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GeneAmp PCR System 9700 Base Module

1. Step Action 3 In the User Name field enter an alphanumeric name up to six characters in length You can take the following action If you want to Then select a character in the list shown in use the Circular Key Pads the upper right portions of the screen put the alphabetic character in the press Enter User Name field enter the numbers directly into the use the numeric keys User Name field go back one space and remove a hold down the Soft key and go back single character multiple spaces 4 Press Accept to accept a name The Security Code screen appears You can take the following action Then press Accept again If you do not want to protect your method want to protect your method see the following section titled Protecting Methods want to return to the Main menu without adding the new user name press Cancel Note An error message appears if you enter a name that already exists Protecting Methods You can protect methods and prevent other users from accidentally overwriting or deleting them by entering a Personal Identification Number PIN on the Security Code screen hank None Unlocked Press PIN to create a Then you set protection to Locked to prevent methods from being overwritten or deleted PIN F1 F2 F3 F4 F5 PIN number Protection User Name Accept Name The following ta
2. To upgrade using a PCMCIA Flash Memory Card continued Step Action 6 If the PCMCIA Flash Memory Card contains a valid firmware upgrade the Upgrade screen appears DO NOT TURN OFF THE INSTRUMENT OR REMOVE THE PC CARD Upgrading the instrument firmware will take approximately 30 seconds Instrument will re boot when complete F1 F2 F3 F4 F5 If successful the Firmware Upgrade Successful screen displays the firmware version to which you have upgraded Pressing the Run key in the lower right corner brings up the Main menu with the new revision number of the software listed on the screen Remove the PCMCIA Flash Memory Card after you have successfully upgraded the firmware Instrument Setup 3 23 Copying Methods How to Copy You can copy methods from a Methods Transportability card to the instrument or from Methods the instrument to a Methods Transportability card P N 940 1064 Runs can be made directly from methods on a Methods Transportability card To copy a method Step Action 1 Insert a Methods Transportability card that contains the updated firmware into the slot at the rear of the right side of the instrument Note The label and arrow on the card face forward and toward the instrument SRAM Recharge PC Card ENTENNIAL Methods Transportability Card Press the card firmly to ensure the card is seated in the slot IMPOR
3. Creating and Editing Methods 5 17 Editing or Deleting Methods Introduction After you create a method you can edit its parameters and store the method by the same name or change its name At some time you may also want to delete a method if you are no longer using it You can access all editing functions from the Main menu The delete screen is accessed through the utility menu Editing a Method The following procedure describes how to edit a method To edit a method Step Action 1 From the Main menu press Edit Note If an SRAM PC Card is detected in the Card slot you will get a choice of editing a method on the PC Card or the instrument The top line of the display continuously cycles between the following three lines Methods on Inst User or on PC card Size Stored or Last Used Used Mem xxx methods xxx segments Free Mem xxx methods xxx segments The following table describes these fields Field Description units for the Size field Based on a calculation of the complexity and length of a method relative to a maximum size of 1102 size segments for the storage capacity of the instrument Used Mem field Displays the number of segments used by all stored methods Free Mem field Displays the number of segments available to store created methods Select one of the methods displayed on the screen or select another method as f
