Epson C82302/04 (Serial I/F) Manual do Utilizador Página 1

GeneAmp® PCR System 9600User’s Manual

S-8! WARNING !Grounding circuit continuity is vital for safe operation of equipment. Never operate equipment with grounding conductor disconnected.! A

3-22Starting a Trial RunIn the following steps, you will learn how to load a tray and run the program you just stored, then stop it after a few moment

3-23Figure 3-5Sliding the heated cover forward for a trial run.

3-24Running the Program1Look at the display. The main menu (shown below) should be displayed. If not press the STOP key one or two times.2With the cur

3-255Before 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

3-267Press MORE again to return you to the first run-time display. The illustration below shows you how the MORE key works.8After a few moments, press

3-2710You can now return to the main menu. Press the OPTION key to move the cursor to HOME, then press ENTER.The Next StepIn this tutorial, you have l

Software Basics 4IntroductionThis chapter presents an overview of the GeneAmp® PCR System 9600 software and describes the HOLD, CYCL, and, AUTO progr

4-2Reviewing Keypad BasicsIf you haven’t already done so, go through the Tutorial in Chapter 3 to learn how to use the keys. The following section sum

4-3Use of the KeysThere are two types of keys: run-time keys and editing keys. Run-time keys are used while running samples, for example, to start and

S-9Electrical Safety TestingCAUTIONRoutine safety testing of analytical instruments (e.g., high potential voltage testing) may be required by various

4-4A Close Look at the Main MenuThe main menu (shown above) appears a few seconds after the instrument is first turned on. If the instrument is alread

4-5Selecting a Function1Press OPTION to move the cursor from one option to the next. When the cursor reaches UTIL, pressing OPTION again will move it

4-6An Overview of PCR Programs and MethodsA program is a set of instructions in which you specify how the instrument should heat and cool your samples

4-7Figure 4-3HOLD, CYCL, AUTO, and METH programsStoring Programs and MethodsBy storing the programs and methods you can easily access and run them lat

4-8The HOLD ProgramDuring a HOLD program the temperature of the sample block (and the sample) is held at one temperature for either a fixed time inter

4-9Figure 4-4A HOLD program held for an indefinite time.Figure 4-5A HOLD program held for a specific time interval.

4-10CYCL: The Cycle ProgramA CYCL program contains the thermal ramp and hold segment patterns for PCR cycling. It contains up to nine setpoints. Each

4-11Figure 4-6A common CYCL program

4-12The AUTO ProgramAn AUTO program allows the user to automatically increment or decrement the setpoint times and temperatures a fixed amount every c

4-13Figure 4-7An AUTO program used to increase hold time.

S-10Operating PrecautionsThis manual contains important information regarding potential hazards that may arise during the operation of the instrument.

4-14PCR MethodsPCR methods are used to automatically link together up to 17 programs for a specific PCR application. To create a method, you use the M

Setting Up PCR Programs and Methods 5IntroductionThis chapter describes how to use the HOLD, CYCL, and AUTO programs to create your own PCR programs.

5-2Setting Hold Times on the GeneAmp® PCR System 9600If you have used the DNA Thermal Cycler or DNA Thermal Cycler 480, read the following information

5-3Figure 5-1Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600

5-4Tables 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

5-5Figure 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 de

5-6Table 5-2 After Down Ramps: Converting Hold Times Greater than One Minute (DNA Thermal Cycler to GeneAmp PCR System 9600)For down ramps, determine

5-7In 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 startin

5-8Editing KeysTo create, view, or edit programs and methods, you will use the following keys.Figure 5-4Editing KeysThe function of each key is descri

5-9Creating and Editing ProgramsThe main steps involved in creating and editing programs are summarized below. These steps are explained in detail in

S-11Instrument CoverCAUTIONThis unit contains protective circuitry. Contact Applied Biosystems before performing any AC line tests.! WARNING !To reduc

5-10Creating a Program1Access the main menu.2Press the OPTION key to select CREATE, then press ENTER.The following display appears3Press the OPTION ke

5-11Storing the Program1Press the OPTION key to move the cursor beneath STORE, then press ENTER.The following display appears:The number “x” is the ne

5-12If you select YES, the following display will appear:In this display, you can specify any number from 1 to 9999 for your user identification numbe

