GeneAmp® PCR System 2400
Contents
1. users from accidentally overwriting or deleting methods you store under a user name PIN Number None Protection Unlocked Accept Cancel Fi F2 F3 F4 F5 Figure 3 3 Security Code screen To enter a security code 1 From the Security Code screen press F3 PIN Thisdisplaysthe New PIN Number screen Figure 3 4 You will be required to enter this 4 digit PIN before your method can be overwritten or deleted New PIN Number Enter Your New PIN Number Cancel F1 F2 F3 F4 F5 Figure 3 4 The New PIN Number screen In the New PIN Number field use the numeric keys to enter a four digit PIN number Press Enter This displays a confirmation screen Confirm your PIN number by re entering it asin step 2 Press Enter This displays the Protection Status screen Figure 3 5 3 Adding Users April 2001 Applied Biosystems Press PIN and set the protection level to locked to guard against your methods being overwritten or deleted User Name lisa PIN Number XXXX Protection Unlocked Accept cancel F1 F2 F3 F4 F5 Figure 3 5 The Protection Status screen 6 Press F4 Lock to toggle between a Locked and Unlocked state 7 Press F1 Accept This displays the Select U ser Name screen Figure 3 6 The name you entered should display on the screen Editing User Names To add your name to an instrument you can also edit existing names by changing a user name or if 19 names have already been entered2. 31 0 180 331400 31 0 180 331409 United Kingdom Warrington 44 0 1925 825650 44 0 1925 282502 Cheshire All other countries not listed 44 0 1925 282481 44 0 1925 282509 Warrington UK Japan Japan Hacchobori Chuo Ku Tokyo 81 3 5566 6230 81 3 5566 6507 Latin America Del A Obregon Mexico 305 670 4350 305 670 4349 1 Introduction April 2001 Applied Biosystems April 2001 To Reach Technical Support Through the Internet We strongly encourage you to visit our Web site for answers to frequently asked questions and for more information about our products You can also order technical documents or an index of available documents and have them faxed or e mailed to you through our site The Applied Biosystems Web site address is http www appliedbiosystems com techsupp To submit technical questions from North America or Europe Step Action 1 Access the Applied Biosystems Technical Support Web site 2 Under the Troubleshooting heading click Support Request Forms then select the relevant support region for the product area of interest 3 Enter the requested information and your question in the displayed form then click Ask Us RIGHT NOW blue button with yellow text 4 Enter the required information in the next form if you have not already done so then click Ask Us RIGHT NOW You will receive an e mail reply to your question from one
3. Biosystems Web site please see the section To Obtain Documents on Demand following the telephone information below To Contact Technical Support by E Mail Contact technical support by e mail for help in the following product areas Product Area E mail address Genetic Analysis DNA Sequencing galab appliedbiosystems com Sequence Detection Systems and PCR pcrlab appliedbiosystems com Protein Sequencing corelab appliedbiosystems com Peptide and DNA Synthesis Biochromatography PerSeptive DNA tsupport appliedbiosystems com PNA and Peptide Synthesis systems CytoFluor FMAT Voyager and Mariner Mass Spectrometers LC MS apisupport sciex com Applied Biosystems MDS Sciex or api3 support sciex com Chemiluminescence Tropix tropix appliedbiosystems com 16 1 Introduction April 2001 Applied Biosystems April 2001 H ours for Telephone Technical Support In the United States and Canada technical support is available at the following times Product Hours Chemiluminescence 8 30 a m to 5 30 p m Eastern Time Framingham support 8 00 a m to 6 00 p m Eastern Time All Other Products 5 30 a m to 5 00 p m Pacific Time To Contact Technical Support by Telephone or Fax In North America To contact Applied Biosystems T echnical Support use the telephone or fax numbers given below To open a service call for other support needs or
4. This removes the name from the Select User Name screen 3 Adding Users April 2001 Applied Biosystems 4 Creating and Editing Methods 6 12 95 In the GeneAmp PCR System 2400 you run all PCR samplesaccording to methods GeneAmp PCR System 2400 you can Create and Edit by Current Ver 2 10 Current User bart 1 Pressing F2 C reate or F3 Edit from the Main menu 2 Entering temperature control parameters on the Create screen 3 Storing the method Figure 4 1 The Main menu Creating Methods The System 2400 comes with a default PCR method You can run this method or use it as a template to create anew method Figure 4 2 Number of Number of Number of temperature contro cycles the PCR temperature parameters in the segment will run control Number of PCR segment parameters in the temperature control jost PCR parameters in the segment pre PCR segment Temperature 1Hld 3 Tmp 25 Cycles parameter C 94 0 Up ramp Hold time parameter Pre PCR segment PCR segment Post PCR segment Figure 4 2 Create screen default method April 2001 4 Creating and Editing Methods 4 1 Applied Biosystems se 1 From the Main menu press F2 Create This displays the Create screen Figure 4 3 2 From the Create screen you can 1 Hild 3 Tmp 25 Cycles 2 Holds F1 F2 F3 F4 F5 Figure 4 3 The Create screen e Press F1 Start and start running the default method Press F2 Store and store the method under a user name
5. ni Stop Key Arrow Keys Enter Key Clear Entry Key Figure 1 1 The System 2400 control panel Note f the calculated sample temperature exceeds 50 C the word HOT Hashes in the upper right corner of the display screen April 2001 1 Introduction 1 3 Applied Biosystems 14 U sing the Keys The keys on the control panel have the following functions Soft Keys Selects the function specified above the key The function F1 F5 of each key is defined on the display screen above the key and is redefined as you view different screens Stop Key Stops a method while it is running Arrow Keys Moves the highlight box to different fields on the display screen in the direction of the arrow Enter Key Enters information typed into a field and advances the highlight box to the next field on a screen Clear Entry Key Removes information from a field CE Numeric Keys Entersnumbersfrom left to rightinto afield you highlight Selecting a Field You use the above keys to edit or perform functions on information in fidds You select a field by moving the highlight box to it There are two ways to select a field 1 Use the arrow keys to freely move the highlight box in one of four directions 2 Press the Enter key and advance the highlight box to the next field Entering Numeric Values When entering numeric values for temperature control parameters you do not type decimals or colons Entered numbers display on the screen from
6. Hours for Telephone Technical Support To Contact Technical Support by Telephone or Fax To Reach Technical Support Through the Internet To Obtain Documents on Demand Running Methods Selecting a Method Viewing Method Parameters Sorting Methods Searching for Methods by User Name Starting aRun Run Time Screen Profile Viewing Method Information Pausing a Run Stopping a Run Before it Completes Completing aRun Reviewing History of a Run 3 Adding Users April 2001 Adding aNew User Name Entering a User Name l 1 1 1 1 1 1 2 1 3 14 14 14 1 5 1 6 1 6 1 6 1 7 1 7 1 11 1 12 2 1 2 1 2 2 2 3 3 1 3 1 Applied Biosystems Protecting Your Methods 3 2 Editing User Names 3 3 Changing a User Name 3 3 Deleting a User Name 3 4 4 Creating and Editing Methods 4 Creating Methods 4 1 Entering Temperature Control Parameters 4 2 Modifying Cycles 4 4 Editing Programmed Pauses 4 14 Storing Methods 4 14 Editing Methods 4 15 Deleting a Method 4 16 5 Using Utilities 5 1 Configuring the Instrument 5 1 Setting the Time 5 2 Setting the Date 5 3 Enabling or Disabling the Optional Printer 5 3 Turning the Beep On or Off 5 4 Setting the Pause Time Out 5 4 Defining the Idle State Setpoint Temperature 5 5 Defining the Baud Rate for your Printer Port 5 5 ii April 2001 Applied Biosystems April 2001 Introduction About This Manual IMPORTANT Before using the GeneAmp PCR System 2400 thoroughly read all