4. Infinity hold not allowed in cycle A method can have an infinity hold segment as the last segment in the method This message occurs when you tried to enter an infinity time in a CYCLE segment Use finite values for cycle segments within the method Invalid password pin You entered an incorrect PIN Enter the correct PIN LCD screen timed out System error Display screen and firmware have a faulty connection Call a Technical Support List of user names is full The maximum number of users has been entered into the system Delete unused user names Maximum of 6 segments allowed You tried to insert more than six temperature control parameters into a hold or cycle Do not assign more than six hold or cycle parameters to a method Method battery RAM initialized Stored methods have been reset due to hardware or software failure Not all methods may be lost Check method directory Call Technical Support Method requires at least one segment You deleted all temperature control parameters in a method A method must have at least one time and temperature parameter Review and correct the method to include the temperature parameter s No seconds in time field You did not include seconds in the time field Include seconds when entering the time Not enough method memory left This error occurs When you attempt to exceed the limit of 137 meth
5. CAUTION Hazardous waste Read the waste profile if any in the site preparation guide for this instrument before handling or disposal ATTENTION D chets dangereux Lire les renseignements sur les d chets avant de les manipuler ou de les liminer CAUTION Hazardous waste Refer to MSDS s and local regulations for handling and disposal ATTENTION D chets dangereux Lire les fiches techniques de s ret de mat riels et la r gulation locale associ es la manipulation et l limination des d chets WARNING Hot lamp AVERTISSEMENT Lampe br lante WARNING Hot Replace lamp with an Applied Biosystems lamp AVERTISSEMENT Composants br lants Remplacer la lampe par une lampe Applied Biosystems CAUTION Hot surface ATTENTION Surface br lante DANGER High voltage DANGER Haute tension 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 viter les risques d lectrocution ne pas retirer les capots dont l ouverture n cessite l utilisation d outils L instrument ne contient aucune pi ce r parable par l utilisateur Toute intervention doit tre effectu e par le personnel de service qualifi de Applied Biosystems CAUTION Moving parts ATTENTION Parties mobiles Introduction and Safety 1 5
6. Creating and Editing Methods 5 1 Adding or Changing Users Introduction The GeneAmp PCR System 9700 stores methods by user s names You can add up to 19 different user names to the instrument Once you ve added your name to a list of users and stored a method under that name you can run the method at any time by selecting it from the Stored Methods screen See Selecting a Method on page 4 3 Use the User function on the Main menu to add new users or edit existing user names The name you add or the name you select from a list of existing user names becomes the current user name All new methods that you create are stored by default under the current user name Adding a New User You add a new user name by entering an alphanumeric name on the User Name Name Screen To add a new user name Step Action 1 From the Main menu press User The Select User Name screen appears A list of names of all users who have been added to the instrument displays in a 4 x 5 matrix Select User Nam lt lt pe gt gt adrian doug Delete F1 F2 F3 FA F5 2 Press New to add a new name to the above list The User Name screen appears Note The blank space after the z is used to insert the blank spaces abcdefghi jklmnopqgrj stuvwxyZ User Name ee i Use ENTER key to select a character 5 2 Creating and Editing Methods To add a new user name continued
7. Note Even after you delete the last method stored under a User name the name is removed from the instrument To delete the name see Deleting a User Name on page 5 5 Creating and Editing Methods 5 21 Converting Hold Times Overview About This Chapter This chapter provides information about setting hold times for the GeneAmp PCR System 9700 compared to the DNA Thermal Cycler or DNA Thermal Cycler 480 This information is based upon differences in how the instruments heat and cool samples Note Protocols using sample volumes between 5 uL and 50 pL developed on either the GeneAmp PCR System 2400 or 9600 may be transported to the GeneAmp PCR System 9700 without change when using the 9600 emulation mode In This Chapter The following topics are covered in this chapter Topic See page About Setting Hold Times 6 2 Guidelines for Converting Hold Times 6 3 Converting Hold Times 6 1 About Setting Hold Times Introduction The hold times specified for the GeneAmp PCR System 9700 are shorter than those used for the Step Cycle or ThermoCycle files on the DNA Thermal Cycler and the DNA Thermal Cycler 480 This is because the DNA Thermal Cycler and the DNA Thermal Cycler 480 starts counting the hold time when the block reaches a temperature one degree before the target temperature while the GeneAmp PCR System 9700 starts counting the hold time when the samples reach a temperature one degree before