5-13Editing a ProgramWhen 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

5-14NoteIf 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

5-15b. Type the original number for the program, then press ENTER. This allows you to replace the original program with the new edited version. The su

5-16Printing a ProgramIf the instrument is configured for a printer, you can obtain a printout of the parameters in a program. For more information on

5-17Creating and Editing MethodsThe main steps involved in creating and editing methods are summarized below. These steps are explained in more detail

5-18Creating a MethodA method is a series of up to 17 programs linked together. For example, you can link a HOLD program to a CYCL program and conclud

5-19NoteIf 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 allow

S-12Pollution DegreeThis equipment will operate safely in environments that contain nonconductive foreign matter up to Pollution Degree 2 in IEC 1010–

5-208The last display to appear when you are creating a method allows you to run, store, or print the method:9In most cases, you will want to store th

5-21Storing the Method1Press the OPTION key to move the cursor beneath STORE, then press ENTER.The following display appears:X is the next available n

5-22In 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

5-23Editing a MethodWhen you want to view a stored method or change it so it includes a different sequence of linked programs, you use the Edit functi

5-24NoteIf 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 allow

5-25If the original method was protected, you will need to enter the user identification number that was specified when the method was first created b

5-263Select 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 th

5-27AB GeneAmp PCR System 9600 Ver 2 June 1, 1992 10:59 amMETH Program #???HOLD Program #1 - Program ParametersHold at 95.0CHold for 5:00Beep wh

5-28Software ShortcutsBelow are some hints to getting around quickly in the software while you are creating or editing programs.Using the STOP KeyWhil

5-29A shortcut to the above procedure is:1With any of the program displays shown, press STOP.The following display appears:2Instead of selecting HOME

S-13Fuses and Power InterruptionIf power to the instrument fails or is turned off while the instrument is running, turn the instrument off and wait fi

5-30Recalling Programs: A ShortcutOnce you have finished editing or running a program, you can quickly recall another program without needing to retur

5-31The HOLD ProgramDuring a HOLD program, the temperature of the sample block (and the sample) is held at one temperature for either a fixed time int

5-325Description of HOLD Program DisplaysThis display allows you to set the temperature at which the sample will be held and the length of time this t

5-33CYCL: The Cycle ProgramA CYCL program contains the thermal ramp and hold segment patterns for PCR cycling. It contains up to nine setpoints. Each

5-34Description of CYCL Program DisplaysDefines the number of incubation temperatures or setpoints used in the PCR cycle. A typical PCR cycle consists

5-35You 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:1For th

5-36Setpoint #3 in a typical cycle program is used for primer extension. This display sets the ramp time, target temperature, and hold time for the th

5-37The 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

5-38The last display in the program indicates the program type, followed by “???,” which means that the program has not yet been stored and assigned a

5-39The AUTO ProgramAn AUTO program allows the user to automatically increment or decrement the setpoint times and temperatures a fixed amount every c

S-14Technical SupportContactingTechnical SupportYou can contact Applied Biosystems for technical support by telephone or fax, by e-mail, or through th

5-40Description of AUTO Program DisplaysDefines the number of incubation temperatures or setpoints used in the PCR cycle. A typical PCR cycle consists

5-411For the setpoint temperature, enter the temperature in decimal form. You do not type a decimal point. For example, to specify 89.0 degrees C, pre

5-42♦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,

5-43These 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 s

5-44The 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

5-45The last display in the program indicates the program type, followed by “???,” which means that the program has not yet been stored and assigned a

Running PCR Samples6IntroductionTo run samples, turn on the instrument and follow these procedures, which are explained in this chapter.♦Loading Sampl

6-2Loading SamplesThe GeneAmp PCR System 9600 uses a 96-position sample tray (MicroAmp Tray) and retainer (MicroAmp Retainer) for 0.2-mL MicroAmp Reac

6-3Figure 6-1Setting up the 96-position sample tray.

S-15To ContactTechnical Supportby Telephone orFaxIn North AmericaTo contact Applied Biosystems Technical Support, use the telephone or fax numbers giv

6-4NoteWhen using MicroAmp Reaction Tubes with Caps, place the required number of tubes into a MicroAmp Base, then fill each tube with PCR reagents an

6-5Placing the Sample Tray in the BlockLift the sample tray and retainer assembly from the sample tray base and place it in the sample block. Make cer

6-6Make certain that the cover knob is completely counterclockwise, which fully raises the platen, before you attempt to slide the heated cover forwar

6-7Turn 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).

