GeneAmp® PCR System 9600 User’s Manual
© Copyright 2001, Applied Biosystems. All rights reserved. For Research Use Only. Not for use in diagnostic procedures. Notice AUTHORIZED THERMAL CYCLER NOTICE This GeneAmp PCR System 9600 is an Authorized Thermal Cycler. Its purchase price includes the up-front fee component of a license under the patents of the Polymerase Chain Reaction (PCR) process, which are owned by Roche Molecular Systems, Inc. and F. Hoffmann-La Roche Ltd.
Safety and Regulatory Information S Conventions Used in This Manual ! WARNING ! A warning indicates an operation that could cause personal injury if precautions are not followed. CAUTION A caution indicates an operation that could cause instrument damage if precautions are not followed. Note Notes emphasize significant information in a procedure or description.
Symbols and Conventions Used on the Instrument There are three different types of warning symbols that appear on the instrument. This symbol indicates an operation (or condition on the instrument) that could cause personal injury or instrument damage if precautions are not followed. This can be any type of hazard. When you see this symbol, refer to the safety pages in the manual for further information. AVERTISSEMENT. Consulter les documents d'accompagnement.
Additional graphic symbols used on the instrument are the following: Indicates alternating current. Indicates the primary protective grounding terminal. Indicates the off position of the main power switch. Indicates the on position of the main power switch.
Warnings on the Instrument The following sections present the warning labels affixed to the instrument. 100, 120, and 220/230 Volt Models The following warning labels are affixed to the front, the left side and the back of the instrument as shown in the figures on the following pages for all three voltage models (100, 120, and 220/230). Front of Instrument ! WARNING ! Hot Surface. Use care when working around this area to avoid being burned by hot components. ! AVERTISSEMENT ! Surface chaude.
Back of Instrument ! WARNING ! Grounding circuit continuity is vital for safe operation of equipment. Never operate equipment with grounding conductor disconnected. ! AVERTISSEMENT ! Risque de choc électrique. Pour un fonctionnement sans danger. Ne jamais utiliser l'équipment si le fil de terre n'est pas raccordé. ! WARNING ! To avoid electrical shock, disconnect power cord before servicing. ! AVERTISSEMENT ! Pour éviter les chocs électriques, débrancher le cordon d'alimentation avant le dépannage.
! WARNING ! Hot Surface. Use care when working around this area to avoid being burned by hot components. ! AVERTISSEMENT ! Surface chaude. ! WARNING ! To reduce the chance of electrical shock do not remove covers that require tool access. No user serviceable parts are inside. Refer servicing to Applied Biosystems qualified service personnel. ! AVERTISSEMENT ! Pour réduire le risque de chocs électriques, ne pas ouvrir les couvercies si un outil est nécessaire.
! WARNING ! For protection against fire hazard, replace only with same type and rating of fuse. ! AVERTISSEMENT ! Afin d'assurer la protection contre les risques d'incendie, remplacer uniquement par un fusible de même type et de même courant nominal.
! WARNING ! Grounding circuit continuity is vital for safe operation of equipment. Never operate equipment with grounding conductor disconnected. ! AVERTISSEMENT ! Risque de choc électrique. Pour un fonctionnement sans danger. Ne jamais utiliser l'équipment si le fil de terre n'est pas raccordé. ! WARNING ! To avoid electrical shock, disconnect power cord before servicing. ! AVERTISSEMENT ! Pour éviter les chocs électriques, débrancher le cordon d'alimentation avant le dépannage.
Electrical Safety Testing CAUTION Routine safety testing of analytical instruments (e.g., high potential voltage testing) may be required by various safety agencies. Testing should only be carried out by qualified personnel after seeking advice from the Applied Biosystems Service Department. Internal AC line surge suppressors may need to be disconnected before a test is performed. On completion of the tests, it is essential to reconnect the surge components.
Operating Precautions This manual contains important information regarding potential hazards that may arise during the operation of the instrument. It is essential that this information is read and thoroughly understood by all potential users of the instrument. This section describes precautions that must be observed in order to assure safe operation. If used otherwise, the protections provided by the instrument can be impaired.
Instrument Cover CAUTION This unit contains protective circuitry. Contact Applied Biosystems before performing any AC line tests. ! WARNING ! To reduce the chance of electrical shock, do not remove covers that require tool access. There are no user-serviceable components inside the instrument. Refer servicing to Applied Biosystems qualified service personnel. Temperature, Humidity, and Environment CAUTION This instrument is designed for indoor use.
Pollution Degree This equipment will operate safely in environments that contain nonconductive foreign matter up to Pollution Degree 2 in IEC 1010–1, CSA 1010.1 and UL 3101–1. Storage Conditions The PCR 9600 may be stored under the following conditions: ♦ ambient temperature is –20 to + 60°C (–4 to 140°F), ♦ ambient relative humidity is 20 to 80%, without condensation, ♦ altitude is in the range 0 to 12,000 meters.
Fuses and Power Interruption If power to the instrument fails or is turned off while the instrument is running, turn the instrument off and wait five minutes before restarting. If you do not wait, or if the power is restored quickly after a power failure, a fuse may blow. This does not mean that there is anything wrong with the instrument. It is caused by the refrigeration motor stalling because it is unable to start until the pressure bleeds away, which takes about five minutes.
Technical Support Contacting You can contact Applied Biosystems for technical support by telephone Technical Support 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 Biosystems Web site (please see the section “To Obtain Documents on Demand” following the telephone information below).
To Contact Technical Support by Telephone or Fax In North America To contact Applied Biosystems Technical Support, use the telephone or fax numbers given below. (To open a service call for other support needs, or in case of an emergency, dial 1-800-831-6844 and press 1.) Product or Product Area Telephone Dial... Fax Dial...
Product or Product Area Telephone Dial... Fax Dial...
Telephone Dial... Region Fax Dial...
Telephone Dial... Fax Dial... United Kingdom (Warrington, Cheshire) 44 (0)1925 825650 44 (0)1925 282502 All other countries not listed (Warrington, UK) 44 (0)1925 282481 44 (0)1925 282509 Region Japan Japan (Hacchobori, ChuoKu, Tokyo) 81 3 5566 6230 81 3 5566 6507 Latin America Del.A.
To Obtain Free, 24-hour access to Applied Biosystems technical documents, Documents on including MSDSs, is available by fax or e-mail or by download from our Demand Web site. To order documents... Then... by index number a. Access the Applied Biosystems Technical Support Web site at http://www.appliedbiosystems.com/techsupp b. Click the Index link for the document type you want, then find the document you want and record the index number. c.
Users Manual Summary If You Have Used the Applied Biosystems DNA Thermal Cycler or DNA Thermal Cycler 480 Describes the differences between the GeneAmp PCR System 9600 and the DNA Thermal Cycler/DNA Thermal Cycler 480. Preface Describes how to use this manual. Chapter 1. Introducing the GeneAmp PCR System 9600 Describes instrument operation, the hardware, and the software. Chapter 2. Installation Describes how to install the instrument and connect it to a printer Chapter 3.
Chapter 7. Utilities Describes how to obtain a history of the run, configure the instrument, run diagnostics, and update the file directory. Chapter 8. Maintenance Describes periodic maintenance procedures. Chapter 9. Troubleshooting Describes how to solve common problems and what to do in case of instrument power loss. Chapter 10. Specifications Lists and describes instrument specifications.
If You Have Used the Applied Biosystems DNA Thermal Cycler or DNA Thermal Cycler 480 You will find that the GeneAmp PCR System 9600 is in many ways similar in operation to the DNA Thermal Cycler and DNA Thermal Cycler 480, but there are several important differences.
Sample Block CAUTION Do not use mineral oil or glycerine in the sample block of the GeneAmp PCR System 9600. The GeneAmp PCR System 9600 is designed for oil-free operation. The MicroAmp Reaction Tubes fit tightly in the wells and a heated cover exerts an even pressure on all tubes. Mineral oil is not used on the sample surface because the heated cover eliminates condensation in the tubes. Sample Tubes The GeneAmp PCR System 9600 uses 0.2-mL MicroAmp Reaction Tubes or 0.
Comparing Files and Programs In the GeneAmp PCR System 9600 software, PCR files are referred to as programs. The following table lists the differences between DNA Thermal Cycler PCR files and GeneAmp PCR System 9600 PCR programs. Function File on the DNA Thermal Cycler Program on the GeneAmp PCR System 9600 PCR INCUBATIONS SOAK (File #1): An incubation file. HOLD: Set the hold time to the FOREVER option for an indefinite soak. TIME DELAY (File #2): An incubation file.
Function Keys 4 To do this: On the DNA Thermal Cycler On the GeneAmp PCR System 9600 Begin a run Press START from the first display in the file. Select RUN on the main menu, enter the program number, then press ENTER. Access a file Press FILE, press the numeric key(s) corresponding to the desired file number, then press ENTER. Select EDIT on the main menu, enter the desired program number, then press ENTER. Access the File Directory Press FILE. Then press ENTER. Select UTIL on the main menu.
File Storage With the GeneAmp PCR System 9600, you can store up to 150 programs. (A method is assigned a program number and is considered an individual program.) The Thermal Cycler stores up to 93 user files. Operation On the DNA Thermal Cycler, the run-time display counts down the number of cycles. On the GeneAmp PCR System 9600, the run-time display counts up the number of cycles. To pause a run on the DNA Thermal Cycler, press the STOP key once.
Setting Hold Times on the GeneAmp PCR System 9600 These general guidelines are based upon differences in how the instruments operate to heat and cool samples. The hold times that you specify in your PCR CYCL and AUTO programs for the GeneAmp PCR System 9600 will be shorter than those you used for your Step-Cycle or Thermo-Cycle files on the DNA Thermal Cycler.
Graphic Figure 1 Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600.
Tables 1 and 2 show some guidelines for converting hold times for the DNA Thermal Cycler or DNA Thermal Cycler 480 to hold times for the GeneAmp PCR System 9600. The table you use will depend on whether you are using an up ramp (the temperature is higher than that used in the previous segment) or a down ramp (the temperature is lower). ♦ If you are using an up ramp, you will base the new hold time on the change in temperature required to reach the next target temperature. See Table 1.
Note If methods developed on the GeneAmp PCR System 9600 are to be used on the DNA Thermal Cycler, you can use Table 1 to convert the hold times from GeneAmp PCR System 9600 to DNA Thermal Cycler. Simply add the indicated times instead of subtracting them. For down ramps, determine the change in temperature required to reach the next target temperature, then round off this value to the closest value given below.
Contents Preface: 1 Using the Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-1 Using the Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-1 Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-3 Software Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-3 Notes and Warnings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-4 Chapter 1.
Setting Up the Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6 Installing the 115-VAC Printer . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6 Installing the 230-VAC Printer . . . . . . . . . . . . . . . . . . . . . . . . . 2-10 Configuring the Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12 Configuring the GeneAmp PCR System 9600 . . . . . . . . . . . . . . . 2-14 Summary of Configuration Parameters . . . . . . . . . . . . . . . . . .
Chapter 4. Software Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1 Reviewing Keypad Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2 Use of the Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3 A Close Look at the Main Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4 Selecting a Function. . .
Software Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28 Using the STOP Key . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28 Recalling Programs: A Shortcut . . . . . . . . . . . . . . . . . . . . . . . . 5-30 The HOLD Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-31 The Displays in a HOLD Program . . . . . . . . . . . . . . . . . . . . . . 5-31 Description of HOLD Program Displays . . . . . . . . . . . . . .
Indicator Lights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-16 Run-Time Displays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-17 CYCL and AUTO Program Run-Time Displays . . . . . . . . . . . . 6-17 HOLD Program Run-Time Display . . . . . . . . . . . . . . . . . . . . . . 6-19 Pausing a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-20 Stopping a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
THIN Time Constant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-32 Printing the Configuration Parameters . . . . . . . . . . . . . . . . . . 7-34 The Diagnostic Function (DIAG) . . . . . . . . . . . . . . . . . . . . . . . . . . 7-35 Selecting the Diagnostic Tests . . . . . . . . . . . . . . . . . . . . . . . . . 7-36 Reviewing the History file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-38 About The History File . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Testing the Temperature Uniformity . . . . . . . . . . . . . . . . . . . . 8-13 Test Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-17 Changing External Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-18 Chapter 9. Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1 Troubleshooting . . . . . . . . .