7. Pause function will not display on the Insert screen if the highlighted segment already has a pre programmed pause Figure 4 14 Insert screen To insert holds Note A hold can only be inserted as the last hold time in a method 1 From the Create screen use the arrow keys to a select a time or temperature parameter to the right of where you want to insert a hold 2 Pres F4 More Depending on the parameter you select in step 1 one of three screens display from which you can access the insert function Figure 4 4 3 Press F2 Insert This displays the Insert screen Figure 4 14 Note The Pause function will not display on the Insert screen if the highlighted segment already has a pre programmed pause or if the highlight box Is not on a PCR segment parameter 4 Press F1 Hold to insert a hold of 4 0 C for 30 seconds to the left of the parameter you selected in step 1 2 Pre PCR 3 Tmp 25 Cycles Holds insert to left of selected parameter Figure 4 15 Inserted hold 5 Typein a value for the hold temperature 6 Press Enter This selects the hold time parameter April 2001 4 Creating and Editing Methods 4 11 Applied Biosystems se a E OW 7 Typein a value for the hold time 8 Press Enter 9 Press F4 More to return to the Create screen which now displays your modified method Use the CE key to clear an entry To insert cycles 1 From the Create screen use the arrow keys to select a t
8. Run You can review a record of the events and errors History of method test2 N i User bart Reaction Volume 25pL that occurred during a run by displaying the Run started at 11 35 00 AM 6 12 94 H istory File screen Figure 2 10 Run ended at 1 00 00 PM 6 12 94 Length ofrun 1 25 00 No exceptions F1 F2 F3 F4 F5 Figure 2 10 The History File screen To review the history of a run 1 From the Stop screen or the Post Run screen press F 1 H ist to display the History File screen 2 Press F2 PageU p to page up or F3 PageDn to page down through the record If the run completes without any errors or exceptions then the PageU p or PageDn soft keys do not display April 2001 2 Running Methods 2 7 Applied Biosystems To print the record press F4 Print Note You can only print a record If you have installed and contigured a printer Press F5 C ancel to return to the previous screen 2 8 2 Running Methods April 2001 Applied Biosystems 3 Adding Users 6 12 95 The GeneAmp PCR System 2400 stores methods GeneAmp PCR System 2400 by user snames You can add your name to alist of Current Ver 2 10 users by Current User bart Adding anew user name or dding a new user name o F1 F2 F3 F4 F5 e Editing an existing user name Figure 3 1 The Main menu Adding a New User Name You can add up to 19 different user names to the bedefghi instrument by jklmnopqr stuvwxyz 1 Pressing F5 U
9. This selects the next temperature parameter 10 Repeat steps 6 through 9 until you have time and temperature values for each of the temperature control parameters you defined in step 2 Use the CE key to clear an entry Press F5 Cancel to return to the Main menu Defining Post PCR Holds The Holds field on the Create screen defines the number of temperature control parameters in the post PCR segment of your method To define post PCR holds Select the Holds field In the Holds field type in the number of post PCR steps for your method Press Enter to select the first post PCR temperature parameter Type in a temperature value between 4 0 C and 99 9 C Press Enter to select the first post PCR hold time parameter Sy OF Ne Type in ahold time value between 00 00 and 98 59 minutes seconds The hold time indicates a hold that lastsindefinitely You can enter aco hold time by typing ahold time value of 99 00 or greater 7 Press Enter This selects the next temperature parameter 8 Repeat steps4 through 7until you have time and temperature values for each of the post PCR hold parameters you defined in step 2 Use the CE key to clear an entry Press F5 Cancel to return to the Main menu Modifying Cycles In addition to customizing valuesfor 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 d
10. by deleting a user name and adding anew name Changing a User Name Select User Name If you know the PIN number for a user name you lt sab gt gt lisa can use the arrowkeysto select aname and change al peter bart steve it hank Accept Cancel F1 F2 F3 F4 F5 Figure 3 6 The Select User Name screen To change the name of a user 1 From the Main menu press F5 U ser This displays the Select User Name screen Figure 3 6 Use the arrow keys to select the name you want to change Press F3 Edit This displays the Security Check screen Type in the four digit PIN number of the user name you selected Press Enter This displays the Security Code screen Figure 3 3 DUU FW Press F2 Name to display the User Name screen Figure 3 2 April 2001 3 Adding Users 3 3 Applied Biosystems 34 a ag a 2 7 Press the CE key to clear the previous name 8 Enter a new user name 9 Press F1 Accept This displays the Security Code screen again You can either protect your method or press F1 Accept again and accept the new name without a PIN This displays the Select U ser Name screen showing the changed name Deleting a User Name If there are not any methods stored in a directory you can delete the user name from the Select User Name screen To delete a user name From the Main menu Press F5 U ser Use the arrow keys to select a user name Press Enter ee eS Press F4 Delete to delete the name
11. e Press F3 Print and print the method Note You can only print a record if you have installed and configured a printer when setting up the instrument e Enter temperature control parameters on the Create screen and create a new method e Press F4 More to display functions for modifying created methods The F4 More key only displays when you select a time or temperature parameter Press F5 Cancel to return to the previous screen Left and right arrows display on the Create screen when the method exceeds the screen display To scroll you can use the arrow keys or press the Enter key repeatedly Entering Temperature C ontrol Parameters When you enter temperature control parameters you define valuesfor parameters in each of the three segments of a method pre PCR PCR and post PCR Figure 4 2 You enter all temperature control parameters on the Create screen by selecting fields and using the numeric keys to type in values Pressing Enter accepts a value and selects fields on the screen 4 2 4 Creating and Editing Methods April 2001 Applied Biosystems April 2001 Defining Pre PCR Holds When you first display the Create screen the Hla field is highlighted The Hid field defines the number of holds for the pre PCR segment of your method To define prePCR holds In the Hid field typein the number of pre PCR holds for your method Press Enter to select the first pre PCR temperature parameter Type in a temperat