6-8Using the Cap-Installing ToolUse the MicroAmp Cap-Installing Tool, supplied with your instrument, to cap a single sample tube or a row of sample tu

6-9Removing Samples from the TrayThe following procedure describes how to remove the sample tubes from the tray:1Place the sample tray back on the bas

6-10Specifying a Program or MethodTo specify the time and temperature pattern you want to use to run PCR samples, you can create a new program or meth

6-11Starting the RunRun KeysThe following keys are used to start a run or are used during the run.Figure 6-7Run-Time KeysThe function of each key is d

6-12Running a Stored ProgramTo run a program that you have previously stored: 1Access the main menu.CAUTIONBefore you start a run, make sure the “Star

6-134If the “Special Tube?” parameter in the Configuration function (see Chapter 7) has been set to “NO,” pressing the OPTION key will change the tube

S-16Outside North AmericaVoyager MALDI-TOF Biospectrometry and Mariner ESI-TOF Mass Spectrometry Workstations1-800-899-5858,then press 131-508-383-7

6-14♦If you have a printer and it has been enabled (using the Configuration function), the following display appears:This display lets you select the

6-15Figure 6-8An example printout of a CYCL program using the SETPOINT option.! WARNING !During a sample run, keep the heated cover pulled forward and

6-16Indicator LightsThe three indicator lights on the control panel of the instrument indicate the operating status, as described below.♦Heating, when

6-17Run-Time DisplaysDuring a run, you will see a run-time display that is continuously updated for the program being run.CYCL and AUTO Program Run-Ti

6-18Figure 6-10Using the MORE key.The parameters in the second run-time display are explained in Figure 6-11.Figure 6-11More run-time information in a

6-19HOLD Program Run-Time DisplayFigure 6-12 shows the run-time displays for a HOLD program. Use the MORE key to view the second run-time display. Pre

6-20Pausing a RunOnce a run has started, you can manually pause a run, in order to add a reagent to your samples, for example, using the PAUS E key. N

6-21Press the STOP key again.The run is aborted and a display similar to the one shown below appears:This display occurs in a CYCL program.3If you cha

6-22Reviewing the History of the RunOnce a run has been completed (or aborted), you can obtain a record of the run called a History file. If you want

Utilities 7IntroductionThis chapter explains the Utilities functions. The Utilities functions let you:♦display or print programs by their number, thei

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7-2Getting to the Utilities MenuTo get the Utilities menu:1Get to the Main menu. Press the STOP key once or twice until the Main menu appears:2Press t

7-3Selecting a Utilities Function To select one of the Utilities functions:1Press OPTION to move the cursor from one function to the next. When the cu

7-4The Directory Function (DIR)The Directory function lets you display or print programs according to:♦program number♦type, or♦user identification num

7-53Press 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

7-6Figure 7-2Example of a list of programs listed according to program number.Directory Enter program # 1HOLD #1CYCL #2AUTO #3Stepto move to

7-7Listing 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

7-8For example, if your first HOLD program is HOLD #14, the following display appears:4Press STEP to view the next display in your program listing. In

7-9Figure 7-3Example of a list of programs listed according to program type.HOLD #14HOLD #26HOLD #31to move to the previous displayto move forward to

7-10Listing Programs by their User Number (USER)The USER selection lets you list all programs that have been stored under a previously specified user

7-114Press STEP to view the next display. In our example, CYCL program #6 is listed:5Press STEP to view the next display, which will list the next pro

© Copyright 2001, Applied Biosystems. All rights reserved.For Research Use Only. Not for use in diagnostic procedures.NoticeAUTHORIZED THERMAL CYCLER

S-18To ReachTechnical SupportThrough theInternetWe strongly encourage you to visit our Web site for answers to frequently asked questions and for more

7-12Figure 7-4Example of a list of programs listed according to user number.HOLD #16HOLD #25AUTO #4 to move to the previous displayto move forward to

7-13Printing a Directory of Your Programs (PRINT)The PRINT selection of the Directory function lets you print a directory of your programs organized b

7-14♦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 wi

7-15Figure 7-5 shows all the displays in the PRINT selection of the Directory function.Figure 7-5The PRINT selection of the Directory function.