8. Max F1 F2 F3 F4 F5 96 Well Select 9600 or STD mode first and then select volume Aluminum S Block Select Method Options Reaction Volume 50 uL Ramp speed 9600 Enter a value from 5 to 50 uL Start 9600 STD FL F2 F3 FA F5 4 If the displayed reaction volume differs from your reaction volume enter the volume of your reactions in the Reaction Volume field The reaction volume range is dependent on the mode selected For The range is 9600 mode 5 to 50 pL MAX STD mode 5 to 100 pL Note Each method remembers the reaction volume Press the CE key to clear an entry To start a run continued Step Action 5 Press Start to start a run If the temperature of the heated cover is less than 103 C this message Cover is heating appears Please wait Cover is heating Current temperature 65 C The run will begin when the heated cover reaches 103 C F1 F2 F3 FA F5 When the heated cover reaches 103 C the Run Time screen displays and the method you selected starts running For a description of this screen see About the Run Time Screen on page 4 7 Sample 56 7 Cycle 1 of 25 94 0 94 0 72 0 72 0 Horizontal lines flash as Cycles count up when hold times decrement run is in PCR segment About the Run Time You can use the Run Time screen to chart progress at any time during the run The Screen Run Time screen displ
9. Use the Circular Key Pad advance the box to the next field Press the Enter key Entering Numeric The following table lists how to enter numeric values for the Temperature and Hold Values Time parameters Parameter Description Temperature Enter values for temperature in decimal form It is not necessary parameters to type a decimal point For example to specify 89 0 C press 8 9 O then press Enter Hold Time parameters A hold time is the length of time the samples will be maintained at a specified temperature Specify all hold times in minutes and seconds then press Enter For example to specify one minute and five seconds press 1 0 5 then press Enter Product Overview 2 3 Transfer or Storage You can transfer or store methods using a Methods Storage Card The instrument can of Methods run a method from its own software or from the methods stored on a Methods Storage card Use To See Methods Storage Card transfer methods from the Copying Methods on page Centennial 256kb SRAM Methods Storage card to the 3 24 P N 0940 1064 instrument or from the instrument to the card for storage Upgrading the There are two ways to upgrade the firmware Firmware 4 with a serial cable connection PC communication cable P N N805 1327 or Macintosh communication cable P N N805 1328 from the instruments RS485 ports With a PCMCIA Flash Memory Card
10. You can obtain from Applied Biosystems the MSDS for any chemical supplied by Applied Biosystems This service is free and available 24 hours a day To obtain MSDSs 1 Go to https docs appliedbiosystems com msdssearch html 2 In the Search field type in the chemical name part number or other information that appears in the MSDS of interest Select the language of your choice then click Search 3 Find the document of interest right click the document title then select any of the following Open To view the document Print Target To print the document Save Target As To download a PDF version of the document to a destination that you choose 4 To have a copy of a document sent by fax or e mail select Fax or Email to the left of the document title in the Search Results page then click RETRIEVE DOCUMENTS at the end of the document list 5 After you enter the required information click View Deliver Selected Documents Now For chemicals not manufactured or distributed by Applied Biosystems call the chemical manufacturer Introduction and Safety 1 7 About Waste Disposal 1 8 Introduction and Safety As the generator of potentially hazardous waste it is your responsibility to perform the actions listed below Characterize by analysis if necessary the waste generated by the particular applications reagents and substrates used in your laboratory Ensure the health and safety of all personnel in yo