12. example If the Time field is Then F2 Then F3 24 AM PM AM 24 PM PM AM 24 2 Pressthe F2 or F3 soft keys until the format you want for the current time displays inthe Time field 3 Use the numeric keys to type in the hours followed by minutes 4 Press Enter to accept the entry CE clears an entry Press F5 Cancel to cancel all entries and return to the previous screen 5 2 5 Using Utilities April 2001 Applied Biosystems Setting the Date To set the date 1 Select the Date field There are three fields to set in the Date field the days field the month field and the year field The F2 and F3 soft keys provide a three way toggle that allows you to define the format of the date as D M Y day month year Y M D year month day or M D Y For example If the Date field is Then F2 Then F3 Y M D D M Y M D Y D M Y Y M D M D Y M D Y D M Y Y M D 2 Press the F2 or F3 soft keys until the format you want for the current date displays in the Date field 3 Usethe numeric keysand typein anumber for each of the three fields days months and years pressing Enter after each entry The order of these three fields depends on the format you chose in step 2 CE clears an entry Press F5 C ancel to cancel all entries and return to the previous screen Enabling or Disabling the O ptional Printer Enabling the printer allows you to print method parameters or records of run time events directly from t
13. in case of an emergency dial 1 800 831 6844 and press 1 Product or Product Area Telephone Dial Fax Dial 3700 DNA Analyzer 1 800 831 6844 then press 8 1 650 638 5981 DNA Synthesis 1 800 831 6844 then press 21 1 650 638 5981 Fluorescent DNA Sequencing 1 800 831 6844 then press 22 1 650 638 5981 Fluorescent Fragment Analysis includes GeneScan applications 1 800 831 6844 then press 23 1 650 638 5981 Integrated Thermal Cyclers 877 and Catalyst 800 instruments 1 800 831 6844 then press 24 1 650 638 5981 3100 Genetic Analyzer 1 800 831 6844 then press 26 1 650 638 5981 Biolnformatics includes BioLIMS BioMerge and SQL GT applications 1 800 831 6844 then press 25 1 505 982 7690 1 Introduction 1 7 Applied Biosystems Product or Product Area Telephone Dial Fax Dial Peptide Synthesis 433 and 43X Systems 1 800 831 6844 then press 31 1 650 638 5981 Protein Sequencing Procise Protein Sequencing Systems 1 800 831 6844 then press 32 1 650 638 5981 PCR and Sequence Detection 1 800 762 4001 then press 1 for PCR 2 for the 7700 or 5700 6 for the 6700 or dial 1 800 831 6844 then press 5 1 240 453 4613 Voyager MALDI TOF Biospectrometry and Mariner ESI TOF Mass Spectrometry Workstations 1 800 899 5858 then press 13 1 508
14. the safety information detailed in the Safety and Regulatory Information section in the front of the GeneAmp PGR System 2400 User s Manual This manual contains abbreviated instructions for operating the GeneAmp PCR System 2400 thermal cycler It isnot intended for first time users but for users already familiar with the System 2400 It gives succinct steps for using most of the instrument s functions Revision C of this manual documents enhancements made to version 2 0 of the firmware including programmable up ramp rates This manual doesn t include tutorial information or some of the more detailed information about sample preparation instrument maintenance and troubleshooting This type of information can be found in TheGeneAmp PCR System 2400 User s M anual User Attention Words Please note the following user attention words that appear in this manual Note This word s used to call attention to information IMPORTANT This information is given because it is necessary for correct operation of the instrument 1 Introduction 1 1 Applied Biosystems 12 Accessing Functions From the Main Menu A few seconds after you turn on the instrument the Main menu appears You can access all functions of the System 2400 from the Main menu If you need to return to the Main menu while using other functions press F5 Cancel until it appears Main Menu 6 12 95 GeneAmp PCR System 2400 Current
15. to delete a test4 lisa 6 11 95 8 6 11 95 method after you create it Cancel F1 F2 F3 F4 F5 Figure 4 21 The Edit screen To edit a method 1 From the Main menu press F3 Edit This displays the Edit screen Figure 4 21 2 Select the method you want to edit a Press F2 View to view the parameters of a method before making a selection Refer to Section 2 Running Methods Viewing M ethod Parametes b Press F3 U ser to search for a method by user name Refer to Section 2 Running Methods Searching for a M hod by User Name c Press F4 Sort to sort methods by different criteria Refer to Section 2 Running Methods Sorting M ethods 3 Press F1 Edit This displays the Create screen April 2001 4 Creating and Editing Methods 4 15 Applied Biosystems 4 Edit temperature control parameters Editing temperature control parameters on the Create screen involves the same tasks and uses the same key combinations as creating a method The same functionsfor modifying methods are also available See Creating Methodson page 4 1 5 Press F2 Store and store the method Deleting a Method You delete methods from the Delete screen You test2 lisa 9 6 12 95 access the Delete screen from the Main menu by XL PCR lt lt ab gt gt 11 6 11 95 test4 lisa 8 6 11 95 pressing F4 Util EZ RNA PCR lt lt ab gt gt 8 6 11 95 Cancel F1 F2 F3 F4 F5 Figure 4
16. 2 2 593 6470 6471 82 2 593 6472 Malaysia Petaling Jaya 60 3 758 8268 60 3 754 9043 Singapore 65 896 2168 65 896 2147 Taiwan Taipei Hsien 886 2 2358 2838 886 2 2358 2839 Thailand Bangkok 66 2 719 6405 66 2 319 9788 Europe Austria Wien 43 0 1 867 35 750 43 0 1 867 35 75 11 Belgium 32 0 2 712 5555 32 0 2 712 5516 Czech Republic and Slovakia Praha 420 2 61 222 164 420 2 61 222 168 Denmark Naerum 45 45 58 60 00 45 45 58 60 01 Finland Espoo 358 0 9 251 24 250 358 0 9 251 24 243 France Paris 33 0 1 69 59 85 85 33 0 1 69 59 85 00 Germany Weiterstadt 49 0 6150 101 0 49 0 6150 101 101 Hungary Budapest 36 0 1 270 8398 36 0 1 270 8288 Estonia Warszawa Italy Milano 39 0 39 83891 39 0 39 838 9492 Norway Oslo 47 23 12 06 05 47 23 12 05 75 Poland Lithuania Latvia and 48 22 866 40 10 48 22 866 40 20 1 Introduction 1 9 Applied Biosystems 1 10 Telephone Fax Region Dial Dial Portugal Lisboa 351 0 22 605 33 14 351 0 22 605 33 15 Russia Moskva 7 095 935 8888 7 095 564 8787 South East Europe Zagreb Croatia 385 1 34 91 927 385 1 34 91 840 Spain Tres Cantos 34 0 91 806 1210 34 0 91 806 1206 Sweden Stockholm 46 0 8 619 4400 46 0 8 619 4401 Switzerland Rotkreuz 41 0 41 799 7777 41 0 41 790 0676 The Netherlands Nieuwerkerk a d lJssel
17. 22 The Delete screen To delete a method 1 From the Main menu press F4 Util This displays the Utilities screen 2 From the Utilities screen press F1 Delete to display the Delete screen Figure 4 22 3 Select one of the methods displayed on the screen or select another method as follows e Press F2 View to view method parameters Refer to Section 2 Running M eth ods Viewing M ethod Parametas e PressF3 U ser to search for amethod by user name Refer to Section 2 Running Methods Searching for M ethods by User Name e PressF4 Sort to sort methods by different criteria Refer to Section 2 Running Methods Sorting M ethods 4 Press F1 Delete This displays the Delete Confirmation screen If the method is protected enter the four digit PIN number and press F1 Accept when the number is correct 5 Press F1 Yes to confirm the deletion This deletes the method and returns you to the Delete screen Press F5 Cancel at any time during the delete process to return to the previous screen 4 16 4 Creating and Editing Methods April 2001 Applied Biosystems 5 Using Utilities 6 12 95 You can access all utility functions by pressing F4 Util on the Main menu By using utilities you GeneAmp PCR System 2400 can Current Ver 2 10 Current User bart 1 Delete a method discussed in the previous section un reate F1 F2 F3 F4 F5 2 Configure the instrument Figure 5 1 The Main menu 3 Run diagnostic tests discu