7-16The Configuration Function (CONFIG)The Configuration function lets you customize the instrument by editing the configuration parameters. These par

7-17Figure 7-6The Configuration function.ConfigurationEDIT-PRINTRuntime printer OFFRuntime beeper ONTime HH:MMDate MM/DD/YYPause time-out limitx

7-18Setting the Time and DateThe Configuration function lets you set the time in hours and minutes and the date in months, days, and years.To set the

7-194To set the date, type in the appropriate numbers for the month, day, and year and press ENTER. The display will automatically separate the month,

7-20Turning the Run-Time Printer Mode and Run-Time Beeper On or OffThe Configuration function lets you turn the run-time printer mode on or off and th

7-214The default condition of the run-time beeper is on. To turn the beeper off, press OPTION (ON changes to OFF), then press ENTER.5Press STEP to dis

S-19To ObtainDocuments onDemandFree, 24-hour access to Applied Biosystems technical documents, including MSDSs, is available by fax or e-mail or by do

7-22Changing 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 ap

7-23Changing the Allowed Setpoint ErrorThe allowed setpoint error is the number of degrees the actual sample temperature may vary from the setpoint be

7-244Press STEP to display the next configuration parameter or press BACK to display the previous configuration parameter. Press STOP to return to the

7-25Entering an Idle State Setpoint ValueThe idle state setpoint is the temperature of the block when a program is not running (the idling temperature

7-26Changing the Temperature Interval for the Setpoint ClockWhenever you run a program, there is an interval before the setpoint temperature is attain

7-272Press ENTER, then press STEP five times.The following display appears:This example shows the default temperature interval of 1 degree C. This mea

7-28Changing the Sample Tube TypeThe Configuration function lets you specify a future sample tube type by defining the tube time constant characterist

7-294To 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 t

7-30Setting Sample Tube Time Constants There are two additional parameters in the Configuration function that let you change the time constants for Mi

7-315Press ENTER.The following display appears:This display lets you change the sample tube time constant. There are two default values for sample tub

7-32THIN Time ConstantThis parameter works the same way as the MICRO time constant. except that the default time constant values are different. Change

7-33These displays let you change the sample tube time constant. There are two default values for sample tube time constants on this display: one for

7-34CAUTIONIf your instrument has software version 1.04 or lower, configure the THIN tube time constant for a default response time of 12.0 seconds fo

7-35The Diagnostic Function (DIAG)The Diagnostic function gives you access to five different diagnostic tests. These tests are: ♦review the most recen

7-36Selecting the Diagnostic TestsThere are two ways to select a diagnostic test:♦You can enter the number of the test you want to runor ♦You can use

7-372Press STEP to scroll forward through the remaining four Diagnostic test displays; press BACK to scroll backward through all four of the test disp

7-38Reviewing the History fileDiagnostic Test #1 lets you review the History file for the most recent run. About The History FileThe History file reco

7-39Status Records in a History FileAs mentioned earlier, a status record contains general information about a run. Every run has at least four status

7-40Any one of the following messages can appear on a status record display:“Tube Type xxxx” This message shows the sample tube type, and will always

7-41Figure 7-9 shows an example status record display for a successful run. Figure 7-9,A typical status record display.The example in the figure tells

Users Manual SummaryIf You Have Used the Applied Biosystems DNA Thermal Cycler or DNA Thermal Cycler 480Describes the differences between the GeneAmp

7-42Data Records in a History FileAs mentioned earlier, a data record contains all pertinent numerical data about a run. Every program has at least on

7-43Any one of the following error messages can appear on a data record display:Figure 7-10 shows an example of a data record display for successful r

7-44Figure 7-10A 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 meth

7-45The 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 f

7-46Figure 7-11Viewing (ALL) the records in a History file for a two-temperature CYCL program.C# 2 29.9C 5Cyc 1 Setpt 1 0:10CYCL# 2 2Reaction

7-47Figure 7-12Viewing the status (STAT) records, data records with error messages (ERROR), and printing records (PRINT).If no error occurs during a r