11. continued Step Action 5 Using the Circular Key Pad and Enter key enter up to a 16 character name for identifying the instrument on the network abcdefghi jklmnopqr IP Name Cycler 01 stuvwxyz MAI Press ENTER key to select a character F1 F2 F3 F4 F5 6 Press Accept when finished entering a name The software returns to the previous screen and displays the new name in the Name field Use the Circular Key Pad to select the last IP field Set the IP field by using the numeric keys to enter an IP address for the instrument Instrument Configuration Set IP RS485 Name Cycler 01 LP 0 0 0 Mi F1 F2 F3 F4 F5 9 Press Accept when all information on this screen is correct Running Instrument Diagnostics Overview Viewing the Diagnostic Screen The instrument provides a number of internal diagnostic utilities tests you can run to verify that the instrument hardware and software components meet performance specifications The following procedure describes how to view the Diagnostic screen To view the Diagnostic screen Step Action 1 From the Main menu press Util The Utilities screen appears Utilities Diag Instrument diagnostics TmCalc Calculates melting temp Config Instrument configuration Diag TmCalc Config More F1 F2 F3 F4 F5 2 From the Utilities screen press Diag The Diagnostics screen appears Diag
12. A Temp C 35 55 56 75 76 96 10 39 sec 39 sec 40 sec 15 45 sec 47 sec 48 sec 20 49 sec 52 sec 53 sec 30 56 sec 59 sec 40 57 sec 62 sec 50 mE 62 sec 60 60 sec In the example below the temperature was decreased by 22 C This value was rounded to 20 C According to Table 6 2 with a starting temperature of 94 C we should subtract 53 seconds from the hold time on the DNA Thermal Cycler or the DNA Thermal Cycler 480 resulting in a new hold time of 27 seconds Note If the methods developed on the GeneAmp PCR System 9700 will be used on the DNA Thermal Cycler or the DNA Thermal Cycler 480 use Table 6 2 to convert the hold times Add the indicated times instead of subtracting them DNA Thermal Cycler gt GeneAmp PCR System 9700 Temp Starting Temp 94 Temp Starting Temp 94 C 94 MN Hold 72 A temp 22 round to 20 80 sec Time C 94 uw Hold 72 A 27 sec Time Converting Hold Times 6 5 Routine Maintenance Overview About This Chapter This chapter describes how to perform routine maintenance on the GeneAmp PCR System 9700 N BD AN eldi ELECTRICAL SHOCK HAZARD Severe electrical shock can result from operating the GeneAmp PCR System 9700 Base Module without its instrument panels in place Do not remove instrument panels High voltage contacts are exposed when instrume
13. Note Upgrade firmware can be ordered from the Applied Biosystems web site or by contacting PCR Technical Support For more information about upgrading the firmware see the following If you are using See a serial cable connection RS485 ports Upgrading Through the Serial Port on page 3 18 a PCMCIA Flash Memory Card Upgrading Firmware from a PCMCIA Flash Memory Card on page 3 22 Microsoft Windows 95 or Windows NT9 Downloading Firmware Using Windows 95 or Windows NT on page 3 20 Windows 3 1 Downloading Firmware Using Windows 3 1 on page 3 21 2 4 Product Overview How the 9700 Differs The GeneAmp PCR System 9700 differs from the GeneAmp PCR System 9600 in from the GeneAmp the following ways PCR System 9600 Reaction volumes of up to 50 pL only can be run and in the 9600 Mode as opposed to 100 uL in the GeneAmp PCR System 9600 Methods are stored under a user name allowing users to keep track of and protect their own methods Hold Cycle and Auto programs no longer exist as menu items under the Create function Instead of linking programs together to create a method you create a single method on the GeneAmp PCR System 9700 If the allowed pause time elapses during a manual pause of a method the method will continue running instead of stopping The last method run cannot be re run or edited unless it is first saved The history file no lo
14. P N N808 0175 The AmpliTaq Gold protocol specifies a 5 minute pre PCR heat step required for the activation of AmpliTaq Gold DNA Polymerase This additional step provides seamless hot start PCR and replaces labor intensive methods such as manual hot start or wax bead mediated hot start techniques 1Hld 3 Tmp 35 Cycles 2 Holds 95 0 95 0 72 0 72 0 5 00 0 15 05 45 oco Method AmpliTaq Gold BigDye Terminators General PCR Utilizing hot start techniques helps to minimize the formation of primer dimers or non specific products thus increasing specificity and sensitivity of PCR You can find further information on AmpliTaq Gold DNA Polymerase in the product insert P N N808 0241 or at the Applied Biosystems website The BigDye method consists of cycle sequencing parameters for dideoxy Sanger terminator sequencing using ABI PRISM BigDye Terminator Cycle Sequencing Ready Reaction Kits available from Applied Biosystems It consists of 25 cycle three temperature cycle sequencing followed by an infinite hold at 4 C 3 Tmp 25 Cycles 1 Hld 96 0 0 05 Method BigDye F1 F2 F3 FA F5 The pre coded conditions in the BigDye method are optimized for AmpliTaq DNA Polymerase FS and the cycle sequencing reagents supplied with the BigDye terminator kits This process is further described in the AB Prism BigDye Terminator Cycle Sequencing Ready Reaction Kits Protocol P N 4303237 The General PCR