18. 383 7855 Biochromatography BioCAD Workstations and Poros Perfusion Chromatography Products 1 800 899 5858 then press 14 1 508 383 7855 Expedite Nucleic acid Synthesis Systems 1 800 899 5858 then press 15 1 508 383 7855 Peptide Synthesis Pioneer and 9050 Plus Peptide Synthesizers 1 800 899 5858 then press 15 1 508 383 7855 PNA Custom and Synthesis 1 800 899 5858 then press 15 1 508 383 7855 FMAT 8100 HTS System and Cytofluor 4000 Fluorescence Plate Reader 1 800 899 5858 then press 16 1 508 383 7855 Chemiluminescence Tropix 1 800 542 2369 U S only or 1 781 271 0045 1 781 275 8581 Applied Biosystems MDS Sciex 1 800 952 4716 1 650 638 6223 1 Introduction April 2001 Applied Biosystems April 2001 Outside North America Region Telephone Dial Fax Dial Africa and the Middle East Africa English Speaking and West Asia Fairlands South Africa 27 11 478 0411 27 11 478 0349 South Africa Johannesburg 27 11 478 0411 27 11 478 0349 Middle Eastern Countries and North Africa Monza Italia 39 0 39 8389 481 39 0 39 8389 493 Eastern Asia China Oceania Australia Scoresby Victoria 61 3 9730 8600 61 3 9730 8799 China Beijing 86 10 64106608 86 10 64106617 Hong Kong 852 2756 6928 852 2756 6968 Korea Seoul 8
19. 7 AutoX function of 4 6 B Backsp function of 3 2 baud rate setting 5 5 beep during apause 4 13 run time 54 turning off 5 4 turning on 5 4 blinking on Run Time screen 2 5 C calculated sample temperature See sample temperature Cancel function of 1 2 2 2 cap installing tool See disposables CE See Clear Entry key Clear Entry key definition of 1 4 Config function of 5 1 configuring April 2001 Index 1 the instrument 5 1 control panel display screen 1 3 keys See keys numeric keys 1 3 using 1 3 cooling 2 5 Create function of 4 1 create screen default method 4 1 customer support See technical support 1 6 cycles editing parameters 4 16 inserting 4 11 4 12 D date setting 5 3 Delete function of 3 4 4 16 deleting methods See methods user names See user display screen definition of 1 3 disposables cap installing tool 1 5 eight strip MicroAmp caps 1 5 eight strip MicroAmp reaction tubes 1 5 MicroAmp 2400 base 1 5 MicroAmp 2400 full plate cover 1 5 MicroAmp 2400 retainer 1 5 MicroAmp 2400 tray 1 5 MicroAmp reaction tubes 1 5 Applied Biosystems MicroAmp reaction tubes with caps 1 5 Hold Documents on Demand 1 12 E Edit function of 3 3 4 1 4 15 editing cycle parameters See cycles methods See methods programmed pauses 4 14 eight strip MicroAmp caps See disposables eight strip MicroAmp reaction tubes See disposables e mail address for technical support 1 6 Enter key definition
20. GeneAmp PCR System 2400 Quick Reference Guide KS Be Copyright 2006 Applied Biosystems All rights reserved Printed in the United States of America NOTICE TO PURCHASER PLEASE REFER TO THE GENEAMP PCR SYSTEM 2400 USER S MANUAL FOR LIMITED LABEL LICENSE OR DISCLAIMER INFORMATION The information contained in this document is subject to change without notice Applied Biosystems makes no warranty of any kind with regard to this material including but not limited to the implied warranties of merchantability and fitness for a particular purpose Applied Biosystems shall not be liable for errors contained herein or for incidental consequential damages in connection with the furnishing performance or use of this material Reproduction or publication of this document in any form or format is prohibited without written permission of Applera Corporation Applied Biosystems and MicroAmp are registered trademarks of Applera Corporation or its subsidiaries in the U S and certain other countries AmpliTag GeneAmp and AmpliWax are registered trademarks of Roche Molecular Systems Inc Applied Biosystems Contents l Introduction About This M anual User Attention Words Accessing Functions From the Main Menu Using the Control Panel Using the Keys Selecting a Field Entering Numeric Values A Look at the MicroAmp Disposables Technical Support Contacting Technical Support To Contact Technical Support by E Mail
21. R segment PCR segment Post PCR segment Figure 2 6 Run Time screen profile From the Run Time screen you can View method information e Pause arun Stop arun before it completes Viewing Method Information At any time during arun you can display 11 36 AM Information information about the method currently running Run started at 11 35 00 AM Run will end at 1 00 00 PM Reaction Volume 25 uL F1 F2 F3 F4 F5 Figure 2 7 The Method Information screen To view information about a method during a run 1 Startarun 2 Press F4 Info This displays the Method Information screen Figure 2 7 Press F4 Return to return to the Run Time screen April 2001 2 Running Methods 25 Applied Biosystems 2 6 Pausing a Run At any time during a run you can manually pause a run for a ten minute period of time Setting the Pause Time Out on page 5 4 describes howto specify a time period for a pause To Pausea Run 1 Start arun 2 From the Run Time screen press F1 Pause For the duration of the pause your samples will remain at the temperature of the instrument when you paused the run The time remaining in a pause is displayed 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 Press F1 Pause again to resume running a method before a pause expires Stopping a Run Before it Completes The Stop Run screen appears when
22. Ver Current User Running Methods User Size Stored fenton 9 06 02 95 Fl F2 F3 F4 F5 Press F1 Run select the method you want to run press F1 Start Creating and Editing Methods 3 Tmp 25 Cycles 2 Holds F1 F2 F3 F4 F5 Press F2 Create or F3 Edit edit the default method press F2 Store 1 Introduction 2 10 bart Adding Users Select User Name lt lt ab gt gt lisa peter steve Accept Cancel F1 F2 F3 F4 F5 Press F5 User press F2 New enter a new user name Using Utilities Ver 2 10 Delete Delete a method Config Instrument configuration Diag Instrument diagnostics Hist Display history of last run F1 F2 F3 F4 F5 Press F4 Util press one of the soft keys F1 F3 to select a utility function April 2001 Applied Biosystems Using the Control Panel The System 2400 control panel consists of a display screen and 22 keys The display screen shows a graphical representation of PCR events before during and after a run You use the keys to enter information into fields on the display screen IMPORTANT Before running PCR methods make sure you have properly loaded the sample tray in the System 2400 This ensures proper operation of the heated cover Calculated sample Display Screen temperature Numeric Keys 1 Hld 3 Tmp 25 Cycles 2 Holds Highlight Box Insert Delete PPRS T am ow OX
23. d 9 Inthe Cycles For field typein the length of the pause in minutes seconds 00 01 98 59 format 10 Press Enter This selects the next field 11 Inthe Beep During The Pause field press F2 Yes or F3 No 12 Press F1 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 1 Hid 4 Tmp 25 Cycles 2 Holds 94 0 Pause 0 30 90 00 72 0 72 0 55 0 0 30 7 00 0 30 Fl F2 F3 F4 F5 Figure 4 18 Inserted pause Use the CE key to clear an entry Note Only one pause can be inserted in each cycle April 2001 4 Creating and Editing Methods 4 13 Applied Biosystems Editing Programmed Pauses If you have inserted a programmed pause in your method you can edit the parameters for the pause at any time To edit programmed pauses 1 From the Create screen use the arrow keysto highlight the word Pause This dis plays the F5 Edit soft key 4 Tmp 25 Cycles 2 Holds 04 0 BE 0 30 90 00 72 0 72 0 55 0 0 30 7 00 4 0 3 F1 F2 F3 F4 F5 Figure 4 19 Editing programmed pauses 2 Press F5 Edit to access the programmed pause screen Figure 4 17 From this screen you can change any of the pause parameters Or use the arrow keys to select the pause time parameter on the screen and edit it by entering a different time Use the CE key to clear an entry Press F5 Cancel to cancel all entries and return to the previou