7-48Printing the History fileTo print the History file:1Select DIAG on the Utilities menu as described on page 7-3.The following display appears:2Pres

7-494Press OPTION to move the cursor to your desired selection, then press ENTER.The following display appears:Figure 7-13 shows a History file printo

7-50Running the Heater TestDiagnostic Test #2 is the Heater Test, which verifies the performance of the sample block heater and electronics by stabili

7-51The following display appears:♦When the temperature stabilizes, full power is applied to all heaters. The display then reads “ramping...”, then “t

Chapter 7. UtilitiesDescribes how to obtain a history of the run, configure the instrument, run diagnostics, and update the file directory.Chapter 8.

7-52Running the Chiller TestDiagnostic Test #3 is the Chiller Test, which verifies the performance of the refrigeration system by calculating the cool

7-53♦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

7-54Running the System Performance TestDiagnostic Test #4 is the System Performance Test. The System Performance Test is a series of comprehensive tes

7-553Press ENTER. The following display appears:This display lets you choose one of the following options:4Press the OPTION key once to move the curso

7-56Running the Verify Calibration Test Diagnostic test #5 is the Verify Calibration test. Run this test to verify that your instrument is still calib

7-57The Delete Function (DEL)The Delete function lets you:♦delete unprotected programs one by one by specifying their program numbers,♦delete protecte

7-58The following display appears:“xxx” on the display pictured above represents the program number of the program you want to delete.3Press the numer

7-59Deleting Programs by User NumberTo delete all of the programs stored under a specified user number1Select DEL on the Utilities menu as described o

7-60The following display will appear, showing in which method the program is linked: The number “xxx” on the top line of the display pictured above r

7-61Deleting All Unprotected ProgramsYou can delete any program, provided that it is not linked in a method or protected under a user number.To delete

If You Have Used the Applied BiosystemsDNA Thermal Cycler or DNA Thermal Cycler 480You will find that the GeneAmp PCR System 9600 is in many ways simi

Maintenance 8IntroductionThis chapter describes how to perform routine maintenance on the GeneAmp® PCR System 9600 without the aid of an Applied Biosy

8-2Cleaning the Sample WellsThe sample wells should be cleaned once a month or as needed.! WARNING !During instrument operation, the sample block can

8-3Cleaning the Heated CoverThe heated cover should be cleaned once a month or as needed. ! WARNING !During instrument operation, the heated cover can

8-4Temperature Calibration Verification TestUse this procedure to verify that your Applied Biosystems GeneAmp PCR System 9600 still meets the temperat

8-52Using a cotton swab, coat wells D1 and E1 with mineral oil. Figure 8-1 shows the location of these wells.Figure 8-1Location of sample wells E1 and

8-6Figure 8-2Placing the probe assembly into the sample wells. 5Slide the heated cover forward and turn the cover knob clockwise until the white mark

8-79Press the OPTION key twice to move the cursor to DIAG, then press ENTER. The following display appears:10Run the Verify Calibration Diagnostic Tes

8-8♦When the clock reaches three minutes, the following display appears:11Measure the temperature of well E1 using the digital thermometer and record

8-9When the clock reaches three minutes, the following display appears:13Measure the temperature of well E1 using the digital thermometer and record t

2Sample BlockCAUTIONDo not use mineral oil or glycerine in the sample block of the GeneAmp PCR System 9600.The GeneAmp PCR System 9600 is designed for

8-10Test ResultsPerform the following steps to calculate the results of the test. You will need to refer to the calibration label that you pasted into

8-11♦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 tem

8-124Clean 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

8-13Temperature Uniformity TestUse this procedure to test the temperature uniformity of the sample block in the GeneAmp PCR System 9600.Equipment Requ

8-14Figure 8-5The probe assembly in sample wells A1 and A2. 5Slide the heated cover forward and turn the cover knob clockwise until the white mark on

8-158On the third cycle, measure the temperature of well A1 90 seconds into Setpoint #1 (95 degrees C setpoint temperature) using the digital thermome

8-1610After you measure the second temperature of well A1, turn the cover knob completely counterclockwise, then slide the heated cover back.11Move th

8-1714When you have completed all measurements, remove the probe assembly from the sample block and turn off the digital thermometer.15Clean the oil f