15. accessories and disposables from Applied Biosystems Numbers To order this part Use P N GeneAmp PCR System 9700 Base Module N805 0200 60 Well 0 5 mL Sample Block Module 4309131 Auto Lid Sample Block Module 4312904 96 Well Gold Sample Block Module 4314443 96 Well Aluminum Sample Block Module 4314445 Dual 384 Well Sample Block Module N805 0400 Temperature Verification System N801 0435 PC method storage card 940 1064 Printer cable N805 1326 PC communication cable N805 1327 Macintosh communication cable N805 1328 Note See the nterchangeable Sample Block Module Users Manual for part numbers of disposable items 3 2 Instrument Setup Setting Up your Laboratory Choosing a Location Operating Temperature What to Avoid Do Not Block Air Vents To prevent vibration place the GeneAmp PCR System 9700 on a solid stable level surface that allows free airflow overhead and around the sides and back You should keep all ventilation slots in the instrument cover free of obstruction for example from excess printer paper The instrument will meet performance specifications when the ambient temperature is 15 C to 30 C 59 to 86 Fahrenheit and the ambient relative humidity is 20 to 80 When setting up the instrument avoid Placing the instrument under overhanging shelves especially when there is a wall behind the unit Proximity to other instruments on the sam
16. b Type in a hold time value between 00 00 and 98 59 minutes seconds Repeat step 3 and step 4 until you have time and temperature values for each of the segment temperature control parameters you defined in step 1 Defining Post PCR On the Create screen the Holds field defines the number of temperature control Holds parameters in the post PCR segment of your method The post PCR incubation temperature and hold time parameters define how to hold your samples at a specified temperature until you are ready to analyze them Note If the idle state setpoint or the last hold of the Method are below 15 C then the heated cover will automatically set to 50 C Post PCR Parameter Settings Typical Post PCR parameter settings Temperature Time min sec Use For 72 C 7 00 Complete extension of all amplicons 72 C 99 59 x AmpErase applications 4 C 99 59 x General storage Follow the procedure below to define Post PCR Holds To define post PCR holds Step Action 1 Select the Holds field In the Holds field type in the number of post PCR steps for your method Press Enter to select the first post PCR temperature parameter Type in a temperature value between 4 0 C and 99 9 C Press Enter to select the first post PCR hold time parameter o c5 0 M Type in a hold time value between 00 00 and 98 59 min sec Note The hold time x indicates a hol
17. printer connecting and configuring 3 26 specifications A 4 system firmware upgrading 3 18 to 3 23 system specifications A 2 Ty calculator how to use 3 17 turning on instrument 3 6 unpacking 3 2 General PCR 4 2 B 2 General PCR about supplied method B 3 grounding 1 10 H Hard soft key function of 3 13 hazards and warnings 1 3 to 1 8 1 9 to burns danger of 1 10 Index 2 instrument warnings 1 9 heated cover screen 4 7 heating of samples 5 8 history of run reviewing history file records 4 11 history formats 4 10 procedure 4 10 hold time converting from DNA Thermal Cycler 6 2 to 6 5 parameters defined 2 3 holds deleting 5 14 inserting 5 13 humidity 1 11 I Idle State Setpoint temperature setting 3 10 input voltage table of 3 4 inserting holds 5 13 K keyboard softkey function of 3 14 keypad testing 3 16 L labels safety 1 9 laboratory environmental requirements 1 11 laboratory setting up 3 3 to 3 4 air vents air circulation 3 3 choosing a location 3 3 fuse service configuration 3 4 input voltage table of 3 4 interchangeable block module about 3 4 operating temperature 3 3 what to avoid 3 3 LCD pixels turning on and off 3 15 locking unlocking methods about 5 4 LSM2 4 2 B 2 M maintenance routine 1 11 Memory Used field definition of 4 3 5 20 Method Not Stored screen actions if displayed 4 12 methods adding or changing users 5 2 to 5 5 adding users 5 2 to 5 3 changing user name 5