24. eaction tubes See disposables modifying cycles 44 ramp rates 4 8 to 4 10 More function of 4 2 N Name function of 3 3 New function of 3 1 notes See user attention words Numeric keys definition of 14 April 2001 O overwriting of methods 3 2 P parameter hold time definition of 2 4 PCR 4 3 post PCR 4 4 pre PCR 4 3 temperature 2 5 definition of 2 4 PCR 4 3 post PCR 4 4 pre PCR 4 3 Pause function of 2 6 4 12 pause time out setting 5 4 pausing arun 2 6 PCR parameters defining See parameter steps see steps PIN number definition of 3 2 entering See security code PIN function of 3 2 post PCR parameters defining See parameter post PCR extension 4 1 44 predefined methods 2 1 pre PCR parameters defining See parameter Index Applied Biosystems steps see steps pre PCR denaturation 4 3 Print function of 2 8 4 2 printer disabling 5 3 enabling 5 3 printer port defining See baud rate printing methods 4 2 profile 2 5 programmed pauses inserting 4 11 4 12 programming pauses 4 12 R ramps flashing of 2 5 reaction volume enteringa 2 4 Resume function of 2 6 Run function of 2 1 2 4 run completion of 2 7 pausing See pausing reviewing history of See history starting 2 4 stopping See stopping Run Time screen 2 5 running methods See methods S sample block 2 5 sample temperature 2 5 4 scrolling 4 2 scrolling methods See methods searching methods See m
25. ecrement time and temperature parameters e Modify up ramp ratesin the cycling segment of a method 4 Creating and Editing Methods April 2001 Applied Biosystems Insert holds cycles and programmed pauses e Delete temperature control parameters The time or temperature parameter you select on the create screen determines which modification function you can access when you Press F4 More Figure 4 4 The F4 More soft key displays 1 Hld 3 Tmp 25 Cycles 2 Holds when you select a time or temperature parameter Pressing F4 More displays different modification options when you select parameters in different segments 7 Press F4 More with a pre PCR 3 Press F4 More with a post PCR ume or temperature parameter tme or temperature e parameter highlighted highlighted 1 Hild 3 Tmp 25 Cycles 1 Hild 3 Tmp 25 Cycles 2 Holds 94 0 94 0 94 0 94 0 From the above screen you Can press From the above screen you Can press F2 Insert and insert holds cycles and F2 Insert and insert holds cycles and programmed pauses or F3 Delete and programmed pauses or F3 Delete and delete the delete the selected temperature control selected temperature control parameters parameters 2 Press F4 More with a PCR time or y temperature parameter highlighted 1 Hld 3 Tmp 25 Cycles 2 Holds 94 0 94 0 From the screen above you can press F2 Insert and insert holds cycles and programmed pauses or press F1 Modity and modity c
26. ems Searching for Methods by User Name You can find any method that has been stored under a user name To search for methods by different user names 1 From the Stored Methods screen press F3 U ser This displays the Search for Methods screen Select User Name lisa peter steve F1 F2 F3 F4 F5 Figure 2 4 The Search tor Methods screen All user names that have methods stored under them displayin a 4 x 5 matrix Note You can not add delete or modity a user name from this screen 2 Choose how you want to search for a particular method List the methods of a particular user a Usethe arrow keys to select the appropriate user name b Press F1 Acceptto accept a selection Thisreturns you to the Stored Methods screen which now displays the methods of the user you selected e List all methods currently stored on the instrument e Press F2 All to list all methods currently stored on the instrument Press F5 C ancel to return to the Main menu April 2001 2 Running Methods 2 3 Applied Biosystems Starting a Run You can start a run after you select a stored method from the Stored Methods screen see Figure 2 2 To start a run 1 From the Main menu press F1 Run to display stored methods 2 Use the up and down arrow keys to select the method you want to run 3 Press F1 Start This displays the Reaction Volume screen Figure 2 5 Reaction Volume 100 pL Enter The Reaction Volume 5 100
27. ercentage of its maximum rate of increase The default maximum up ramp rate is 100 To modify up ramp rates 1 From the Modify screen press F1 Modify This displays the Select Modification screen Figure 4 7 2 Press F2_Ramp This displays the Ramp Rate Modification screen Figure 4 9 1 Hld 3 Tmp 25 Cycles 2 Holds Accept Cancel F1 F2 F3 F4 F5 Figure 4 9 The Ramp Rate Modification screen For the three temperature cycling method shown in Figure 4 9 you can modify the rate at which the instrument ramps up from 72 0 C to 94 0 C or from 55 0 C to 72 0 C 48 4 Creating and Editing Methods April 2001 Applied Biosystems 3 Usethe arrow keys to select an up ramp that you want to modify If you select a ramp rate value preceded by a higher temperature you cannot modify the down ramp rate Note that ramp modification functions do not display for the F2 or F3 softkeys when a down ramp rate is highlighted Figure 4 10 1 Hld 3 Tmp 25 Cycles 2 Holds Accept Cancel F1 F2 F3 F4 F5 Figure 4 10 Selection of a down ramp rate If you move the highlight box to the third temperature in the cycling segment of the default method you can modify the highlighted up ramp rate The third up ramp rate defines the rate at which the instrument increaes from 55 C to 72 06 each time the method cycles Figure 4 11 1 Hld 3 Tmp 25 Cycles 2 Holds Accept Cancel F1 F2 F3 F4 F5 Figure 4 11 Selection of an up ramp
28. ethods securing protecting methods See methods security code entering 3 2 segments inserting cyclesinto 4 12 PCR 4 1 4 2 post PCR 4 1 4 2 pre PCR 4 1 4 2 selecting a cycle modification function 4 5 a method to edit 4 15 a name for storing a method 4 15 fields 1 4 4 2 methods 2 1 setting baud rate See baud rate date See date pause time out See pause time out temperature control parameters 4 2 the time See time Soft keys definition of 1 4 Sort function of 2 2 4 16 sorting methods See methods Start function of 2 2 2 4 4 2 starting a run See run steps PCR 43 pre PCR 4 3 Stop key Index April 2001 Applied Biosystems definition of 14 stopping arun 2 6 Store function of 2 6 4 2 4 14 4 16 storing methods See methods y W Util function of 4 16 5 1 View function of 2 2 4 15 T WWW address technical support 1 6 to 1 12 e mail address 1 6 Internet address 1 11 regional sales offices 1 9 to 1 10 telephone fax North America 1 7 temperature auto incrementing decrementing automatic segment extension 4 6 parameters See parameter three temperature PCR Incubation steps See steps time setting 5 2 U unlocking methods See methods U ser function of 2 3 3 3 4 15 user name changing 3 3 deleting 3 4 entering 3 1 new 3 1 user attention words important 1 1 note 1 1 users adding 3 1 April 2001 Index Applied Biosystems 1 11 Documents on Demand 1 12 Headqua
29. he Second Con figuration screen Figure 5 4 2 Uthe numeric keys and type in the minutes followed by the seconds for the Pause Time Out 3 Press Enter This accepts your selection and selectsthe Idle State Set Point field CE clearsan entry 5 Using Utilities April 2001 Applied Biosystems Defining the Idle State Setpoint Temperature The idle state setpoint temperature is the temperature the instrument will remain at when powered up and idle Note After a run completes or s terminated there s 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 To set the idle state setpoint temperature 1 Selectthe Idle State Set Point field 2 Use the numeric keys and type in a temperature between 4 0 C and 99 9 C CE clears an entry 3 Press Enter to accept your entry Defining the Baud Rate for your Printer Port Define the printer port value in the Baud Rate field To set the baud rate 1 Select the Baud Rate field 2 Pres F2 Up or F3 Down to increase or decrease the baud rates Available baud rates are 19200 9600 4800 2400 1200 600 and 300 3 Press Enter to accept your entry April 2001 5 Using Utilities 5 5 Applied Biosystems Index A Accept function of 2 2 adding users See users Arrow keys definition of 14 asterisk meaning of 4