Changing External FusesThere are two slow-blow fuses accessible from the left side of the instrument. Use the following procedure to change these fuse

Troubleshooting 9IntroductionThis chapter contains troubleshooting information to help you correct any problems you experience in operating the GeneA

3Comparing Files and ProgramsIn the GeneAmp PCR System 9600 software, PCR files are referred to as programs. The following table lists the differences

9-2Table 9-1 Troubleshooting InformationProblem Possible Cause Check and / or RemedyThe power switch is on but there is no response.The power cable is

9-3The system will not cool down to subambient temperatures.The laboratory is either too humid or too hot.Move the instrument to an air-conditioned ro

9-4Upon power-up or returning to an instrument that has been running unattended, the following display appears:This is normal if the power has been in

9-5If the Instrument Turns OffIf power is interrupted and the instrument turns off while you are operating it, the following will occur when you turn

Specifications 10DimensionsThe physical dimensions of the instrument are:Height: 30.5 cm (12 in.)Width: 52 cm (20 in.)Depth: 61 cm (24 in.)Weight: 40.

10-2Power RequirementsThere are three versions of the GeneAmp PCR System 9600. The power requirements of these instrument versions are:♦120VAC, 60 Hz,

10-3Sample Temperature RangeThe temperature range of the sample block is:4.0 degrees to 99.9 degrees C.Sample Temperature AccuracyThe displayed sample

10-4Figure 10-1Sample temperature overshoot after ramping up.Ramp Time RepeatabilityThermal setpoints are achieved within +/–5 seconds (not including

10-5Printer InterfaceThe GeneAmp PCR System 9600 uses an RS-232C serial port as its printer interface. In addition, the following specifications apply

4Function KeysTo do this: On the DNA Thermal CyclerOn the GeneAmp PCR System 9600Begin a run Press START from the first display in the file. Select RU

IndexNoteA page number in italics (e.g., 5-26) indicates an illustration.AAborting a run, 6-20—6-21ALL history file display option, 7-45, 7-46ALL hist

Index-2Cleaning the sample block cover, 8-3Clear Entry key. See CE keyCondensation. See Loading samplesCONFIG function. See Configuration functionConf

Index-3setpoints in, 3-3, 4-10, 5-33specifying the number of cycles in, 3-18storing, 3-20target temperatures in, 3-4CYCLE print option, 6-14Cycle prog

Index-4Displayed sample temperature, 10-3Documents on Demand S-19Dot-matrix printer. See Printer setup and configurationEEdit function, 5-13EDIT optio

Index-5viewing data records with error messages in, 7-47viewing status records in, 7-47viewing, 7-44—7-47HOLD programdefining values in, 5-32definitio

Index-6MMain menu, 3-6CREATE option, description of, 4-4cursor on, 3-6description of, 3-6, 4-4—4-5EDIT option, description of, 4-4getting to the, 4-4o

Index-7PCR programs and methodsoverview of, 4-6—4-7setting up, 5-1—5-45PCR techniqueannealing step, 1-2Denaturing step, 1-2description of, 1-2Extendin

Index-8Program numbersassigning to methods, 5-21assigning, 5-11use in creating methods, 5-18, 5-45use in deleting programs, 7-57viewing a directory of

Index-9Run-time displays, 6-17—6-19Run-time keys, 4-3, 6-11Run-time printer modeturning on and off, 7-20turning on, 2-13SSample block covercleaning, 8

5File StorageWith the GeneAmp PCR System 9600, you can store up to 150 programs. (A method is assigned a program number and is considered an individua

Index-10default value, 7-26temperature interval, 7-26, 7-26SETPOINT print optionexample printout, 6-15SETPOINT print option, 6-14Setpoint time. See Ho

Index-11TTarget temperatureSee also Sample temperature, Setpointsin CYCL programs, 3-4See also Sample temperatureTechnical support S-14—S-19E-mail add

Index-12UUnpacking the instrument, 2-2Unprotected programs, deleting, 7-61User diagnostics. See Diagnostic testsUser identification number. See User n

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S-1Safety and Regulatory InformationSConventions Used in This Manual! WARNING !A warning indicates an operation that could cause personal injury if pr