11 Illustrations Figure 1-1 The GeneAmp PCR System 9600. . . . . . . . . . . . . . . . . . . . . . . . . . 1-1 Figure 1-2 Sample block and heated cover. . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3 Figure 1-3 The control panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4 Figure 2-1 DIP switch Settings on the Epson C82302 serial interface card. . .
Figure 5-2 Sample conversion of hold times for up ramps (DNA Thermal Cycler to GeneAmp PCR System 9600) . . . . . . . . . . . . . . 5-5 Figure 5-3 Sample conversion of hold times for down ramps (DNA Thermal Cycler to GeneAmp PCR System 9600) . . . . . . . . . . . . . . . . . . . . . 5-7 Figure 5-4 Editing Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8 Figure 5-5 Example of a printout for a CYCL program. . . . . . . . . . . . . . . . . .
Figure 7-4 Example of a list of programs listed according to user number. . . 7-12 Figure 7-5 The PRINT selection of the Directory function. . . . . . . . . . . . . . . . 7-15 Figure 7-6 The Configuration function. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-17 Figure 7-7 Diagram of a 1-degree C temperature interval. . . . . . . . . . . . . . . . 7-26 Figure 7-8 Initial displays for the five diagnostic tests. . . . . . . . . . . . . . . . . . .
Preface: Using the Manual P The GeneAmp PCR System 9600 is a highly sophisticated, yet easy-to-use temperature cycling instrument designed specifically to automate the PCR technique. Using the Manual The main function of this manual is to give you all the information needed to operate the GeneAmp PCR System 9600 in as productive a way as possible, utilizing all of the instrument's features. Note The unpacking and setup procedures for the GeneAmp PCR System 9600 are included in Chapter 2 of this manual.
We recommend that you follow this approach to learn about the GeneAmp PCR System 9600: P-2 1 Read this chapter to learn about the conventions used in the manual. 2 Read Chapter 1 to familiarize yourself with the instrument hardware and software. 3 If you are installing the instrument yourself, use this chapter as a guide. 4 Use the tutorial in Chapter 3 to learn the basic operation of the system in about 30 minutes.
Conventions The following conventions are used in this manual. Software Conventions ♦ The instrument display is pictured as follows. This display shows the main menu. Select Option 9600 RUN-CREATE-EDIT-UTIL ♦ In displays where the current temperature of the samples is indicated, the temperature is shown in the manual as xx.xC, as in the display below. CYCL# 26 PAUSE 10:00 xx.xC ♦ Messages seen on the display and referred to in the text are enclosed in quotation marks.
Notes and Warnings The following conventions are used in this manual: ! WARNING ! A warning indicates an operation that could cause personal injury if precautions are not followed. CAUTION A caution indicates an operation that could cause instrument damage if precautions are not followed. Note Notes emphasize significant information in a procedure or description.
1 Introducing the GeneAmp® PCR System 9600 1 Introduction This chapter describes the principles of instrument operation, the hardware, and the software. Figure 1-1 The GeneAmp PCR System 9600.
Principles of Operation The GeneAmp PCR System 9600 automates the Polymerase Chain Reaction (PCR) technique for amplifying DNA. The Polymerase Chain Reaction (PCR) technique is conceptually a very simple method for amplifying nucleic acids. It mimics the natural DNA replication process in that the number of DNA molecules generated by the Polymerase Chain Reaction doubles after each cycle.
restriction sites. Dideoxy sequencing can also be performed on the amplified product. Instrument Description The GeneAmp PCR System 9600 contains a programmable heating and cooling block, which rapidly and uniformly heats and cools PCR samples. A Look at the Sample Block The sample block is a 96-well aluminum block. Up to 96 samples in MicroAmp Reaction Tubes (0.2 mL) are loaded in a sample tray and placed in the block.
the power density at the edges is greater than that at the center to compensate for losses that may occur at the edges. A Look at the Control Panel The instrument control panel consists of a 40-character blue fluorescent display; three indicator lights that show you when the sample block is heating, cooling, or hot; and the keypad. The keypad includes standard numeric keys and eight function keys used for creating, storing, editing, or running PCR cycles. Figure 1-3 1-4 The control panel.
Instrument Features Features of the GeneAmp PCR System 9600 include: ♦ reproducibility of cycle times ♦ uniformity of PCR yields for samples ♦ sample tray accommodating up to 96 samples in an 8 x 12 format ♦ thin-walled MicroAmp Reaction Tubes allowing efficient heat transfer and improving equilibration times ♦ high speed of heating and cooling so that more samples can be run in a fixed amount of time, increasing productivity ♦ heated cover assuring that tubes fit tightly in the wells ♦ oil-fre
The software lets you: 1-6 ♦ create, store, and modify your own customized time and temperature programs and protect these programs with a user number, if desired ♦ link several programs together to create and store a PCR method ♦ automatically increment or decrement the setpoint time and/or temperature a fixed amount every cycle ♦ view the current status of your PCR cycle on one of two runtime displays ♦ review comprehensive run-time information in a history of the run ♦ run software diagnosti
Installing the GeneAmp PCR System 9600 2 2 I Introduction This chapter describes how to install the GeneAmp PCR System 9600. If your instrument has already been installed by an Applied Biosystems Service Representative, disregard these instructions.
Unpacking Inspect the GeneAmp PCR System 9600, and all other parts supplied, for any damage that may have occurred during shipment. If there has been any damage during transit, notify the carrier and Applied Biosystems immediately. Save the shipping container and all packing materials in case it becomes necessary to reship the instrument. Do not attempt to lift or move the instrument without the assistance of others. Safety training for proper lifting techniques is recommended.
Item Part No. Quantity 230-220V Conversion Kit (shipped with 230V unit) N801-0110 1 100V 50Hz to 60Hz Conversion N801-0111 Kit (shipped with 100V unit) 1 PCR System 9600 Video (Domestic and Japan) N801-0661 1 PCR System 9600 Video (Europe) N801-0660 1 Users Manual 0993-8660 1 Quick Reference Guide 0993-8690 1 Brochures 0993-8813 1 Supplies, Accessories, and Replacement Parts For Sales Assistance and Information: 1-800-345-5224. For Technical Assistance: 1-800-762-4001.
Power Requirements CAUTION Before the power is turned on for the first time at installation, be sure that the unit has been upright for at least four hours at normal indoor temperatures (15 degrees C to 30 degrees C). The GeneAmp PCR System 9600 operates on one of the following input voltages: Part No. Voltage (volts) Freq.
All 230VAC instruments are wired for single-ended line service. 230VAC instruments installed in locations that have double-ended line service or locations that have unpolarized power receptacles (as in Germany) must be rewired using the instructions provided with the 230V to 220V Conversion Kit, Applied Biosystems Part No. N801-0110. The 220/230 VAC units are supplied with a power cord that has a Continental European style plug (also known as Schuko or CEE 7/7).
Setting Up the Printer The GeneAmp PCR System 9600 can be used with an optional Epson LX-810 printer or other Epson-compatible printers with a serial (RS-232C) interface board. The printer is shipped with an Epson C82302 serial adapter card when ordered as part of Printer Kits (N801-0313 for 115VAC operation or N801-0314 for 230VAC operation). The card must be installed in the printer as instructed in pages 5-38 to 5-51 of the Epson LX-810 Instruction Manual (as explained below).
4 Connect one end of the cable (Applied Biosystems Part No. N801-0421) to the 25-pin (D shell) RS-232C connector on the side panel of the GeneAmp PCR System 9600. Connect the other end of the cable to the connector on the serial adapter card you just installed. Note When you are printing, the printer ON LINE/OFF LINE button must be in the ON LINE position. See page 3-3 of the Epson LX-810 User's manual.
Figure 2-1 2-8 DIP switch Settings on the Epson C82302 serial interface card.
RS-232 Communications Parameters for users who do not have an LX-810: 9600 Baud No Parity 8 data bits 1 stop bit GeneAmp PCR System 9600 Instrument Power Cord Connection Printer Dip Switch settings Fuse Holders Serial Port ON Cable N801-0421 ON/OFF Switch Epson LX-810 Printer Rear Panel 1 SW1 8 1 SW2 4 Epson LX-810 Printer Right Side Panel Note: When installing the serial interface card in the Epson LX-810, see pages 5-38 to 5-51 in the Epson LX-810 Users Manual.
Installing the 230-VAC Printer The Printer Kit for the 230-VAC GeneAmp PCR System 9600 (Part No. N801-0314) contains a printer (Part No. 0942-1015), with a serial adapter card. It also includes a printer cable (N801-0421) and a 230-volt adapter (Part No. 0942-1002). To set up and install the printer, proceed as follows: 2-10 1 Set the DIP switches on the Epson C82302 serial adapter card as shown in Figure 2-1.
Note When you are printing, the printer ON LINE/OFF LINE button must be in the ON LINE position. See page 3-3 of the Epson LX-810 User's manual. After you have installed and connected the printer, you must configure the GeneAmp PCR System 9600 for the printer as described on the following pages.
Configuring the Printer 1 Turn on the power switch located on the lower left side of the instrument. A beeper sounds and all three indicator lights flash. Two displays appear briefly. Finally, the instrument main menu appears: Select Option 9600 RUN-CREATE-EDIT-UTIL The cursor appears under the "R" in RUN. 2 Press the OPTION key three times. The cursor moves under UTIL. Select Option 9600 RUN-CREATE-EDIT-UTIL 3 Press ENTER.
The following display appears: Time Date HH:MM MM/DD/YY This display is used to set the time and date. 5 To set the time, press the appropriate numeric keys for hours and minutes (HH:MM), then press ENTER. The software will place the colon for you. Press ENTER after making each entry. 6 To set the date, press the appropriate numeric keys for month, day and year (MM/DD/YY), then press ENTER. The software will separate the numbers for you. 7 Press STEP.
Configuring the GeneAmp PCR System 9600 The final procedure in installing the GeneAmp PCR System 9600 is checking the instrument configuration.
Summary of Configuration Parameters Configuration EDIT-PRINT This display lets you edit or print the configuration parameters. Press ENTER to select EDIT. The first configuration screen, used to set the time and date, is displayed. Time Date HH:MM MM/DD/YY Set the time in hours and minutes (HH:MM), and the date in month, day, and year (MM/DD/YY). Press STEP to move to the next display.
Idle state setpoint 25C Set the temperature at which the block will be maintained when a program is not running. As factory set, the instrument will heat to 25 degrees C while idling and the heating indicator will flash. The default idling temperature may be changed to a new value. For operator safety, this value should be close to room temperature. Press STEP to move to the next display. Or, press BACK to move to the previous display. Start clock within x.
a. To change the default condition, press the OPTION key. “NO” will change to “YES” on the display and you will be able to select a different tube type when you start a run (see Chapter 6 for more information). b. Press ENTER. The following display appears: Rxn vol=100uL T= 9.5 Rxn vol= 50uL T= 7.0 This display lets you change the sample tube time constant.
There are two additional configurable parameters that let you change the time constants for MicroAmp Reaction Tubes and Thin Walled GeneAmp Reaction Tubes. We recommend that you only change these values if instructed to do so by future documentation. For more information, see pages 7-28 to 7-33.
Heater and Chiller Tests After you have configured the GeneAmp PCR System 9600, perform the heater and chiller tests as described in the following sections to verify that the instrument is operating correctly. Heater Test The heater test verifies that the sample block heaters and electronics are operating correctly. At the conclusion of the test, the display indicates whether the test was successful or not. The test takes approximately three minutes to run.
3 Press the OPTION key twice to move the cursor under DIAG and press ENTER. A display referring to the first diagnostic test appears: Enter Diag test # 1 REVIEW HISTORY FILE 4 Change the "1" to a "2" by pressing 2. Then press ENTER. The following display appears and the test begins: Enter Diag test # 2 HEATER TEST If “Heater Test Passed” appears on the display as shown below, proceed to the chiller test. If “Heater Test Failed” appears on the display, notify an Applied Biosystems Service Engineer.
Chiller Test The chiller test verifies that the refrigeration system is operating correctly. CAUTION Before you begin this test, make sure you place an empty MicroAmp Tray (MicroAmp Tray/Retainer Set, Part No. N801-0530) on the sample block, then slide the heated cover forward and turn the cover knob clockwise until the white mark on the knob lines up with the white mark on the cover. 1 The following display should appear. If not, follow Steps 1 through 3 in the heater test procedure on page 2-19.