18. screen Screen Saver Options The following table lists the screen saver options Use This Option To Activate the Screen Saver Smart After 15 minutes unless a method is running Always After 15 minutes Never Never You can use the fourth Configuration screen to set the IP address for the instrument The instrument can be linked to a network via the RS485 ports located on the right rear side of the instrument see the figure on page 3 18 Once connected and configured the instrument will be visible from the network under the IP address and instrument name you select in the following procedure Note See the System 9700 Networking Software User s Manual P N 4309575 for more information about networking GeneAmp PCR System 9700 instruments To set the IP Address for an instrument Step Action 1 Select More to display the second configuration screen Instrument Configuration Set IP RS485 Name Cycler 01 LP 0 0 FL F2 F3 F4 F5 2 Set the Set IP field using the and keys The following settings are available Setting Definition RS485 Activates the RS 485 ports Must be used with the networking software Off Turns off the networking capability and turns on the RS232 ports 3 Use the Circular Key Pad to select the Name field 4 Select Name Instrument Setup 3 11 3 12 Instrument Setup To set the IP Address for an instrument
19. 0 cece eee eh 1 11 Introducthon a a ese 8s ieee pes A es DA pe E ON ee RS 1 11 Temperature Humidity and Environment 00 0002 00 00 0005 1 11 POU bis festa ieee di 1 11 Emission Immunity Statement e 00 cee eee ne 1 11 Routine Maintenance for Safe Operation 0 0 0 eee eee eee 1 11 U S and Canadian Safety Standards 0 0 0 0 eee eee eee 1 12 Canadian EMC Standard lecce ee eaves e xe RR RR RR aes 1 12 European Safety and EMC Standards 1 12 Australian EMC Standards 0 0 0 eee eene ee 1 12 2 Product Overview OVELVICW 5o di ni ea 2 1 About This Chapters tic i352 octet seb it ed Aca Ue OP eis 2 1 In Ihis Chapter eee A A A a ae ET 2 1 About the GeneAmp PCR System 9700 2 0 ec cee eee 2 2 About the Instrument suspa iopo ie ee GR ER RE a RU Mal EE ER ES 2 2 Control Pane tad bed eh tes ee ied EE Rs 2 2 Control Panel Diagt mi x RSS S Te R RRR ERa ccc eee ees 2 2 Using the Keys senesced eet si ea ee ee a wed a 2 3 Selecting a Field necu e RA RR Ree hee ees 2 3 Entering Numeric Values 0 0 0 6 R r ea rr 2 3 Transfer or Storage of Methods 0 0 cece eee eee 2 4 Upgrading the Firmware cocer t Ra E R RRR RT R TR RR ee eee ees 2 4 How the 9700 Differs from the GeneAmp PCR System 9600 2 5 3 Instrument Setup OVERVICW SN Sci E EA ee DOS ene ak di Salk ee srk eet 3 1 About This Chapter ed eek dee A Re Baa 3 1 In This Chapter oder Aira 3 1 Unpacking the Instrumen
20. 0 cee eee 5 18 Introduction 204 443 ea ae eee Ge ad dee SA doh Rod dean 5 18 Editing a Method tot Es tratte MEER QE A IRE S SP 5 18 Deleting a Method sihire enn E ES E LA Sea eA ee eed 5 20 6 Converting Hold Times OVERVIEW 5 Lee eed eee UP Rx NEL ECL LA P MENU so BS das 6 1 About Ihis Chapter eR Rer ROI eae ae ee aS 6 1 In This Chapter ceci rd ESPECIE be RO E RR 6 1 About Setting Hold Times desse ges a Rady Roe econ gree e Eus 6 2 Introduction eire bp e e re Rer IU RECIEN 6 2 Hold Time BT 3 cv cue e hem oS WS EE EE EORR TATE 6 2 Guidelines for Converting Hold Times 0 0 0 eee cee eene 6 3 Introd ction Lee RD ee iho eS HR ete eios eere hg 6 3 What to Base the New Hold Times On 0 0 0 cee eee eee eee 6 3 Setting Up Ramps lt Te rR eo bero EUREN HEN PE E PE UE 6 3 Table of Conversions o RR e eee ee eee x A e eR RO EI sn 6 3 Up Ramp Example eror E c RR nals a PER DER RE ES 6 4 Setting Down Ramps 20 20 cece cee eee mh be he 6 4 Table Of Conversions 3 ce5 3ge8 ees avenge gags ales doe gee ES 6 5 Down Ramp Example aaa a RR RRR 0 0 RE R y Ie RID RPG gee ae ores 6 5 7 Routine Maintenance OVERVIEW 3 con ered see es NOD RIDERS PANT Ae ays WP eee 7 1 About This Chapter ita ta ew aia eth ale eee 7 1 In This Chapter avoir a oe HA es th rt 7 1 Changing the External Fuses 0 0 0 2 eee cece eee nes 7 2 Introduction i i E i e I AAA A an ea eee 7 2 Power Entry Module Diagram eee
21. 230 10 50 60 Hz 1 3 14 a Acceptable AC line voltage tolerances 100 120 220 230 1096 240 VAC 6 10 50 60 Hz 1 Note The Volt Amp number for this instrument is 725 Volt Amps The instrument features an interchangeable sample block module allowing portability and versatility in sample configuration Sample Block Module Part Number 96 Well Gold Sample Block Module 4314443 96 Well Aluminum Sample Block Module 4314445 60 Well 0 5 mL Sample Block Module 4309131 Dual 384 Well Sample Block Module N805 0400 Auto Lid Sample Block Module 4312904 Note The GeneAmp PCR System 9700 will not operate without an interchangeable sample block module installed For an example refer to the GeneAmp PCR System 9700 96 Well Sample Block Module User Guide for instructions on how to install a block and configure the samples Double Line Fuse Introduction AN Mabel FIRE HAZARD For continued protection against the risk of fire replace fuses only with listed and certified fuses of the same type and rating as those currently in the instrument IMPORTANT For proper operation you must know the power source s available and determine if the instrument fuse configuration is correct The instrument is shipped configured for single line operation Fuse Part Number The correct fuse is an 8 amp Type T 250 V 5x20 mm fuse P N 0999 1683 Power Entry Module The following is a diagram of the Power