6Setting Hold Times on the GeneAmp PCR System 9600These general guidelines are based upon differences in how the instruments operate to heat and cool

7Figure 1Heating ramps on the DNA Thermal Cycler 480 and GeneAmp PCR System 9600.Graphic

8Tables 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

9NoteIf 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

Contents 1Preface: Using the Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . P-1Using the Manual . . . . . . . .

iiSetting Up the Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6Installing the 115-VAC Printer . . . . . . . . . .

iiiChapter 4. Software Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1Introduction . . . . . . . . . . .

ivSoftware Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28Using the STOP Key . . . . . . . . . . . . . . . .

vIndicator Lights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-16Run-Time Displays . . . . . . . . . . . . . . . . .

S-2Symbols and Conventions Used on the InstrumentThere are three different types of warning symbols that appear on the instrument.This symbol indicate

viTHIN Time Constant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-32Printing the Configuration Parameters . . . . . . . . . . . . .

viiTesting the Temperature Uniformity . . . . . . . . . . . . . . . . . . . . 8-13Test Results . . . . . . . . . . . . . . . . . . . . . . . . . .

ixIllustrations 11Figure 1-1 The GeneAmp PCR System 9600. . . . . . . . . . . . . . . . . . . . . . . . . . 1-1Figure 1-2 Sample block and heated cov

xFigure 5-2 Sample conversion of hold times for up ramps (DNAThermal Cycler to GeneAmp PCR System 9600) . . . . . . . . . . . . . . 5-5Figure 5-3 Samp

xiFigure 7-4 Example of a list of programs listed according to user number. . . 7-12Figure 7-5 The PRINT selection of the Directory function. . . .

Preface: Using the Manual PThe GeneAmp PCR System 9600 is a highly sophisticated, yet easy-to-use temperature cycling instrument designed specifically

P-2We recommend that you follow this approach to learn about the GeneAmp PCR System 9600:1Read this chapter to learn about the conventions used in the

P-3ConventionsThe following conventions are used in this manual.Software Conventions♦The instrument display is pictured as follows. This display show

S-3Additional graphic symbols used on the instrument are the following: Indicates alternating current.Indicates the primary protective grounding termi

P-4Notes and WarningsThe following conventions are used in this manual:! WARNING !A warning indicates an operation that could cause personal injury if

Introducing the GeneAmp® PCR System 9600 1Introduction This chapter describes the principles of instrument operation, the hardware, and the software.F

1-2Principles of OperationThe GeneAmp PCR System 9600 automates the Polymerase Chain Reaction (PCR) technique for amplifying DNA. The Polymerase Chain

1-3restriction sites. Dideoxy sequencing can also be performed on the amplified product.Instrument DescriptionThe GeneAmp PCR System 9600 contains a p

1-4the 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 PanelT

1-5Instrument FeaturesFeatures of the GeneAmp PCR System 9600 include:♦reproducibility of cycle times♦uniformity of PCR yields for samples♦sample tray

1-6The software lets you:♦create, store, and modify your own customized time and temperature programs and protect these programs with a user number, i

Installing the GeneAmp PCR System 9600 2IIntroduction This chapter describes how to install the GeneAmp PCR System 9600. If your instrument has alread

2-2UnpackingInspect the GeneAmp PCR System 9600, and all other parts supplied, for any damage that may have occurred during shipment. If there has bee

2-3Supplies, Accessories, and Replacement PartsFor Sales Assistance and Information: 1-800-345-5224. For Technical Assistance: 1-800-762-4001. Supplie

S-4Warnings on the InstrumentThe following sections present the warning labels affixed to the instrument.The following warning labels are affixed to t

2-4Power RequirementsCAUTIONBefore the power is turned on for the first time at installation, be sure that the unit has been upright for at least fo

2-5All 230VAC instruments are wired for single-ended line service. 230VAC instruments installed in locations that have double-ended line service or lo

2-6Setting Up the PrinterThe GeneAmp PCR System 9600 can be used with an optional Epson LX-810 printer or other Epson-compatible printers with a seria

2-74Connect 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 PC

2-8Figure 2-1DIP switch Settings on the Epson C82302 serial interface card.