Tutorial: Customizing a PCR CYCL Program 3 3 Introduction This tutorial explains how to set up a time and temperature profile for PCR. To do this, you will customize the CYCL (Cycle) program stored in instrument memory.
Before You Start Before you start this tutorial: 3-2 1 The system should be properly installed either by an Applied Biosystems service representative or according to the supplied instructions in Chapter 2, Installation, in this manual. 2 Read Chapter 1 in this manual. 3 Unwrap one of the MicroAmp Trays supplied with the instrument.
What is a CYCL Program? A CYCL program is a set of instructions in which you specify how the instrument should heat and cool your samples in a PCR cycle. The CYCL program is stored in the instrument software. You view the CYCL program by scrolling through a series of displays on the front panel screen. By entering the times and temperatures for your PCR application, you can easily customize the program to your needs. The CYCL program is a common type of PCR thermal profile.
For each setpoint, you specify a target temperature, a ramp time, and a hold time (see Figure 3-1). The ramp time is the time it takes to change from one temperature to another. The hold time is the length of the samples will be held at the specified temperature. With the GeneAmp PCR System 9600, the hold time begins when the samples, not the block, reach the target temperature. Figure 3-2 Setting temperature and time values for Setpoint #1.
Starting Up the Instrument Press the power switch (see Figure 1-3) to the ON position. Figure 3-3 Location of power switch. A beeper sounds, and all three indicator lights on the control panel flash. The screen lights up and a series of displays appear.
Getting to the CYCL Program 1 After you start the instrument, the main menu (shown below) appears on the screen. Select Option 9600 RUN-CREATE-EDIT-UTIL Think of the main menu as your “home base.” It gives you access to the major functions of the instrument. You can easily get to the main menu from any of the other displays by pressing the STOP key one or two times. Note If you press the wrong key in the steps that follow, press STOP one or two times to return to the main menu and start again.
3 To select an option on the main menu, you use the OPTION key. To learn how the OPTION key works, follow these steps: a. Press the OPTION key to move the cursor from one selection to the next: b. When the cursor reaches the last selection (UTIL), press OPTION to move the cursor to the first selection again: The OPTION key is used the same way on many different displays.
4 To create a program, you need to select the CREATE option. Press the OPTION key once to move the cursor under CREATE: Select Option 9600 RUN-CREATE-EDIT-UTIL Cursor 5 Press ENTER The next display appears: You have now learned how to make a menu selection. Using the OPTION key, you mark your selection, then you press ENTER to accept it. You’ll do this again in the next step. Create program HOLD-CYCL-AUTO-METH 6 Press the OPTION key to move the cursor under CYCL.
A Look at the CYCL Program In the following steps, you will look at the main displays in the CYCL program. In each display, you will see the default parameters (e.g., times and temperatures) that make up a common PCR cycle. Using the STEP key, you will quickly step through all the displays and accept the default values. Keep in mind, however, that default values can be changed, which you will do later on in this tutorial.
3 Press STEP to accept all of the default values and move to the next display. The display for Setpoint #2 appears: Setpt #2 Ramp 0:00 55.0C Hold 0:30 This display sets the ramp time, temperature, and hold time for Setpoint #2 — used for primer annealing. For a three-temperature cycle, the second PCR setpoint is commonly 55 degrees C and is held for 30 seconds. 4 Press STEP to accept the default ramp time, temperature, and hold time for Setpoint #2.
The following display appears: Total cycles = 25 Pause during run? NO 6 Press the BACK key to review the display for Setpoint #3. The illustration below shows you how the BACK key works. Setpt #3 Ramp 0:00 72.0C Hold 0:30 Press Back To display the previous screen Total cycles = 25 Pause during run? No 7 Now, press STEP to move forward again to the next display: Total cycles = 25 Pause during run? NO “Total cycles” specifies the number of times the three-temperature cycle will be repeated.
8 Press STEP to accept the default values in the display. The following display appears: CYCL#??? xx.xC RUN-STORE-PRINT-HOME This is the last display in the program. From here, you have the option of running, storing, or printing the program, or reviewing it again. In the next procedure, you will go through the program again to customize it with new PCR parameters.
Figure 3-4 Moving through the CYCL program displays.
Customizing the CYCL Program In the steps below, you will customize the CYCL program by changing some of the default parameters. Although we suggest some new temperatures and times to use, you may want to choose values relating to a current PCR application in your lab. Defining the Number of Setpoints 1 The first display in the CYCL program (shown below) should appear on your display. If it does not, press STOP one or two times to return to the main menu.
Defining Values for Setpoint # 1 Setpt #1 Ramp 0:00 94.0C Hold 0:30 In the following steps, you will change some of the default values for Setpoint #1. 1 Look for the cursor on the display. It appears under the ramp time. The default time of 0:00 is most commonly used. This causes the sample to be heated or cooled to the target temperature as fast as possible. 2 For this example, we will not change the default ramp time. Press ENTER to accept 0:00 minutes. The cursor moves to the temperature entry.
The cursor moves to the hold time: Setpt #1 Ramp 0:00 96.0C Hold 0:30 4 Sometimes, you may want to change an entry after you have pressed ENTER. To move back to the previous entry, you press the BACK key. The cursor is now at the hold time. Press BACK to move the cursor back to the temperature: Setpt $1 Ramp 0:00 94.0C Hold 0:30 Press Back To move the cursor back to the previous parameter 5 Now press ENTER to move the cursor forward again to the hold time.
Defining Values for Setpoint #2 Setpt #2 Ramp 0:00 55.0C Hold 0:30 1 Use the default ramp time by pressing ENTER 2 Enter 52.5 degrees C for the temperature by pressing 5, then 2, then 5. Then press ENTER. 3 We will not change the hold time, Press STEP to skip over this entry, The display for Setpoint #3 appears. Defining Values for Setpoint #3 Setpt #3 Ramp 0:00 72.0C Hold 0:30 1 Use the default ramp time by pressing ENTER. 2 Enter 74.5 degrees C for the temperature. Press ENTER.
Specifying the Number of Cycles Total cycles = 25 Pause during run? NO The first entry in the above display specifies the number of times the cycle will be repeated. 1 Enter 30 cycles: press 3 then press 0. When the entry is correct, press ENTER. The cursor moves to the entry, “Pause during run?” This allows you to pause a run to add a reagent to your sample solutions, for example. 2 The OPTION key is also used to change a NO selection to a YES and vice versa.
The next display (the last display in the program) is: Program Type CYCL Program Number not yet assigned O CYCL#??? xx.xC RUN-STORE-PRINT-HOME O “CYCL” in this display means that the type of program you have set up is a CYCL program. “#???” means that the program doesn’t have a program number yet since it hasn’t been stored. Store the program following the procedure on the next page. This will allow you to run the program you have customized at any time in the future without needing to set it up again.
Storing Your CYCL Program 1 The following display should appear on your screen: CYCL#??? xx.xC RUN-STORE-PRINT-HOME 2 Press the OPTION key to move the cursor beneath STORE, then press ENTER. The following display appears: Store Enter program # x At the cursor, x is the next available program number. If this is the first program stored on the instrument, x would be a “1” on the display. 3 Press ENTER to store the program under the displayed number.
The following display appears: Prog# x OK to store? YES 5 Press ENTER to store the program The following display appears: Program Type CYCL Assigned Program Number (1) O CYCL# 1 xx.xC RUN-STORE-PRINT-HOME On this display, CYCL is the type of program you have set up. The number of the program appears on the display following the program type. Your program is stored with the parameters you have entered. From this display, you could print the program parameters if a printer is available.
Starting a Trial Run In the following steps, you will learn how to load a tray and run the program you just stored, then stop it after a few moments. You will not be loading any samples in the tray for this exercise, but will be able to see how a run is initiated. Loading a Tray (without samples) Load an empty tray in the sample block by following these steps. 3-22 1 Turn the cover knob fully counterclockwise (see Figure 3-5).
Figure 3-5 Sliding the heated cover forward for a trial run.
Running the Program 1 Look at the display. The main menu (shown below) should be displayed. If not press the STOP key one or two times. Select Option 9600 RUN-CREATE-EDIT-UTIL 2 With the cursor beneath RUN, press ENTER. The following display appears: Run Enter program # _ 3 Press the key for the number of the program you created and stored earlier in this tutorial. (If it was the first program stored on the system, press 1.) Then press the ENTER key.
5 Before the run starts, a display will appear that reminds you to close and tighten the heated cover, When the run starts, you will see a run-time display that is continuously updated for the program being run. During ramp segments, you will see the following display: Setpoint temperature Current sample temperature O Ramp to 96.5C xx.
Current setpoint number Total cycles in program O Setpt #1 Tot Cyc 30 Hrs left 0.7 Prog 1 Estimated time left in program Current program # 7 Press MORE again to return you to the first run-time display. The illustration below shows you how the MORE key works. O Ramp to 96.5C xx.xC 0:30 Cycle 1 Press More Setpt #1 Tot Cyc 30 Hrs left 0.7 Prog 1 8 To move between the two run-time displays After a few moments, press the STOP key to abort the run. The following display appears: CYCL# 1 xx.
CYCL# 1 Abort xx.xC RUN-STORE-PRINT-HOME 10 You can now return to the main menu. Press the OPTION key to move the cursor to HOME, then press ENTER. Select Option 9600 RUN-CREATE-EDIT-UTIL The Next Step In this tutorial, you have learned how to set up a threetemperature PCR CYCL program. You may now want to try creating a CYCL program to perform two-temperature PCR. Start by selecting CREATE on the main menu, Then, select CYCL for the type of program you want to create.
Software Basics 4 4 Introduction This chapter presents an overview of the GeneAmp® PCR System 9600 software and describes the HOLD, CYCL, and, AUTO programs and PCR methods.
Reviewing Keypad Basics If you haven’t already done so, go through the Tutorial in Chapter 3 to learn how to use the keys. The following section summarizes the functions of the keys. On the left side of the keypad are function keys used to select the thermal cycling parameters and run programs. The right side of the keypad is used to specify numeric values, for example, time and temperatures for an analysis, or the number of cycles. After you type a numeric value, you press the ENTER key.
Use of the Keys There are two types of keys: run-time keys and editing keys. Runtime keys are used while running samples, for example, to start and stop an analysis. Editing keys are used to move through the different displays and select program options. The ENTER key is also considered an editing key. After you select an item by marking it with the cursor, pressing ENTER accepts your selection.
A Close Look at the Main Menu Select Option 9600 RUN-CREATE-EDIT-UTIL The main menu (shown above) appears a few seconds after the instrument is first turned on. If the instrument is already on and the main menu is not shown, you can always access the main menu by pressing the STOP key until it is displayed. Note If the display on your screen has the following options: “RUNSTORE-PRINT-HOME,” you can select HOME to get to the main menu. (Press the OPTION key to move the cursor under HOME, then press ENTER.
Selecting a Function 1 Press OPTION to move the cursor from one option to the next. When the cursor reaches UTIL, pressing OPTION again will move it back to RUN. 2 When the cursor is at the desired selection, press ENTER. You will then see the first display for the option you selected. For example, when you select RUN or EDIT, you will be asked to enter the number of a program. When you select CREATE, you then select the type of program you want to use.
An Overview of PCR Programs and Methods A program is a set of instructions in which you specify how the instrument should heat and cool your samples for PCR. Three types of programs are stored in the instrument software HOLD, CYCL, and AUTO. You can view each program by scrolling through a series of displays on the front panel screen. Each program contains default parameters, which you can change as necessary to customize the program.
Figure 4-3 HOLD, CYCL, AUTO, and METH programs Storing Programs and Methods By storing the programs and methods you can easily access and run them later. Up to 150 programs be stored on the GeneAmp PCR System 9600. A program can be a method (a series of linked programs) or an individual program. Both methods and programs are assigned program numbers.
The HOLD Program During a HOLD program the temperature of the sample block (and the sample) is held at one temperature for either a fixed time interval or an indefinite period. Figures 4-4 and 4-5 show the two common types of HOLD programs. A HOLD program would normally be used before or after running a CYCL program. For example a high temperature (e.g., 94 degrees C) HOLD might be used before cycling and a low temperature (e.g., 4 degrees C) HOLD might be used after cycling.
Figure 4-4 A HOLD program held for an indefinite time. Figure 4-5 A HOLD program held for a specific time interval.