30. he display screen The default value for the optional printer is off To enable or disable the optional printer 1 Select the Run Time Printer field This changes the functions of the F2 and F3 soft keys 2 Press F2 On to enable the printer or F3 0 ff to disable it 3 Press Enter to accept your entry Press F5 C ancel to cancel all entries and return to the previous screen April 2001 5 Using Utilities 5 3 Applied Biosystems 5 4 Pause Time Out 10 00 00 01 99 59 Idle State Set Point 25 0C 4 0 99 9 Baud Rate 9600 Accept Turning the Beep On or Off When turned on the run time beeper beeps during a pause and once at the completion of arun The default value is of To turn the run time beep on or off 1 Selectthe Run Time Beep field This changes the value of the F2 and F3 soft keys 2 Press F2 0n to turn the beeper on or F3 0 ff to turn it off Press F5 Cancel to cancel all entries and return to the previous screen Setting the Pause Time O ut The Pause Time Out field sets the time in Instrument Configuration minutes seconds format for the length of a manual pause You setthe Pause Time Out field from the Second Configuration screen From this screen you can Cancel also define 1 The idle state setpoint temperature 2 The printer port Figure 5 4 The Second Configuration screen To set the pause time out 1 From the First Configuration screen press F4 More This displays t
31. ime or temperature parameter to the right of where you want to insert a hold See Figure 4 4 2 Press F4 More 3 Press F2 Insert This displays the Insert screen 4 Press F2 Cycle to insert a cycle to the left of the segment you selected in step 1 Figure 4 16 inserted cycle 3 Tmp 25 Cycles 94 0 Figure 4 16 Example of Inserted cycle Use the CE key to clear an entry Press F5 Cancel to cancel your entry and return to the previous screen To insert a programmed pause 1 From the Create screen use the arrow keys to select a PCR segment time or temperature parameter where you want to insert a programmed pause 2 Press F4 More 3 Press F2 Insert This displays the Insert screen 4 From the Insert screen press F3 Pause This displays the Programmed Pause screen Figure 4 17 4 12 4 Creating and Editing Methods April 2001 Applied Biosystems Displays number of Start first Pause at Cycle 7 of 25 cycles programmed Pause Every 3 Cycles For 0 30 Beep During The Pause Yes Cancel F1 F2 F3 F4 F5 Figure 4 17 The Programmed Pause screen 5 IntheStart lst Pause at Cycle field type in the cycle number where you want the method to first pause 1 98 6 Press Enter This selects the next field 7 Inthe Pause Every field typein the pause frequency in cycles 1 98 The pause frequency specifies the number of cycles that will run between each pause 8 Press Enter This selects the next fiel
32. me or temperature parameter that you want modified when you run your method Note From the AutoX screen you cannot modality the number of parameters in each segment or the number of cycles 6 Use the numeric keys to type in the fixed amount that you want the value of the parameter to increase or decrease each time your method completes a cycle Values for times can be between 0 01 and 9 59 minutes seconds Values for temperatures can be between 0 1 and 9 9 C 7 Press F2 to increase the value every cycle A plus sign displays in the current field or Press F3 to decrease the value every cycle A minus sign displaysin the current field An asterisk appears on the AutoX screen and the Modify screen for parameters that will be modified as the method runs 8 Press F1 Accept to accept all entries on the AutoX screen Use the CE key to clear an entry Press F5 C ancel to cancel all entries and return to the previous screen April 2001 4 Creating and Editing Methods 47 Applied Biosystems a ira Modifying Ramp Rates The ramp time is the time it takes the instrument to change from one temperature to another U sing functions accessible from the Modify screen you can modify the up ramp rate of the instrument that is the rate at which the instrument heats your samples from one temperature setting to the next You can decrease up ramp rates for the cycling segment of amethod by defining the up ramp rate as a p
33. of 1 4 entering numeric values 1 4 erasing methods See deleting methods user names See user name deleting error message 3 2 Exit function of 2 6 F fields See selecting H heated cover 2 4 heating 4 1 profile 2 5 help Seetechnical support 1 7 highlight box definition of 1 3 moving See selecting function of 4 11 hold time auto incrementing decrementing 4 6 parameters See parameter hold times display of 2 5 holds inserting 4 11 HOT indicator 2 5 I idle state temperature defining 5 5 important See user attention words Info function of 2 5 Insert function of 4 11 4 12 Internet address Documents on Demand 1 12 K keys functions of 1 4 L list of users 3 1 Lock function of 3 3 locking methods See methods M Hist Main menu function of 2 6 2 7 accessing functions from 1 2 history Method of arun 2 7 function of 4 15 2 Index April 2001 Applied Biosystems methods changing the name of 4 15 default 4 1 deleting 4 16 editing 4 15 locking 3 3 printing See printing protecting 3 2 running 2 1 scrolling arrows 4 2 searching for 2 3 sorting 2 2 stored 2 1 storing 2 6 4 14 unlocking 3 3 viewing information about 2 5 viewing parameters 2 1 MicroAmp 2400 base See disposables MicroAmp 2400 full plate cover See disposables MicroAmp 2400 retainer See disposables MicroAmp 2400 tray See disposables MicroAmp reaction tubes with caps See disposables MicroAmp r
34. of our technical experts within 24 to 48 hours 1 Introduction 1 11 Applied Biosystems To Obtain Documents on Demand Free 24 hour access to Applied Biosystems technical documents including MSDSs is available by fax or e mail or by download from our Web site To order documents Then by index number a Access the Applied Biosystems Technical Support Web site at http www appliedbiosystems com techsupp Click the Index link for the document type you want then find the document you want and record the index number Use the index number when requesting documents following the procedures below by phone for fax From the U S or Canada call 1 800 487 6809 or Internet for fax or e mail delivery delivery from outside the U S and Canada call 1 858 712 0317 b Follow the voice instructions to order the documents you want Note There is a limit of five documents per request through the a Access the Applied Biosystems Technical Support Web site at Note There is a limit of five documents per request for fax delivery but no limit on the number of documents you can order for e mail delivery http www appliedbiosystems com techsupp Under Resource Libraries click the type of document you want Enter or select the requested information in the displayed form then click Search In the displayed search results select a check box for the method of delivery for each document that matche