2-9 Figure 2-2Side panel of the GeneAmp PCR System 9600 and rear panel of the printer showing DIP switch settings and cable connections.GeneAmp PCR Sy

2-10Installing the 230-VAC PrinterThe Printer Kit for the 230-VAC GeneAmp PCR System 9600 (Part No. N801-0314) contains a printer (Part No. 0942-1015

2-11NoteWhen 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 manu

2-12Configuring the Printer1Turn on the power switch located on the lower left side of the instrument.A beeper sounds and all three indicator lights f

2-13The following display appears: This display is used to set the time and date.5To set the time, press the appropriate numeric keys for hours and mi

S-5Back of Instrument! WARNING !Grounding circuit continuity is vital for safe operation of equipment. Never operate equipment with grounding conducto

2-14Configuring the GeneAmp PCR System 9600The final procedure in installing the GeneAmp PCR System 9600 is checking the instrument configuration. Th

2-15Summary of Configuration ParametersConfigurationEDIT-PRINTThis display lets you edit or print the configuration parameters.Press ENTER to select

2-16Idle state setpoint25CSet the temperature at which the block will be maintained when a program is not running. As factory set, the instrument wil

2-17a. 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 tub

2-18There are two additional configurable parameters that let you change the time constants for MicroAmp Reaction Tubes and Thin Walled GeneAmp Reacti

2-19Heater and Chiller Tests After you have configured the GeneAmp PCR System 9600, perform the heater and chiller tests as described in the following

2-203Press the OPTION key twice to move the cursor under DIAG and press ENTER. A display referring to the first diagnostic test appears:4Change the &q

2-21Chiller TestThe chiller test verifies that the refrigeration system is operating correctly. CAUTIONBefore you begin this test, make sure you place

Tutorial: Customizing a PCR CYCL Program 3IntroductionThis tutorial explains how to set up a time and temperature profile for PCR. To do this, you wil

S-6! WARNING !Hot Surface. Use care when working around this area to avoid being burned by hot components.! AVERTISSEMENT !Surface chaude.! WARNING !T

3-2Before You StartBefore you start this tutorial:1The system should be properly installed either by an Applied Biosystems service representative or a

3-3What 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 c

3-4For 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 fr

3-5Starting Up the InstrumentPress the power switch (see Figure 1-3) to the ON position.Figure 3-3Location of power switch.A beeper sounds, and all th

3-6Getting to the CYCL Program1After you start the instrument, the main menu (shown below) appears on the screen.Think of the main menu as your “home

3-73To 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 mov

3-84To create a program, you need to select the CREATE option. Press the OPTION key once to move the cursor under CREATE:5Press ENTERThe next display

3-9A Look at the CYCL ProgramIn the following steps, you will look at the main displays in the CYCL program. In each display, you will see the default

3-103Press STEP to accept all of the default values and move to the next display.The display for Setpoint #2 appears:This display sets the ramp time,

3-11The following display appears:6Press the BACK key to review the display for Setpoint #3. The illustration below shows you how the BACK key works.7

S-7! WARNING !For protection against fire hazard, replace only with same type and rating of fuse.! AVERTISSEMENT !Afin d'assurer la protection co

3-128Press STEP to accept the default values in the display.The following display appears:This is the last display in the program. From here, you have

3-13Figure 3-4Moving through the CYCL program displays.

3-14Customizing the CYCL ProgramIn the steps below, you will customize the CYCL program by changing some of the default parameters. Although we sugges

3-15Defining Values for Setpoint # 1In the following steps, you will change some of the default values for Setpoint #1.1Look for the cursor on the dis

3-16The cursor moves to the hold time:4Sometimes, you may want to change an entry after you have pressed ENTER. To move back to the previous entry, yo

3-17Defining Values for Setpoint #21Use the default ramp time by pressing ENTER2Enter 52.5 degrees C for the temperature by pressing 5, then 2, then 5

3-18Specifying the Number of CyclesThe first entry in the above display specifies the number of times the cycle will be repeated.1 Enter 30 cycles: pr

3-19The next display (the last display in the program) is:O“CYCL” in this display means that the type of program you have set up is a CYCL program. “#

3-20Storing Your CYCL Program1The following display should appear on your screen:2Press the OPTION key to move the cursor beneath STORE, then press EN

3-21The following display appears:5Press ENTER to store the programThe following display appears:On this display, CYCL is the type of program you have