CYCL: The Cycle Program A CYCL program contains the thermal ramp and hold segment patterns for PCR cycling. It contains up to nine setpoints. Each setpoint comprises a ramp segment and a hold segment for the specific target temperature. The pattern can be repeated up to 99 times. A complete cycle for a common profile requires about three or four minutes. Typically, there are two or three setpoints in a CYCL program. The first setpoint is commonly used for DNA denaturation or melting.
Figure 4-6 A common CYCL program 4-11
The AUTO Program An AUTO program allows the user to automatically increment or decrement the setpoint times and temperatures a fixed amount every cycle. By increasing the extension time with each cycle, it may be possible to increase product yield with a fixed amount of enzyme. The enzyme is not initially limiting, but eventually, if more enzyme is not added, longer times may be needed to continue with exponential increases in product.
Figure 4-7 An AUTO program used to increase hold time.
PCR Methods PCR methods are used to automatically link together up to 17 programs for a specific PCR application. To create a method, you use the METH program. An example of a method is shown in Figure 4-8. This method starts with a HOLD file used for pre-PCR denaturation (e.g., 94.0 degrees C for five minutes). This is followed by a CYCL program for three-temperature PCR. A final HOLD program concludes the run, for post-PCR storage overnight (at 4.0 degrees C, for example).
Setting Up PCR Programs and Methods 5 5 Introduction This chapter describes how to use the HOLD, CYCL, and AUTO programs to create your own PCR programs. You will learn how to store, access, edit, and print these programs. This chapter also describes how to setup a PCR method, in which you specify a sequence of programs for a run. For example, pre-PCR incubations, PCR cycling, and post-PCR incubations can be linked together in a single method.
Setting Hold Times on the GeneAmp® PCR System 9600 If you have used the DNA Thermal Cycler or DNA Thermal Cycler 480, read the following information on setting hold times. These general guidelines are based upon differences in how the instruments heat and cool samples. The hold times that you specify in your PCR Cycle and Auto programs for the GeneAmp PCR System 9600 will be shorter than those you used for your Step-Cycle or Thermo-Cycle files on the DNA Thermal Cycler.
Figure 5-1 Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600 5-3
Tables 5-1 and 5-2 show guidelines on how to convert hold times for the DNA Thermal Cycler or DNA Thermal Cycler 480 to hold times for the GeneAmp PCR System 9600. The table you use will depend on whether you are using an up ramp (the temperature is higher than in the previous segment) or a down ramp (the temperature is lower). ♦ If you are using an up ramp, you will base the new hold time on the change in temperature required to reach the next target temperature. See Table 5-1.
Figure 5-2 shows an example of converted hold times. In this example, the temperature was increased by 17 degrees C, This value was rounded to 15 degrees C. According to Table 5-1, we should subtract 45 seconds from the hold time on the DNA Thermal Cycler, giving us a new hold time of 35 seconds.
Table 5-2 After Down Ramps: Converting Hold Times Greater than One Minute (DNA Thermal Cycler to GeneAmp PCR System 9600) For down ramps, determine the change in temperature required to reach the next target temperature, then round off this value to the closest value given below. Then, based on the starting temperature of the ramp, determine the number of seconds to subtract from the DNA Thermal Cycler hold time to arrive at the new hold time.
In the example below, the temperature was decreased by 22 degrees C. This value was rounded to 20 degrees C. According to Table 5-2, with a starting temperature of 94 degrees C, we should subtract 53 seconds from the hold time on the DNA Thermal Cycler, giving us a new hold time of 27 seconds.
Editing Keys To create, view, or edit programs and methods, you will use the following keys. Figure 5-4 Editing Keys The function of each key is described below. 5-8 BACK Moves the cursor to the previous parameter or display. STEP Moves the cursor to the next parameter or display OPTION Moves the cursor to your selection. Changes a YES response to a NO and vice versa. STOP Returns you to the last display in a program when pressed once. When pressed twice, returns you to the main menu.
Creating and Editing Programs The main steps involved in creating and editing programs are summarized below. These steps are explained in detail in the following pages. 1 Start at the main menu. 2 Choose one of the following: a. Select CREATE on the main menu if you want to create a new program. b. On the next display, choose the type of program — HOLD, CYCL, or AUTO — you want to create. OR a.
Creating a Program 1 Access the main menu. Select Option 9600 RUN-CREATE-EDIT-UTIL 2 Press the OPTION key to select CREATE, then press ENTER. The following display appears Create a program HOLD-CYCL-AUTO-METH 3 Press the OPTION key to select the type of program — HOLD, CYCL, or AUTO — you want to create, then press ENTER. (The METH option is used to create a method. See page 5-18.) 4 Specify the thermal cycling parameters for the program.
Storing the Program 1 Press the OPTION key to move the cursor beneath STORE, then press ENTER. The following display appears: Store Enter program # x The number “x” is the next available number. If this is the first file being stored, “x” would be a “1” on the display. Up to 150 programs can be stored. 2 Press ENTER to store the method under the displayed number. OR To use a different number, type the number (1-150), then press ENTER.
If you select YES, the following display will appear: Store Enter user # In this display, you can specify any number from 1 to 9999 for your user identification number. Make a note of the number you choose for later use. Type the number, then press ENTER. The following display appears: Prog # x User #xxxx OK to store? YES Note If you see a display that reads, “Prog #x: OK to (overwrite?,” you typed a number (in Step 2) that has already been used. Press OPTION key to select YES or NO.
Editing a Program When you want to view a program you have stored or make changes to it, you use the Edit function. You can also modify an existing program to create a new one. This can save you time when you need to change only certain program parameters. To edit a program: 1 Access the main menu. Select Option 9600 RUN-CREATE-EDIT-UTIL 2 Press the OPTION key to select EDIT, then press ENTER.
Note If you enter a number for a program that does not exist, you will see a message that reads “Program not found.” The next display allows you to choose the program number you want to edit again. 4 Edit the program as necessary. The displays in each program are described in the tables at the end of this chapter. Press ENTER after you make a numeric entry. Press STEP to advance to the next display. Press BACK to return to a previous parameter or display.
b. Type the original number for the program, then press ENTER. This allows you to replace the original program with the new edited version. The subsequent display will ask “OK to overwrite?” Select YES and the original program will be over-written by the new edited version. If the original program was protected, you will need to enter the user identification number that was specified when the program was first created before you can overwrite it.
Printing a Program If the instrument is configured for a printer, you can obtain a printout of the parameters in a program. For more information on configuring a printer, see Chapter 7, “Utilities.” 1 You can print any program when the last display in the program is on the screen. The last display for the Cycle program is shown below. (To quickly get to this display while you are in a program, press STOP.) CYCL#??? xx.xC RUN-STORE-PRINT-HOME 2 Press the OPTION key twice to select PRINT, then press ENTER.
Creating and Editing Methods The main steps involved in creating and editing methods are summarized below. These steps are explained in more detail on the following pages. 1 Start at the main menu. 2 Choose one of the following: a. On the main menu, select CREATE if you want to create a new method. b. Then select METH on the next display. OR a. Select EDIT on the main menu if you want to view or edit a method you have already stored (and assigned a number). 3 Link together a series of programs.
Creating a Method A method is a series of up to 17 programs linked together. For example, you can link a HOLD program to a CYCL program and conclude your experiment with another HOLD program. To create a method: 1 Access the main menu. Select Option 9600 RUN-CREATE-EDIT-UTIL 2 Press the OPTION key to select CREATE, then press ENTER. You obtain the following display: Create program HOLD-CYCL-AUTO-METH 3 Press the OPTION key to select METH, then press ENTER.
Note If you enter a program number for a program that does not exist, you will see a message that reads “Program not found.” The next display allows you to choose the program number you want to edit again. A program can appear more than one time in a method. Also, the same program can be used in more than one method. 5 Press STEP to move to the next display. If you are linking seven or more programs in a method, the following display appears.
8 Program Type: (Method) The last display to appear when you are creating a method allows you to run, store, or print the method: Program Number (not yet assigned) METH#??? xx.xC RUN-STORE-PRINT-HOME 9 5-20 In most cases, you will want to store the method and assign it a number so that it can be run at any time. Use the following procedure to store the method.
Storing the Method 1 Press the OPTION key to move the cursor beneath STORE, then press ENTER. The following display appears: Store Enter program # x X is the next available number. If this is the first file being stored, x would be a “1” on the display. 2 Press ENTER to store the method under the displayed number. OR To use a different number, type the number (1-150) then press ENTER.
Store Enter user # In this display, you can specify any number from 1 to 9999 for your user identification number. Make a note of the number you choose for later use. Type the number, then press ENTER. The following display appears: Prog # x User #xxxx OK to store? YES Note If you see a display that reads, “Prog #x: OK to overwrite?; you typed a number (in Step 2) that has already been used. Press OPTION key to select YES or NO. YES stores the new file and erases (overwrites) the old one.
Editing a Method When you want to view a stored method or change it so it includes a different sequence of linked programs, you use the Edit function. To edit a method: 1 Access the main menu. Select Option 9600 RUN-CREATE-EDIT-UTIL 2 Press the OPTION key to select EDIT, then press ENTER. You obtain the following display: Edit Enter program # 3 _ Type the number of the method you wish to edit, then press ENTER. The following display appears.
Note If you enter a program number for a program that does not exist, you will see a message that reads “Program not found.” The next display allows you to choose the program number you want to edit again. 5 The last display gives you the option of storing the file. Press the OPTION key to select STORE, then press ENTER. The following display appears: Store Enter program # x The next available number (x) appears at the cursor. 6 To store the method, you have two options.
If the original method was protected, you will need to enter the user identification number that was specified when the method was first created before you can overwrite the method. The following display will appear: Prog x is protected Enter user # Type the correct user number, then press ENTER. The next display will ask “OK to overwrite?” Select YES and the original method will be overwritten by the new edited version.
3 AB GeneAmp Select METHOD to print out a list of the linked program numbers specified in the method (see Figure 5-6). Or, select PROGRAM DATA to print out the complete program parameters for each program linked in the method. PCR System 9600 Ver 2 June 1, 1992 10:55 am METH Program #??? HOLD Program #l CYCL Program #2 HOLD Program #3 Figure 5-6 Example of a method printout using METHOD.
AB GeneAmp PCR System 9600 Ver 2 June 1, 1992 10:59 am METH Program #??? HOLD Program #1 - Program Parameters Hold at 95.0C Hold for 5:00 Beep while Hold? NO CYCL Program #2 – Program Parameters 3 Temperature PCR SetPt #l 94.0C Ramp Hold 0:00 0:30 SetPt #2 55.0C Ramp Hold 0:00 0:30 SetPt #3 72.0C Ramp Hold 0:00 0:30 Total cycles = 25 Pause during run? NO HOLD Program #3 - Program Parameters Hold at 4.
Software Shortcuts Below are some hints to getting around quickly in the software while you are creating or editing programs. Using the STOP Key While you are creating or editing a program, you may want to start over, or use another function of the instrument. You can easily do this by using the STOP key. 1 With any of the program displays shown, press STOP. The following display appears: Program Type: (CYCL) Program Number (not yet assigned) CYCL#??? xx.
A shortcut to the above procedure is: 1 With any of the program displays shown, press STOP. The following display appears: CYCL#??? xx.xC RUN-STORE-PRINT-HOME 2 Instead of selecting HOME on this display, you can immediately return to the main menu by pressing STOP again. However, any changes you have made to a program will be lost.
Recalling Programs: A Shortcut Once you have finished editing or running a program, you can quickly recall another program without needing to return to the main menu. 1 Once you have stored a program, your display will look like this (CYCL program shown): Program Type: Program Number (26) CYCL# 26 xx.xC RUN-STORE-PRINT-HOME 2 Although the cursor appears under RUN, at this point, you can enter any program number. The program number you enter will appear on the top line. Then press ENTER.
The HOLD Program During a HOLD program, the temperature of the sample block (and the sample) is held at one temperature for either a fixed time interval or an indefinite period. These two basic types of programs are shown in Figures 4-4 and 4-5. The Displays in a HOLD Program Figure 5-8 shows the main displays that make up a HOLD program. These displays are described on the following pages. Figure 5-8 The series of displays in a HOLD program.