35. pL Cancel F1 F2 F3 F4 F5 Figure 2 5 The Reaction Volume screen a Ifthe displayed reaction volume isthe same as your reaction volume go to step 4 b If the displayed reaction volume differs from your reaction volume enter the volume of your reactions 5100 uL in the Reaction Volume field To clear an entry press the CE key 4 Press F1 Start to start a run When the heated cover reaches 103 C the Run Time screen displays and the method you selected starts running Press F5 Cancel to return to the previous screen Run Time Screen Profile The Run Time screen displays the method currently running You can chart the progress of a run by viewing the Run Time screen at any time during the run The Run Time screen displays the executing segment and the next segment to execute Figure 2 6 2 4 2 Running Methods April 2001 Applied Biosystems Calculated sample Horizontallines tlashas Cycles count up when run HOT displays when temperature updated hold times decrement 18 in PCR segment the sample block as TUN progresses exceeds 50 C Temperature S parameters are Sample 55 0 C Cycle 1 of 25 displayed above the Aight or left arrows appear on graph 94 0 94 0 elther side of aisplay if method Ramps flash when gt scrollable in that direction system Is approaching next temperature value Post PCR hold times of 99 00 or greater Hold times are display Aas co displayed below the graph Pre PC
36. rate 4 Modify the up ramp rate you selected by defining it as percentage of the maximum of 100 e Press F2 Faster to increase the up ramp rate by 10 up to a maximum of 100 e Press F3_Slower to decrease the up ramp rate by 10 from 100 to 10 and by 5 from 10 to 5 e Usethenumeric keys to enter a value that defines the percentage by which you want to decrease the up ramp rate for each cycle of the method You can enter values between 5 and 95 or 100 Figure 4 12 April 2001 4 Creating and Editing Methods 49 Applied Biosystems 1 Hld 3 Tmp 25 Cycles 2 Holds F1 F2 F3 F4 F5 Figure 4 12 Modified up ramp rate For ramp rates less than 100 an asterisk appears next to modified up ramps The asterisk remains beneath the modified temperature parameter to remind you that the method has been modified Figure 4 13 3 Tmp 25 Cycles 2 Holds Figure 4 13 Method with modified up ramp rate 5 Press F1_Accept to accept all entries and return to the previous screen Note f you enter a numeric value outside the range of acceptable values you will receive the following message Valid range is 5 to 95 and 100 4 10 4 Creating and Editing Methods April 2001 Applied Biosystems Inserting H olds Cycles and Programmed Pauses From the Insert screen Figure 4 14 you can insert holds and cycles and program pauses that the instrument inserts into your method asit runs 1 Hid 3 Tmp 25 Cycles 2 Holds The
37. right to left filling across decimal points or colons For example to specify 89 0 degrees C press 8 9 0 then press Enter Specify all hold times in minutes and seconds then press Enter For example to specify one minute and five seconds press 1 0 5 then press Enter 1 Introduction April 2001 Applied Biosystems A Look at the MicroAmp Disposables The MicroAmp disposables you can use to prepare samples for the GeneAmp PCR System 2400 are shown below in Figure 1 2 Cap Installing Too MicroAmp 22400 Retainer Eight strip MicroAmp Caps MicroAmp 2400 Full Plate Cover MicroAmp 2400 Tray Eight strio MicroAmp Reaction Tubes MicroAmp Reaction Tubes 3 MicroAmp 2400 Base MicroAmp Reaction Tubes with Caps Figure 1 2 MicroAmp disposables for use with the System 2400 For detailed information about the MicroAmp disposables supplied with your instrument and how to use them for loading and unloading samples refer to the GeneA mp PCR System 2400 User s M anual P N 0993 6056 April 2001 1 Introduction 15 Applied Biosystems Technical Support Contacting Technical Support You can contact Applied Biosystems for technical support by telephone or fax by e mail or through the Internet You can order Applied Biosystems user documents MSDSs certificates of analysis and other related documents 24 hours a day In addition you can download documents in PDF format from the Applied
38. rters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free 1 800 345 5224 Fax 1 650 638 5884 Worldwide Sales Offices Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches into 150 countries on six continents For international office locations please call our local office or refer to our web site at www appliedbiosystems com www appliedbiosystems com AR Applied D Biosystems Applera Corporation is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses Printed in the USA 07 2006 Part Number 0993 6057_Rev D an Applera business
39. s screen After you have entered all modifications to the customized method you are creating you must store the method before running it Storing Methods Storing a method completes the creation of it You can store the default method or modify and then User fenton store it Method exp000 Store A Method Free Mem 76 methods 334 segments Accept Cancel F1 F2 F3 F4 F5 Figure 4 20 The Store screen To store a method 1 From the Create screen press F2 Store Thisdisplaysthe Store screen Figure 4 20 4 14 4 Creating and Editing Methods April 2001 Applied Biosystems 2 Select a user name where you want to store the method Ifyou want to store the method under the displayed name go to step 3 To change the name of the user press F2 U ser This displays the Select U ser Name screen See Figure 3 6 on page 3 3 3 Press Enter to select the Method field Ifyou want to keep the name of the method as displayed go to step 4 To change the name of the method press F3 Method This displays the Stored Method screen See Figure 2 2 on page 2 1 4 Press F1 Accept to store the method and return to the previous screen Press F5 Cancel to return to the previous screen without storing the method Editing Methods Matha Taer Datedtor d After you create a meth od you can edit the test2 lisa 6 12 95 parametersin it and store it by the same name or ZL PCR 6 11 95 change its name You may also want
40. s your criteria then click Deliver Selected Documents Now or click the PDF icon for the document to download it immediately Fill in the information form if you have not previously done so then click Deliver Selected Documents Now to submit your order 1 12 1 Introduction April 2001 Applied Biosystems 2 Running Methods The GeneAmp PCR System 2400 runs PCR samples according to stored methods You can run methods by 6 12 95 GeneAmp PCR System 2400 Current Vor 2 10 1 Pressing F1 Run from the Main menu Current User bart E Figure 2 1 2 Selecting a Method F1 F2 F3 F4 Pa 3 Starting a Run Figure 2 1 The Main menu Selecting a Method You select a method by moving the highlight box to Bethe User Bare asa a method listed on the Stored Methods screen 06 02 35 Figure 2 2 If you need help deciding which method to select you can view method parameters sort methods by different categories or search for mg nme F1 F2 F3 F4 F5 Figure 2 2 The Stored Methods screen Viewing Method Parameters Note There are four predefined methods stored under user lt lt ab gt gt that you can select and run or edit modity and store under a new name To view parameters of a method before running 1 From the Main menu press F1 Run This displays the Stored Methods screen Figure 2 2 April 2001 2 Running Methods 2 1 Applied Biosystems OOOO 2 Press F2 View This di