5 Description of HOLD Program Displays Hold at 4.0C Hold FOREVER- 10:00 This display allows you to set the temperature at which the sample will be held and the length of time this temperature will be maintained. Press ENTER to accept the default temperature (4 degrees C), or select a different temperature. Enter the temperature in a decimal form, but do not type the decimal point. For example, to specify 82.0 degrees C, press 8 2 0. Then press ENTER.
CYCL: The Cycle Program A CYCL program contains the thermal ramp and hold segment patterns for PCR cycling. It contains up to nine setpoints. Each setpoint comprises a ramp segment and a hold segment for the specific target temperature. The pattern can be repeated up to 99 times. Typically there are two or three setpoints in a CYCL program. A complete cycle typically requires less than two to four minutes. The Displays in a CYCL Program Figure 5-9 shows the main displays that make up a CYCL program.
Description of CYCL Program Displays 3 Temperature PCR Defines the number of incubation temperatures or setpoints used in the PCR cycle. A typical PCR cycle consists of three (3) setpoints; therefore, #3 is the default value. Press ENTER to accept the default, or type a different number (1-9), then press ENTER. Setpt #1 Ramp 0:00 94.0C Hold 0:30 Setpoint #1 in a typical cycle program is used for DNA denaturation or melting.
You can accept any of the default values for Setpoint #1 by pressing the ENTER key, or you can change the values using the following steps: Setpt #2 Ramp 0:00 55.0C Hold 0:30 1 For the ramp time, use the numeric keys to specify the time (in minutes and seconds). For example, to specify a ramp time of one minute, press 1 0 0, then press ENTER. 2 For the setpoint temperature, enter the temperature in decimal form. You do not type a decimal point. For example, to specify 96.
Setpt #3 Ramp 0:00 72.0C Hold 0:30 Setpoint #3 in a typical cycle program is used for primer extension. This display sets the ramp time, target temperature, and hold time for the third setpoint (Setpt #3). The default values are shown in the display to the left. You can accept any of the default values for Setpoint #3 by pressing the ENTER key, or you can change the values using the same procedure as that for Setpoint #1 (see above). Setpt #n Ramp 0:00 72.
Pause after setpt #1 Beep while pause?YES The display appears only if you specified a pause in the previous display. ln this display, you define the setpoint after which you want to pause the run. Type the number of the desired setpoint, then press ENTER. During the pause, you specify whether or not you want a beeper to sound. Press the OPTION key to change the YES (default) to a NO and vice versa. When the desired response is displayed, press ENTER.
CYCL #??? xx.xC RUN-STORE-PRINT-HOME 5-38 The last display in the program indicates the program type, followed by “???,” which means that the program has not yet been stored and assigned a number. It also displays the calculated sample temperature. The options in this display allow you to run, store, or print the program, or return to the main menu.
The AUTO Program An AUTO program allows the user to automatically increment or decrement the setpoint times and temperatures a fixed amount every cycle. The Displays in an AUTO Program Figure 5-10 The main displays in a three-temperature AUTO program.
Description of AUTO Program Displays 3 Temperature PCR Defines the number of incubation temperatures or setpoints used in the PCR cycle. A typical PCR cycle consists of three (3) setpoints; therefore, 3 is the default value. Type the number of setpoints you wish in your DNA amplification experiment (1-9), then press ENTER. Setpt #1 Hold for 94.0C 0:30 This display sets the following values for the first setpoint (Setpt #1): ♦ Setpoint temperature. The default value is 94.0 degrees C.
Setpt #1 94.0C Change time/temp? NO 1 For the setpoint temperature, enter the temperature in decimal form. You do not type a decimal point. For example, to specify 89.0 degrees C, press 8 9 0, then press ENTER. 2 Specify the hold time in minutes and seconds, then press ENTER. For example, to specify one minute and five seconds, press 1 0 5, then press ENTER. This display allows you to incrementally increase or decrease the hold time or temperature of the first setpoint in successive cycles.
♦ Enter the temperature increment in decimal form, except you do not type a decimal point. For example, to specify a two-degree increment, press 2, then 0. Then press ENTER. OR ♦ Press ENTER to accept the default (0.0) temperature. This will not change the specified temperature of Setpoint #1 in successive cycles. The cursor moves to the hold time increment. Setpt #2 Hold for 55.0C 0:30 Setpt #2 55.
Setpt #3 72.0C Hold for 0:30 Setpt #3 72.0C Change time/temp? NO Setpt #n 0.0C Hold for 0:30 Total cycles = 25 Pause during run? NO These two displays are used to set the temperature and hold time for the third setpoint (Setpt #3) and change the time and temperature values in successive cycles, if desired. To change these displays, use the same procedure as described for Setpoint #1. A display will appear for each setpoint up until the total number of setpoints specified in the first program display.
Pause after setpt #1 Beep while pause?YES The display appears only if you specified a pause in the previous display. In this display, you define the setpoint after which you want to pause the run. Type the number of the desired setpoint, then press ENTER. During the pause, you specify whether or not you want a beeper to sound. Press the OPTION key to change the YES (default) to a NO and vice versa. When the de-sired response is displayed, press ENTER.
AUTO# ??? xx.xC RUN-STORE-PRINT-HOME The last display in the program indicates the program type, followed by “???,” which means that the program has not yet been stored and assigned a number. It also displays the calculated sample temperature. The options in this display allow you to run, store, or print the program, or return to the main menu.
Running PCR Samples6 6 Introduction To run samples, turn on the instrument and follow these procedures, which are explained in this chapter. ♦ Loading Samples in the Tray ♦ Placing the Sample Tray in the Block ♦ Removing the Sample Tray from the Block ♦ Removing Samples from the Tray ♦ Specifying a Program or Method ♦ Starting a Run Note After you turn on the instrument, wait 10 minutes before you run your samples. ! WARNING ! Never run the instrument without a sample tray in place.
Loading Samples The GeneAmp PCR System 9600 uses a 96-position sample tray (MicroAmp Tray) and retainer (MicroAmp Retainer) for 0.2-mL MicroAmp Reaction Tubes. Using the 96-Position Sample Tray with MicroAmp Reaction Tubes To load the 96-position MicroAmp Tray, follow the steps below (refer to Figure 6-1). CAUTION The GeneAmp PCR System 9600 is designed for oil-free operation. It does not use mineral oil or glycerine in the sample block.
Figure 6-1 Setting up the 96-position sample tray.
Note When using MicroAmp Reaction Tubes with Caps, place the required number of tubes into a MicroAmp Base, then fill each tube with PCR reagents and close the caps firmly. Position an empty MicroAmp Tray in the sample block, then place the MicroAmp Reaction Tubes with Caps into the MicroAmp Tray sitting in the sample block. 4 Place the MicroAmp Retainer over the sample tray and tubes (see Figure 6-1). The retainer and the tray are keyed so the retainer can fit only one way.
Placing the Sample Tray in the Block 1 Lift the sample tray and retainer assembly from the sample tray base and place it in the sample block. Make certain that the notch in the sample tray is at the left of the block. The receptacle in the tray labeled A1 will then be in the upper left-hand corner of the block. Once the tray is placed in the block, be sure that the rim of the tray engages with the channel around the block. Figure 6-3 Placing the sample tray in the block.
2 Make certain that the cover knob is completely counterclockwise, which fully raises the platen, before you attempt to slide the heated cover forward. Then slide the cover forward. Figure 6-4 6-6 Sliding the heated cover forward.
3 Turn the cover knob clockwise until the white mark on the knob lines up with the white mark on the cover (indicating the full clockwise position). This lowers the platen onto the tray. Figure 6-5 Turning the cover knob.
Using the Cap-Installing Tool Use the MicroAmp Cap-Installing Tool, supplied with your instrument, to cap a single sample tube or a row of sample tubes as described in the following procedure. 1 Place individual sample tubes or a row of tubes in the sample tray (you don't have to use a retainer). 2 Manually press the cap(s) onto the tube(s) so that the caps are not sitting loosely on the tubes. 3 Use the roller end of the tool to press a row of caps into a row of sample tubes.
Removing Samples from the Tray The following procedure describes how to remove the sample tubes from the tray: 1 Place the sample tray back on the base and remove the sample caps. 2 Remove the tray from the base. 3 Grasp one end of the tray with one hand, and with your other hand, press in the front and back tabs on the retainer (see Figure 6-6). Then push up and remove the retainer. 4 Remove the sample tubes. Figure 6-6 Removing samples from the tray.
Specifying a Program or Method To specify the time and temperature pattern you want to use to run PCR samples, you can create a new program or method, edit an existing one, or recall one you have previously stored. Create a new program or method Select the CREATE option on the main menu and choose a type of program: HOLD, CYCL, or AUTO. Modify the parameters in the program displays by referring to the description of each program in Chapter 4.
Starting the Run Run Keys The following keys are used to start a run or are used during the run. Figure 6-7 Run-Time Keys The function of each key is described below. RUN Starts or restarts a sample run. MORE Displays more information about run-time parameters. PAUSE Interrupts a run so you can add a reagent to your samples, or add or remove samples. STOP Aborts a run.
Running a Stored Program To run a program that you have previously stored: 1 Access the main menu. Select Option 9600 RUN-CREATE-EDIT-UTIL CAUTION Before you start a run, make sure the “Start clock within x.xC of setpoint” parameter in the Configuration function is set correctly. To do this, select “UTIL” on the main menu, then select “CONFIG” on the Utilities menu. Press ENTER, then press the STEP key five times to view the “Start clock...” parameter. See Chapter 7 for complete instructions.
4 If the “Special Tube?” parameter in the Configuration function (see Chapter 7) has been set to “NO,” pressing the OPTION key will change the tube type to Thin-Walled GeneAmp Reaction Tubes. On the display, “MICRO” changes to “THIN.” Note Instructions for the use of sample tubes other than MicroAmp Reaction Tubes will be included in separate documentation.
♦ If you have a printer and it has been enabled (using the Configuration function), the following display appears: Select print mode OFF-CYCLE-SETPOINT This display lets you select the type of printout you want: 7 OFF: Disables data output to the printer for this run. CYCLE: Prints a message that reads “Complete” after each cycle. SETPOINT Prints actual and programmed time and temperature data for each ramp and hold segment during cycling.
Figure 6-8 option. An example printout of a CYCL program using the SETPOINT ! WARNING ! During a sample run, keep the heated cover pulled forward and tightened down at all times. This will guard against burns and guarantee the best temperature uniformity.
Indicator Lights The three indicator lights on the control panel of the instrument indicate the operating status, as described below. ♦ Heating, when lit, indicates that the heater is active. When flashing, it indicates that the system is controlling the sample temperature. ♦ Cooling, when lit or flashing, indicates that ramp cooling is active. Note Both of the above lights will be lit simultaneously when the sample is being held at a subambient temperature.
Run-Time Displays During a run, you will see a run-time display that is continuously updated for the program being run. CYCL and AUTO Program Run-Time Displays The run-time displays for a CYCL program and an AUTO program are the same. If you are in a ramp segment, the display will show “Ramp to. . .” If you are in a hold segment, the display will show “Hold at. . .” These displays are shown in Figure 6-9. Setpoint temperature Current sample temperature Ramp to 94.0C xx.
Ramp to 94.0C xx.xC 0:30 Cycle 1 Press More Setpt #1 Tot Cyc 30 Hrs left 0.5 Prog 1 To move between the two run-time displays Figure 6-10 Using the MORE key. The parameters in the second run-time display are explained in Figure 6-11. Current setpoint Total cycles in program Setpt #1 Tot Cyc 25 Hrs left 1.2 Prog 26 Estimated time left in program Program # Figure 6-11 More run-time information in a CYCL program. Press MORE again to return you to the first run-time display.
HOLD Program Run-Time Display Figure 6-12 shows the run-time displays for a HOLD program. Use the MORE key to view the second run-time display. Press the MORE key again to return to the first run-time display. Programmed target temperature Current sample temperature Hold at 95.0C xx.xC 4:30 Prog 1 Time remaining Current program # Press More To move between the two run-time displays Hrs left 0.2 Prog Time remaining 1 Current program # Figure 6-12 Run-time displays for a HOLD program.
Pausing a Run Once a run has started, you can manually pause a run, in order to add a reagent to your samples, for example, using the PAUSE key. Note that the instrument will automatically pause if you select the Pause option in a CYCL or AUTO program. ! WARNING ! Be careful not to touch the sample block or the bottom of the heated cover during a pause. These areas may be hotter than 100 degrees C. 1 Press the PAUSE key. The instrument beeps and a display similar to the one shown below appears.
Press the STOP key again. The run is aborted and a display similar to the one shown below appears: CYCL# 26 Abort xx.xC RUN-STORE-PRINT-HOME This display occurs in a CYCL program. 3 If you change your mind and do not want to abort the run, press the OPTION key to change “YES” to “NO,” then press ENTER. OR Press the RUN key. The run resumes. 4 To run the program from the beginning, select the RUN option.
Reviewing the History of the Run Once a run has been completed (or aborted), you can obtain a record of the run called a History file. If you want to view the current History file for a run, you must view it before you start the next run, since each time a new run begins, the previous History file is erased. A History file can contain status records or data records. Status records list the status messages received during the run, such as “Method Complete” or various error messages.
Utilities 7 7 Introduction This chapter explains the Utilities functions.
Getting to the Utilities Menu To get the Utilities menu: 1 Get to the Main menu. Press the STOP key once or twice until the Main menu appears: Select Option 9600 RUN-CREATE-EDIT-UTIL 2 Press the OPTION key three times to move the cursor to UTIL, then press ENTER. The Utilities menu appears: Select function DIR-CONFIG-DIAG-DEL The functions available from the Utilities menu are: 7-2 ♦ DIR Select this function to display or print a listing of your programs by program number, type, or user number.
Selecting a Utilities Function To select one of the Utilities functions: 1 Press OPTION to move the cursor from one function to the next. When the cursor reaches DEL, press OPTION to move the cursor back to DIR. 2 When the cursor is under your desired selection, press ENTER. You will then see the first display for the function you selected. Figure 7-1 shows the first displays for the Utilities functions.
The Directory Function (DIR) The Directory function lets you display or print programs according to: ♦ program number ♦ type, or ♦ user identification number Once you view a directory, you can return to Utilities menu or the Main menu using the STOP key. Listing Programs by their Program Number (PROG) The PROG selection lets you list your programs by their program number on a series of displays, starting with the first program number that you enter.
3 Press the numeric keys that correspond to the program number of the program you want to list first, then press ENTER. In our example, the default is shown. Each of the next displays will list a program by its program number and type, beginning with Program #1. 4 Press STEP to view the next display. In our example, Program #1 is a Hold program: HOLD #1 5 Press STEP to view the next display, which will list Program #2.
Directory Enter program # Press Step 1 to move forward to the next display Press HOLD #1 Stop to return to the first display Press Step Back to move to the previous display Press CYCL #2 Stop to return to the first display Step Back Press Stop AUTO #3 to return to the first display Figure 7-2 7-6 Example of a list of programs listed according to program number.
Listing Programs by their Program Type (TYPE) The TYPE selection lets you list all your programs of a specific program type (HOLD, CYCL, or AUTO) in numerical order. To list your programs by their program type: 1 Select DIR on the Utilities menu as described on page 7-3. The Directory display appears: Directory PROG-TYPE-USER-PRINT 2 Press OPTION to move the cursor to TYPE, then press ENTER.
For example, if your first HOLD program is HOLD #14, the following display appears: HOLD #14 4 Press STEP to view the next display in your program listing. In our example, the next HOLD program is HOLD #26: HOLD #26 5 Press BACK each time you want to view the previous program in the list. 6 You can press STOP at any time to return to the display in which you selected the program type. Figure 7-3 on the next page shows an example of a list of programs grouped by program type.
Directory HOLD-CYCL-AUTO-METH Press to move forward to the Step next display Press HOLD #14 Stop to return to the first display Press Step Back to move to the previous display Press HOLD #26 Stop to return to the first display Step Back Press HOLD #31 Stop to return to the first display Figure 7-3 Example of a list of programs listed according to program type.
Listing Programs by their User Number (USER) The USER selection lets you list all programs that have been stored under a previously specified user number. (While storing a program, you have the option of protecting the program by entering a user identification number.) This type of directory will also list the program type and program number. To list your programs by their user number: 1 Select DIR on the Utilities menu as described on page 7-3.
4 Press STEP to view the next display. In our example, CYCL program #6 is listed: CYCL #6 5 User#7777 Press STEP to view the next display, which will list the next program stored under user #7777. In our example, HOLD program #5 is listed: HOLD #5 User#7777 6 Press BACK to view the previous program in the list. 7 You can press STOP at any time to return to the display in which you entered the user number.
Directory Enter user #7777 Press to move forward to the Step next display Press HOLD #16 Stop User#7777 to return to the first display Press Step Back to move to the previous display Press HOLD #25 Stop User#7777 to return to the first display Step Back Press Stop AUTO #4 User#7777 to return to the first display Figure 7-4 7-12 Example of a list of programs listed according to user number.
Printing a Directory of Your Programs (PRINT) The PRINT selection of the Directory function lets you print a directory of your programs organized by program number (PROG), program type (TYPE), or user number (USER). To print a directory: 1 Select DIR on the Utilities menu as described on page 7-3. The Directory display appears: Directory PROG-TYPE-USER-PRINT 2 Press OPTION three times to move the cursor to PRINT, then press ENTER.
Directory Print Enter program # ♦ If the above display is shown, type the program # of the first program in the directory you want to print, then press ENTER. All your programs will be printed, beginning with the program # you entered. Directory Print HOLD-CYCL-AUTO-METH ♦ If the above display is shown, press the OPTION key to move the cursor to the program type of which you want to print a directory, then press ENTER. For example, if you select HOLD, all your HOLD programs will be printed.
Figure 7-5 shows all the displays in the PRINT selection of the Directory function. Figure 7-5 The PRINT selection of the Directory function.
The Configuration Function (CONFIG) The Configuration function lets you customize the instrument by editing the configuration parameters. These parameters include: ♦ time and date ♦ run-time printer mode (on or off) ♦ run-time beeper (on or off) ♦ pause time-out limit ♦ allowed setpoint error ♦ idle state setpoint ♦ temperature interval that triggers the clock start ♦ sample tube time constants Editing the Configuration Parameters There are eleven configuration parameters that you can edit.
Configuration EDIT-PRINT Press Enter Time Date to display the first configuration parameter HH:MM MM/DD/YY Step Runtime printer Runtime beeper OFF ON moves you forward to the next display Pause time-out limit xx:xx Allowed setpt error x.xC Back moves you to the previous display or parameter Idle state setpoint 25C Start clock within x.
Setting the Time and Date The Configuration function lets you set the time in hours and minutes and the date in months, days, and years. To set the time and date: 1 Select CONFIG on the Utilities menu as described on page 7-3. The following display appears: Configuration EDIT-PRINT 2 Press ENTER. The following display appears: Time Date HH:MM MM/DD/YY The cursor appears under the entry field for hours (HH on the display shown above).
4 To set the date, type in the appropriate numbers for the month, day, and year and press ENTER. The display will automatically separate the month, day, and year. 5 Press STEP to display the next configuration parameter or press STOP to return to the first Configuration display.
Turning the Run-Time Printer Mode and Run-Time Beeper On or Off The Configuration function lets you turn the run-time printer mode on or off and the run-time beeper on or off. These parameters appear together on one display. If you have a printer, setting the run-time printer mode to ON lets you print run-time data. When the run-time beeper is on, a beeper will sound at the end of each segment in a run. To turn these parameters on or off: 1 Select CONFIG on the Utilities menu as described on page 7-3.
4 The default condition of the run-time beeper is on. To turn the beeper off, press OPTION (ON changes to OFF), then press ENTER. 5 Press STEP to display the next configuration parameter or press BACK to display the previous configuration parameter. Press STOP to return to the first Configuration display.
Changing the Pause Time-Out Limit The pause time-out limit is the maximum amount of time a program can pause before it automatically aborts; it applies only to the keypad pause. The default value is 10 minutes. This means that if you do not restart a run within 10 minutes after you pause it, the run is aborted. The Configuration function lets you change the pause time-out limit. To change the pause time-out limit: 1 Select CONFIG on the Utilities menu as described on page 7-3.
Changing the Allowed Setpoint Error The allowed setpoint error is the number of degrees the actual sample temperature may vary from the setpoint before the reading is recorded in the history file as an error. The default value is 2.0 degrees C. The Configuration function lets you change the allowed setpoint error value. To change the allowed setpoint error value: 1 Select CONFIG on the Utilities menu as described on page 7-3.
4 7-24 Press STEP to display the next configuration parameter or press BACK to display the previous configuration parameter. Press STOP to return to the first Configuration display.
Entering an Idle State Setpoint Value The idle state setpoint is the temperature of the block when a program is not running (the idling temperature). The Configuration function lets you change the idle state setpoint value. The default value for the idle state setpoint is 25 degrees C. The instrument will automatically heat or cool to this temperature while idling and the Heating light on the control panel will flash.
Changing the Temperature Interval for the Setpoint Clock Whenever you run a program, there is an interval before the setpoint temperature is attained. The clock starts counting the hold time at the beginning of this interval. For example, if the setpoint temperature is 95 degrees C, and the temperature interval is 1 degree C, the clock will actually start counting at 94 degrees C. Figure 7-7 illustrates this example.
2 Press ENTER, then press STEP five times. The following display appears: Start clock within 1.0C of setpoint This example shows the default temperature interval of 1 degree C. This means that the setpoint clock will start counting within 1 degree of the setpoint temperature. 3 To enter a temperature interval different from the default value, press the appropriate numeric keys, then press ENTER. The range of valid entries for the temperature interval is 0.5 to 1.0 degrees C.
Changing the Sample Tube Type The Configuration function lets you specify a future sample tube type by defining the tube time constant characteristics. We recommend not specifying a special tube type unless future sample tube types become available. To change the sample tube type and sample tube time constant value: 1 Select CONFIG on the Utilities menu as described on page 7-3. The following display appears: Configuration EDIT-PRINT 2 Press ENTER, then press STEP six times.
4 To change the default condition, press the OPTION key. “NO” will change to “YES” on the display and you will be able to select a different tube type when you start a run (see Chapter 5 for more information). 5 Press ENTER. The following display appears: Rxn vol=100uL T= 9.5 Rxn vol= 50uL T= 7.0 This display lets you change the sample tube time constant.
Setting Sample Tube Time Constants There are two additional parameters in the Configuration function that let you change the time constants for MicroAmp Reaction Tubes and Thin Walled GeneAmp Reaction Tubes. We recommend that you do not change the time constant values unless instructed to do so by future documentation. MICRO Time Constant To change the sample tube time constant value for MicroAmp Reaction Tubes: 1 Select CONFIG on the Utilities menu as described on page 7-3.
5 Press ENTER. The following display appears: Rxn vol=100uL T= 9.5 Rxn vol= 50uL T= 7.0 This display lets you change the sample tube time constant. There are two default values for sample tube time constants on this display: one for sample tubes with a reaction volume of 100 µL, and one for sample tubes with a reaction volume of 50 µL. There is a time constant default value for sample tubes with a reaction volume of 20 µL that appears on a separate display.
THIN Time Constant This parameter works the same way as the MICRO time constant. except that the default time constant values are different. Change the sample tube time constant value for Thin Walled GeneAmp Reaction Tubes as follows: 1 Select CONFIG on the Utilities menu as described on page 7-3. The following display appears: Configuration EDIT-PRINT 2 Press ENTER, then press STEP until the following display appears: Set THIN tube time constants? NO 3 The default condition of this parameter is no.
These displays let you change the sample tube time constant. There are two default values for sample tube time constants on this display: one for sample tubes with a reaction volume of 100 µL, and one for sample tubes with a reaction volume of 50 µL. There is a time constant default value for sample tubes with a reaction volume of 20 µL that appears on a separate display. ♦ If your instrument has software version 1.05 or higher, press STEP to view the following display: Rxn vol= 20uL T=12.
CAUTION If your instrument has software version 1.04 or lower, configure the THIN tube time constant for a default response time of 12.0 seconds for 20-µL reaction volume. When initiating a PCR program, specify a reaction volume of 20 µL for all experiments using Thin-Walled GeneAmp Reaction Tubes. If your instrument has software version 1.05 or higher, the response time of 12.0 seconds for all three reaction volumes is correct for the Thin-Walled GeneAmp Reaction Tubes.
The Diagnostic Function (DIAG) The Diagnostic function gives you access to five different diagnostic tests. These tests are: ♦ review the most recent instrument run by examining the History file ♦ test the sample block heating system ♦ test the sample block cooling system ♦ test the overall performance of your instrument ♦ verify that your instrument is still calibrated Each of the diagnostic tests are numbered, 1 through 5, and each test appears on a separate display.