41. ser from the Main menu User Name Use the Enter key to select a character 2 Entering a user name Accept Cancel F1 F2 F3 F4 F5 3 Protecting your methods You can then store methods under user names Figure 3 2 The User Name screen To add a new user name 1 From the Main menu press F5 U ser This displays the Select User Name screen 2 Press F2 New This displays the U ser Name screen Figure 3 2 Entering a User Name To enter a user name 1 IntheUser Name field enter a alphanumeric name up to six charactersin length a Use the arrow keys to select a character in the list shown in the upper right portion of the screen b Press Enter to put the character in the field April 2001 3 Adding Users 3 1 Applied Biosystems Use the numeric keys to type numbers directly into the User Name field Press F3 Backsp to go back one space e Press the CE key to clear an entry Press F1 Accept to accept a name you must enter at least one character This displays the Security Code screen Figure 3 3 An error message displays if you enter a name that already exists Press F5 Cancel to return to the previous screen without adding the newuser name Protecting Your Methods ress PIN f and Set the protection To protect a method you can enter a Personal status to Locked to guard against your methods being overwritten or deleted Identification Number PIN and prevent other User Name lisa
42. splays all the parameters of a method After reviewing pre PCR PCR and post PCR parameters of a stored method you can either press F1 Start and start the method or press F5 Cancel and return to the Stored Methods screen Figure 2 2 Note You can not edit parameters trom the View Method screen 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 stored methods by different criteria 1 From the Stored Methods screen press F4 Sort This displays the Sorting Criteria screen Sort Methods by Method Name Date Last Used Date Stored Method Size Cancel F1 F2 F3 F4 F5 Figure 2 3 The Sorting Criteria screen 2 Usthe up and down arrow keys to select the type of sort Method Name sorts methods alphabetically Date Last Used sorts methods chronologically in descending order by date of use The last method used is listed first Date Stored sorts methods chronologically by date stored The last method stored is listed first Method Size sortsmethodsin increasing order by the amount of memory used to store each file The largest size method is listed first 3 Press F1 Accept to accept a selection This returns you to the Stored Methods screen where the displayed methods are sorted according to your selection in step 2 Press F5 Cancel to return to the previous screen 2 2 2 Running Methods April 2001 Applied Biosyst
43. ssed in the User s M anual 4 Reviewthe history of the last run discussed in the previous section Configuring the Instrument eT Configuring the instrument involves setting values Delete Delete a method for operating parametersand enabling or disabling Config Instrument configuration optional features Diag Instrument diagnostics Hist Display history of last run Exit F1 F2 F3 F4 F5 Figure 5 2 The Utilities screen To configure the instrument 1 From the Main menu press F4 Util This displays the Utilities screen Figure 5 2 2 Press F2 Config This displays the First Configuration screen Figure 5 3 April 2001 5 Using Utilities 5 1 Applied Biosystems Setting the Time Instrument Configuration From the First Configuration screen you can set Timer es AM the current time and date for file memory Date 1 12 94 M D Y Run Time Printer oN maintenance and run time displays and enable or Run Time Beep OFF disable the run time printer and the run time beep Accept 24m more cancel si e When all the valueson the screen are correct press F1 Accept Figure 5 3 The First Configuration screen To set the time 1 Select the Time field The F2 and F3 soft keys provide a three way toggle that allows you to define the format of the time in AM PM or 24 hour format Whatever format is displayed for the Time field the F2 and F3 soft keys define the other two formats For
44. ure value between 4 0 C and 99 9 C Press Enter to select the first pre PCR hold time parameter Type in ahold time value between 00 00 and 98 59 minutes seconds Press Enter This selects the next temperature parameter a oO MW FP WN BP Repeat steps 3 through 6 until you have time and temperature values for each of the pre PCR hold parameters you defined in step 1 Use the CE key to clear an entry Press F5 C ancel to return to the Main menu Defining PCR Parameters The Tmp field on the Create screen definesthe number of temperature control parameters in the PCR cycling segment of your method To define PCR parameters 1 Select the Tmp field 2 Inthe Tmp field type in the number of temperature control parameters 1 6 for one cycle of your method Three temperature PCR is the typical setting for most PCR reactions 3 Press Enter Thisselectsthe cycles field In this field you specify the number of times you want the PCR cycling segment of your method to run 4 Inthe cycles field typein the number of cycles you want your method to run 2 99 Twenty five cycles is the default setting 5 Press Enter This selects the first PCR temperature parameter 6 Type in a temperature value between 4 0 C and 99 9 C 7 Press Enter to select the first PCR hold time parameter 4 Creating and Editing Methods 43 Applied Biosystems 44 8 Typein ahold time value between 00 00 and 98 59 minutes seconds 9 Press Enter
45. ycling by auto extending decremeniting time and temperature parameters or by selecting up ramp rates Press F3 Delete and delete the selected temperature con trol parameters Figure 4 4 Using the More function to modify cycling April 2001 4 Creating and Editing Methods 45 Applied Biosystems Auto incrementing decrementing Temperature Control Parameters Using the AutoX function you can automatically increase or decrease the values for any PCR segment parameter a fixed amount every cycle 2 Pre PCR 3 Tmp 25Cycles 2 Holds Accept Figure 4 5 The AutoX screen To auto increment decrement PCR parameters 1 From the Create screen use the arrow keys to select a time or temperature parameter in the PCR segment 2 Press F4 More This displays the Modify screen Figure 4 6 Figure 4 6 The Modify screen 3 Press F1 Modify This displays the Select Modification screen Figure 4 7 Select AutoX to modify Time or Temperature Select Ramp to modify an up ramp rate Cancel F1 F2 F3 F4 F5 Figure 4 7 The Select Modification Screen 4 6 4 Creating and Editing Methods April 2001 Applied Biosystems SS Sk 4 Press F1 AutoX This displays the AutoX screen Figure 4 8 2 Pre PCR 3 Tmp 25 Cycles Accept Figure 4 8 The AutoX screen Note f a programmed pause has been inserted the AutoX screen will display the pause but you can not modity it trom the AutoX screen 5 Select the PCR ti
46. you stop arun before completion of a method Figure 2 8 Method test2 Run Aborted at 10 25 00 AM Length of Run 1 25 00 Exception occured check history file Exit F2 F3 F4 F5 Figure 2 8 The Stop Run screen To stop a run before completion of a method 1 Press the Stop key This displays a Stop confirmation screen The run pauses for the pre programmed period of time When the pause time expires the run will abort You can resume the run by pressing F1 Resume 2 Press the Stop key again This stopsarun and displays the Stop Run screen At this time you can e Press F1 Hist and review the history of the run e Press F5 Exit and return to the Main menu Ifyou have not yet stored the method that was running you can press F2 Store This displays the Store screen 2 Running Methods April 2001 Applied Biosystems If anyerrorsoccur duringarun the message Exception occurred check history file displays You can review the history file by pressing F1 H ist See Reviewing History of a Run below Completing a Run When amethod completes running the SO ee instrument will beep unless you turned off the beep Run completed at 1 00 00 PM when configuring theinstrument At completion of BED tren IN arun the Post Run screen displays Figure 2 9 From the Post Run screen you can perform the same functions as you can after stopping a run Fl F2 F3 F4 F5 Figure 2 9 The Post Run Screen Reviewing History of a
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