Selecting the Diagnostic Tests There are two ways to select a diagnostic test: ♦ You can enter the number of the test you want to run or ♦ You can use the STEP key to scroll forward through the test displays and the BACK key to scroll backward through the test displays. To select a diagnostic test by entering its test number: 1 Select DIAG on the Utilities menu as described on page 7-3.
2 Press STEP to scroll forward through the remaining four Diagnostic test displays; press BACK to scroll backward through all four of the test displays. Press STOP at any time to return to the Utilities menu. Figure 7-8 shows the initial displays for the diagnostic tests.
Reviewing the History file Diagnostic Test #1 lets you review the History file for the most recent run. About The History File The History file records the events that occurred during a run. If a run was terminated, you can view the History file to determine the cause and how much of the run was completed. The History file contains two types of information about a run.
Status Records in a History File As mentioned earlier, a status record contains general information about a run. Every run has at least four status records that contain the sample tube type, the reaction volume, the temperature at which the clock started, and either a message indicating that the run was completed successfully, or a message indicating that an error occurred during the run.
Any one of the following messages can appear on a status record display: 7-40 “Tube Type xxxx” This message shows the sample tube type, and will always be the first record. “Reaction Vol xxxxuL” This message shows the reaction volume used in the run, and will always be the second record. “Clk starts w/in x.xC” This message shows the temperature at which the hold clock starts, and will always be the third record.
“Power Failure xxx.x hrs” This message is also a fatal error message and will appear if a power failure occurred during the run. It shows how long the power was off. “Abort mm/dd/yy hh:mm” This message will appear if you pressed the STOP key during the run. It shows the time and date the run was aborted. “Pause Timeout hh:mm” The pause timeout limit was exceeded during the run. “Fatal Setpoint Error” The sample block did not reach its setpoint in a reasonable period of time. “Pause xx:xx at xx.
Data Records in a History File As mentioned earlier, a data record contains all pertinent numerical data about a run. Every program has at least one data record. A simple HOLD program, for example, has only one data record.
Any one of the following error messages can appear on a data record display: “Setp Error” This message will appear if the setpoint was not reached in a reasonable period of time. “Prog Error” This message will appear if, when you ran an AUTO program, either time became a negative number or the temperature went out of the range of 0.1° to 99.9 °C. “Temp Error” This message will appear if, at the end of a segment, the set-point temperature drifted +/− a previously entered amount.
Program Program # Type C# 2 Cyc 1 Ending Setpoint Temperature 25.2C 6 Setpt 2 0:10 Record # Elapsed Time Cycle # Setpoint # Figure 7-10 A data record display of a CYCL run. The above example tells you that this data record is record #6 of CYCL program #2. There is no method number because this program was not linked in a method. This record also tells you that this is setpoint #2 of cycle #1, the ending setpoint temperature was 25.2 degrees C, and the elapsed time was ten seconds.
The total number of records in the History file appears on the top line of this display. In this example, there are seven records in the History file.
Enter Diag Test #1 REVIEW HISTORY FILE Press Enter History 10 recs ALL-STAT-ERROR-PRINT Press Enter Status Record Data Record The most recent record is displayed first. CYCL# 2 Abort 12/21/90 10 14:47 Press Press Press Step Back Stop C# 2 Cyc 3 26.0C Setpt 1 9 0:05 to move to the next display to move to the previous display to return to the first display C# 2 Cyc 2 25.2C Setpt 2 8 0:10 CYCL# 2 4 Start 12/21/90 14:45 C# 2 Cyc 2 29.8C Setpt 1 7 0:10 CYCL# 2 3 Clk starts w/in 1.
Enter Diag Test #1 REVIEW HISTORY FILE History 10 recs ALL-STAT-ERROR-PRINT Enter Press Stop to return to the first display Enter CYCL# 2 Abort 12/21/90 Status Message 10 14:47 Enter Enter If no error occurs during a run, “No Error records” will appear on the display. If an error occurs during a run, a data record containing an error message will appear here.
Printing the History file To print the History file: 1 Select DIAG on the Utilities menu as described on page 7-3. The following display appears: Enter Diag Test #1 REVIEW HISTORY FILE 2 Press ENTER to select Diagnostic Test #1. The following display appears: History 10 recs ALL-STAT-ERROR-PRINT 3 Press the OPTION key three times to move the cursor to PRINT, then press ENTER.
4 Press OPTION to move the cursor to your desired selection, then press ENTER. The following display appears: History Print printing... Figure 7-13 shows a History file printout of all status and data records (ALL) for a CYCL program. Figure 7-13 Printout of all status and data records (ALL) of a typical History file.
Running the Heater Test Diagnostic Test #2 is the Heater Test, which verifies the performance of the sample block heater and electronics by stabilizing the block temperature at 35 degrees C, then applying full power to the heaters and measuring the temperature rise over a period of time. CAUTION Before you begin this test, make sure you place an empty MicroAmp Tray (MicroAmp Tray/Retainer Set, Part No.
The following display appears: Heater Test Blk=xx.x going to 35C. . . ♦ When the temperature stabilizes, full power is applied to all heaters. The display then reads “ramping...”, then “timing...” and the block temperature is monitored. ♦ When the block reaches the setpoint, the following screen appears: Heater Test Passed This display will show “Passed” if the test was successful. If the test was not successful, the display will show “Failed.
Running the Chiller Test Diagnostic Test #3 is the Chiller Test, which verifies the performance of the refrigeration system by calculating the cooling rate of the sample block. CAUTION Before you begin this test, make sure you place an empty MicroAmp Tray (MicroAmp Tray/Retainer Set, Part No. N801-0530) on the sample block, then slide the heated cover forward and turn the cover knob clockwise until the white mark on the knob lines up with the white mark on the cover.
♦ The system first waits for the coolant temperature to get to 10 degrees C. (If it can't do this within 18 minutes, a failure message will be displayed.) The following display appears: Chiller Test Blk=xx.x going to 50C... The value “xx.x” on the screen pictured above represents the current temperature (in degrees C) of the sample block.
Running the System Performance Test Diagnostic Test #4 is the System Performance Test. The System Performance Test is a series of comprehensive tests of the instrument's heating and cooling systems and is used to help an Applied Biosystems Service Engineer diagnose any special problem you may be having with your GeneAmp PCR System 9600. Run this test when you suspect problems with the instrument and the Heater Test and Chiller Test both pass. The System Performance takes about 30 to 40 minutes to complete.
3 Press ENTER. The following display appears: System Performance VIEW-RUN-PRINT This display lets you choose one of the following options: VIEW: Select this option to view the last test results on a series of displays. Use the STEP key to move forward through the displays; use the BACK key to move backward through the displays. RUN: Select this option to run the test. PRINT: Select this option to print a list of the test results.
Running the Verify Calibration Test Diagnostic test #5 is the Verify Calibration test. Run this test to verify that your instrument is still calibrated. To run this test, you will need the Temperature Verification System for the GeneAmp PCR System 9600, Applied Biosystems Part No. (N801-0435). Refer to Chapter 8, “Maintenance,” for complete instructions on how to verify you instrument's calibration.
The Delete Function (DEL) The Delete function lets you: ♦ delete unprotected programs one by one by specifying their program numbers, ♦ delete protected programs stored under a user number by specifying that user number, and ♦ delete all unprotected programs. In all cases, if a program is linked in a method, that program cannot be deleted until the method is first deleted.
The following display appears: Delete Enter program #xxx “xxx” on the display pictured above represents the program number of the program you want to delete. 3 Press the numeric keys that correspond to the number of the program you want to delete, then press ENTER. You can delete any program or method. Note A program cannot be deleted if it is linked in a method, or if the program is protected (unless the correct user number is entered.
Deleting Programs by User Number To delete all of the programs stored under a specified user number 1 Select DEL on the Utilities menu as described on page 7-3. The following display appears Delete PROGRAM-USER-ALL 2 Press the OPTION key to move the cursor to USER, then press ENTER. The following display appears Delete Enter user # xxxx 3 Press the numeric keys that correspond to the user number of the programs you want to delete, then press ENTER.
The following display will appear, showing in which method the program is linked: Can't delete file xxx Linked in method xxx! The number “xxx” on the top line of the display pictured above represents the program number of the program that cannot be deleted. The number “xxx” on the bottom line represents the method number in which the program is linked. 5 If you want to delete all the unlinked programs under the given user number, press ENTER.
Deleting All Unprotected Programs You can delete any program, provided that it is not linked in a method or protected under a user number. To delete all unprotected programs: 1 Select DEL on the Utilities menu as described on page 7-3. The following display appears: Delete PROGRAM-USER-ALL 2 Press the OPTION key twice to move the cursor to ALL, then press ENTER.
Maintenance 8 8 Introduction This chapter describes how to perform routine maintenance on the GeneAmp® PCR System 9600 without the aid of an Applied Biosystems Service Representative. ! WARNING ! Do not remove the instrument cover. There are no components inside the GeneAmp PCR System 9600 that you can safely service yourself. If you suspect a problem, contact an Applied Biosystems Service Representative.
Cleaning the Sample Wells The sample wells should be cleaned once a month or as needed. ! WARNING ! During instrument operation, the sample block can be heated as high as 100 degrees C. Before performing the following procedure, be sure to wait until the sample block reaches room temperature. To clean the sample wells: 1 Run a 25-degree HOLD program to bring the sample block to room temperature, then turn off the instrument for 15 minutes. 2 Remove the sample tray from the block and set aside.
Cleaning the Heated Cover The heated cover should be cleaned once a month or as needed. ! WARNING ! During instrument operation, the heated cover can be heated as high as 107 degrees C. Before performing the following procedure, be sure to wait until the sample block reaches room temperature. To clean the heated cover, proceed as follows: 1 Run a 25-degree HOLD program to bring the sample block to room temperature, then turn off the instrument for 15 minutes.
Temperature Calibration Verification Test Use this procedure to verify that your Applied Biosystems GeneAmp PCR System 9600 still meets the temperature accuracy specification. Equipment Required You will need the following equipment to perform this procedure: Temperature Verification System, (Part No.
2 Using a cotton swab, coat wells D1 and E1 with mineral oil. Figure 8-1 shows the location of these wells. Figure 8-1 3 Location of sample wells E1 and D1. Place the probe tray on the sample block so that the probe tray notch faces the front of the instrument. The RTD probe assembly consists of two cones, one of which measures the temperature of the sample well. The wire is attached to the cone that does not measure the temperature of the sample well. This cone is a dummy probe.
Figure 8-2 Placing the probe assembly into the sample wells. 5 Slide the heated cover forward and turn the cover knob clockwise until the white mark on the cover knob is aligned with the white mark on the cover. 6 Turn on the digital thermometer by moving the ON-OFF/RANGE switch to the 200 position. 7 Turn on the GeneAmp PCR System 9600. The main menu appears: Select Option 9600 RUN-CREATE-EDIT-UTIL 8 8-6 Press the OPTION key three times to move the cursor to UTIL, then press ENTER.
Select function DIR-CONFIG-DIAG-DEL 9 Press the OPTION key twice to move the cursor to DIAG, then press ENTER. The following display appears: Enter Diag Test #1 REVIEW HISTORY FILE 10 Run the Verify Calibration Diagnostic Test (Test #5) by pressing 5, then ENTER. ♦ The temperature of the sample block and heated cover will go to 40 degrees C, and the following display will appear: Going to 40 ºC... Cvr= xxC Blk = xx.
♦ When the clock reaches three minutes, the following display appears: Record Temperature Time=MM:SS Blk=40.0C 11 Measure the temperature of well E1 using the digital thermometer and record this temperature as T(40). See Figure 8-3 on the next page. 12 Press ENTER. ♦ The temperature of the sample block and heated cover will go to 95 degrees C, and the following display will appear: Going to 95°C... Cvr= xxC Blk = xx.
When the clock reaches three minutes, the following display appears: Record Temperature Time=MM:SS Blk=95.0C 13 Measure the temperature of well E1 using the digital thermometer and record this temperature as T(95). Note To exit the test at any time, press the STOP key. Press 5 and ENTER to return to the Verify Calibration Diagnostic test. Figure 8-3 shows when you should take the two measurements.
Test Results Perform the following steps to calculate the results of the test. You will need to refer to the calibration label that you pasted into Figure 8-4 below, for the High and Low Offset values. PASTE THE CALIBRATION LABEL HERE. Figure 8-4 GeneAmp PCR System 9600 Calibration Label. Note If you have more than one GeneAmp PCR System 9600 in your laboratory, make sure that the serial number on the calibration label matches the serial number on the instrument you are testing.
♦ If the block average is more than 0.75 degree C above or below 95 degrees C, your instrument must be recalibrated. For example: If the measured temperature of well E1 at was 95.2°C, and the High Offset printed on your calibration label is –0.1, then you would use the following formula: Block Average at 95°C = 95.2 – (–0.1) = 95.3°C In this example, since 95.3°C does not differ by +/–0.75°C from your programmed target temperature, your instrument would not need to be recalibrated.
4 Clean the oil from wells D1 and E1 using cotton swabs. This completes the test. The calibration has now been verified. If your instrument needs to be recalibrated, contact an Applied Biosystems Service Representative.
Temperature Uniformity Test Use this procedure to test the temperature uniformity of the sample block in the GeneAmp PCR System 9600. Equipment Required You will need the following equipment: ♦ Temperature Verification System Testing the Temperature Uniformity Perform the procedure as described in the following steps: 1 If the heated cover is in the forward position, turn the cover knob completely counterclockwise, then slide the cover back.
Figure 8-5 The probe assembly in sample wells A1 and A2. 5 Slide the heated cover forward and turn the cover knob clockwise until the white mark on the cover knob is aligned with the white mark on the cover. 6 Turn on the digital thermometer by moving the ON-OFF/RANGE switch to the 200 position.
8 On the third cycle, measure the temperature of well A1 90 seconds into Setpoint #1 (95 degrees C setpoint temperature) using the digital thermometer. The time remaining clock on the run-time display will read “0:30” (30 seconds). Record this temperature. 9 Still on the third cycle, measure the temperature of well A1 90 seconds into Setpoint #2 (40 degrees C setpoint temperature) using the digital thermometer. The time remaining clock on the run-time display will read “0:30” (30 seconds).
10 After you measure the second temperature of well A1, turn the cover knob completely counterclockwise, then slide the heated cover back. 11 Move the probe assembly to wells A4 and A5 with the dummy probe in A5. 12 Slide the heated cover forward and turn the cover knob clockwise until the white marks are aligned. 13 Repeat the measurements on wells A4, A8, A12, C1, C4, C8, C12, E1, E4, E8, and E12, H1, H4, H8, and H12.
14 When you have completed all measurements, remove the probe assembly from the sample block and turn off the digital thermometer. 15 Clean the oil from the sample block. Test Results 1 For the 16 Setpoint #1 measurements (95°C hold) subtract the lowest measured temperature from the highest measured temperature. 2 For the 16 Setpoint #2 measurements (40°C hold), subtract the lowest measured temperature from the highest measured temperature.
Changing External Fuses There are two slow-blow fuses accessible from the left side of the instrument. Use the following procedure to change these fuses. Use 15-Amp slow-blow fuses for the 100 and 120 VAC instruments. Use 8-Amp slow-blow fuses for the 220-240 VAC instruments. See Chapter 10 for information on power requirements. 1 Turn off the GeneAmp PCR System 9600 and disconnect the power cord from the instrument. 2 The fuses are located next to the instrument power cord connection (see Figure 8-8).
Troubleshooting 9 9 Introduction This chapter contains troubleshooting information to help you correct any problems you experience in operating the GeneAmp PCR System 9600. This chapter also explains what happens if a power failure causes the instrument to turn off while you are operating it. Troubleshooting The table that begins on the following page lists instrument problems you may have, the probable causes of these problems, and what you can do to correct them.
Table 9-1 Troubleshooting Information Problem The power switch is on but there is no response. Possible Cause The power cable is loose or not plugged in. There is no display on Fuse is blown. the screen and no noise from the motor or fan. 9-2 Check and / or Remedy Plug the power cable in properly. Replace the fuse. Power is on but the screen is blank and the motor is running. Or, when you press a key, the display does not show the appropriate response or the screen is blank.
Table 9-1 Troubleshooting Information (continued) Problem Possible Cause Check and / or Remedy The system will not cool The laboratory is either down to subambient too humid or too hot. temperatures. Move the instrument to an air-conditioned room. Or run Diagnostic Test #3, the Chiller Test. Call an Applied Biosystems Service Engineer if the test fails. An error message is displayed when you turn on the instrument. One of the main instrument systems has failed.
Table 9-1 Troubleshooting Information (continued) Problem Upon power-up or returning to an instrument that has been running unattended, the following display appears: Possible Cause Check and / or Remedy This is normal if the power has been interrupted or shut off while running a program. Review the history file to determine when the power failed. Note that the system comes up in a 4degree soak to save any samples. The display shows how long power was interrupted.
If the Instrument Turns Off If power is interrupted and the instrument turns off while you are operating it, the following will occur when you turn it back on: ♦ If you were editing a program, you will lose the changes to that program and will have to re-edit it. ♦ The instrument will begin a 4-degree Hold program. If you were editing a program, review the History file to find out how much of your program was run before the instrument turned off (see Chapter 7).
Specifications 10 10 Dimensions The physical dimensions of the instrument are: Height: 30.5 cm (12 in.) Width: 52 cm (20 in.) Depth: 61 cm (24 in.) Weight: 40.5 kg (90 lbs.) Sample Compartment The sample compartment contains an aluminum block with 96 sample positions in an eight by twelve microplate format. A heated cover over the sample vessels eliminates the need for oil. Sample Tubes The sample compartment can hold: 96 MicroAmp Reaction Tubes (0.
Power Requirements There are three versions of the GeneAmp PCR System 9600. The power requirements of these instrument versions are: ♦ 120VAC, 60 Hz, 10 amps, 15-amp slow blow fuse ♦ 220-240 VAC, 50 Hz, 5 amps, 8-amp slow blow fuse ♦ 100 VAC, 50-60 Hz, 12 amps, 15-amp slow blow fuse Control Panel The instrument control panel consists of the display, keypad, and indicator lights. Display The GeneAmp PCR System 9600 uses a 40-character blue luminescent display (20 characters x 2 lines).
Sample Temperature Range The temperature range of the sample block is: 4.0 degrees to 99.9 degrees C. Sample Temperature Accuracy The displayed sample temperature matches the average true sample temperature within +/–0.75 degrees C. Displayed Sample Temperature The displayed sample temperature will match the specified setpoint temperature to within +/–0.2 degrees C, centered around the setpoint temperature two minutes after the sample temperature is within 1 degree C of setpoint.
Figure 10-1 Sample temperature overshoot after ramping up. Ramp Time Repeatability Thermal setpoints are achieved within +/–5 seconds (not including the first cycle). Sample Heating and Cooling Rate The sample temperature ramp rate for heating and cooling is approximately one degree C per second.
Printer Interface The GeneAmp PCR System 9600 uses an RS-232C serial port as its printer interface. In addition, the following specifications apply: Baud Rate: 9600 Setup: no parity, 8 data bits, one stop bit Temperature Calibration The GeneAmp PCR System 9600 has been calibrated to standards traceable to NIST (National Institute for Standards and Technology U.S.).
Index Note A page number in italics (e.g., 5-26) indicates an illustration.
Conventions notes and warnings, S-2, P-4 used in manual, S-1, P-3 Cleaning the sample block cover, 8-3 Clear Entry key. See CE key Condensation. See Loading samples CONFIG function.
setpoints in, 3-3, 4-10, 5-33 specifying the number of cycles in, 3-18 storing, 3-20 target temperatures in, 3-4 CYCLE print option, 6-14 Cycle program. See CYCL program Cycles defining total number in AUTO program, 5-43 defining total number in CYCL program, 5-36 D Data record display, 7-44 error messages in, 7-43 in a history file, 7-42—7-44 information in, 7-42 Decimal values, entering, 5-35 Default values definition of, 3-4 See also HOLD program, CYCL program, AUTO program DEL function.
Displayed sample temperature, 10-3 G Documents on Demand S-19 GeneAmp PCR System 9600 description of software, 1-5—1-6 features of, 1-5 general description of, 1-3 input voltages, 2-4 installing, 2-1—2-21 instrument specifications, 10-1—10-5 Maintenance, 8-1—8-18 ordering accessories and replacement parts for, 2-3 parts supplied with, 2-2 setting hold times, 5-2—5-7 Dot-matrix printer.
viewing data records with error messages in, 7-47 viewing status records in, 7-47 viewing, 7-44—7-47 HOLD program defining values in, 5-32 definition of, 4-8 description of, 4-8—4-9, 5-32 displays in, 5-32, 5-32 hold for a specific time interval, 4-9 in PCR method, 4-14 last display in, 5-32 run-time displays, 6-19, 6-19 turning beeper on, 5-32 types of, 4-8 Hold time default value in HOLD program, 5-32 definition of, 3-4 setting in AUTO program, 5-40 setting in CYCL program 5-34 Hold times converting from
M Main menu, 3-6 CREATE option, description of, 4-4 cursor on, 3-6 description of, 3-6, 4-4—4-5 EDIT option, description of, 4-4 getting to the, 4-4 options on, 4-4, 4-5 RUN option, description of, 4-4 selecting a function on, 4-5—4-6 selecting options on, 3-7, 3-7 using the STOP key to return to, 5-29 UTIL option, description of, 4-4 Maintenance procedures, 8-1—8-18 cleaning the sample block cover, 8-3 cleaning the sample wells, 8-2 temperature calibration verification test, 8-4—8-12 temperature uniformity
PCR programs and methods overview of, 4-6—4-7 setting up, 5-1—5-45 PCR technique annealing step, 1-2 Denaturing step, 1-2 description of, 1-2 Extending step, 1-2 in AUTO program, 4-12 in CYCL program, 4-10 in HOLD program, 4-8 in methods, 4-14 Polymerase chain reaction, definition of, 1-2 Power interruption, 9-5 Power requirements, 2-4—2-5, 10-2 input voltages, 2-4 Power switch, location of, 3-5 Precautions, 2-5 Primer annealing. See PCR technique Primer extending.
Program numbers assigning to methods, 5-21 assigning, 5-11 use in creating methods, 5-18, 5-45 use in deleting programs, 7-57 viewing a directory of programs by, 7-4—7-6, 7-6 Programming a pause in AUTO program, 5-43 in CYCL program, 5-36 Programs creating, 5-10 definition of, 1-5, 4-6 editing, 5-13—5-15 linking in methods, 4-6—4-7 overview of, 4-6—4-7 overwriting, 5-15 printing, 5-16—5-17 recalling, 5-30—5-31 running, 6-1—6-22 storing, 5-11—5-12, 5-14 types of, 1-5, 4-6, 4-7 Protected methods, 5-25 Protect
Run-time displays, 6-17—6-19 Run-time printer mode turning on and off, 7-20 turning on, 2-13 Sample tray 96-position installing, 6-2, 6-3 loading without samples, 3-22—3-23 placing in the block, 6-5, 6-5 removing, 6-8 S Sample tray retainer installing, 6-4, 6-4 Sample block cover cleaning, 8-3 use in sample tray installation, 6-6 use in trial run, 3-23 use of cover knob, 6-7 Sample tube reaction volume, in configuration function, 7-29 Run-time keys, 4-3, 6-11 Sample block temperature idle state setpo
temperature calibration, 10-5 default value, 7-26 temperature interval, 7-26, 7-26 Starting a run, 6-11—6-16 SETPOINT print option example printout, 6-15 Starting up the instrument, 3-5 STAT history file display option, 7-45, 7-47 SETPOINT print option, 6-14 STAT history file print option, 7-48 Setpoint time.
T Target temperature See also Sample temperature, Setpoints in CYCL programs, 3-4 See also Sample temperature use in Verify Calibration test, 7-56 Temperature, requirements for installation, 2-5 Test # 1. See Reviewing the history file Test # 2. See Heater test Technical support S-14—S-19 E-mail address S-14 Internet address S-18 Telephone/fax S-15—S-18 Test # 3.
by user number, 7-10—7-12, 7-12 U Viewing the history file, 7-44—7-47 Unpacking the instrument, 2-2 Unprotected programs, deleting, 7-61 User diagnostics. See Diagnostic tests User identification number.
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