22. 5 protecting methods 5 3 to 5 4 Util function of 3 7 W warning Index 4 chemical hazard 1 6 chemical waste hazard 1 6 warranty damages claims returns D 3 exceptions D 2 for computers with altered configuration D 1 limitations D 2 period D 1 warranty claims D 2 warranty exceptions D 2 warranty period effective date D 2 waste disposal 1 8 Win 3 1 downloading firmware using 3 21 Windows 95 Windows NT downloading firmware using 3 20 X XL PCR 4 2 B 2 about supplied method B 5 Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free In North America 1 800 345 5224 Fax 1 650 638 5884 Worldwide Sales and Support Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches 150 countries on six continents For sales office locations and technical support please call our local office or refer to our Web site at www appliedbiosystems com www appliedbiosystems com A Applied KS Biosystems Applied Biosystems is committed to providing the world s leading technology and information for life scientists 6 2010 Part Number 4304481 Rev H ss
23. Chemical Safety Chemical Hazard Warning Chemical Waste Hazard Warning 1 6 Introduction and Safety Nr CHEMICAL HAZARD Some of the chemicals used with Applied Biosystems instruments and protocols are potentially hazardous and can cause injury illness or death 4 Read and understand the material safety data sheets MSDSs provided by the chemical manufacturer before you store handle or work with any chemicals or hazardous materials Minimize contact with chemicals Wear appropriate personal protective equipment when handling chemicals e g safety glasses gloves or protective clothing For additional safety guidelines consult the MSDS Minimize the inhalation of chemicals Do not leave chemical containers open Use only with adequate ventilation e g fume hood For additional safety guidelines consult the MSDS Check regularly for chemical leaks or spills If a leak or spill occurs follow the manufacturer s cleanup procedures as recommended on the MSDS Comply with all local state provincial or national laws and regulations related to chemical storage handling and disposal Tamma CHEMICAL WASTE HAZARD Wastes produced by Applied Biosystems instruments are potentially hazardous and can cause injury illness or death 4 Read and understand the material safety data sheets MSDSs provided by the manufacturers of the chemicals in the waste container before you store handle or dispose of chemical wa
24. PANELS OR COVERS KEEP FREE OF DEBRIS FAN INTAKE Introduction and Safety 1 9 Danger of Burns ANIN PHYSICAL INJURY HAZARD Hot Surface Use care when working around this area to avoid being burned by hot components Grounding and The system 9700 must be grounded for protection against electrical shock Electrical Safety Ya DUW edi ELECTRICAL HAZARD Do not use an adapter to a two terminal outlet since this does not provide positive ground protection Fuses Improper fuses can damage the wiring system and cause a fire Tamma FIRE HAZARD For continued protection against the risk of fire replace fuses only with fuses of the type and rating specified for the instrument N WelA58 ELECTRICAL SHOCK HAZARD Improper fuses or high voltage supply can damage the instrument wiring system and cause a fire Before turning on the instrument verify that the fuses are properly installed and that the instrument voltage matches the power supply in your laboratory 1 10 Introduction and Safety Laboratory Environmental Requirements Introduction Temperature Humidity and Environment Pollution Emission Immunity Statement Routine Maintenance for Safe Operation Take the precautions described in this section whenever you operate the system 9700 Read this section before you install the instrument Taman The instrument should be used according to the instructions provided in this manual If us
25. PCR for the amplification of the control target a 20 8 kb product from Lambda DNA supplied in the kit This process is further described in the product insert for the GeneAmp XL PCR Kit P N N808 0192 Supplied Methods B 5 Contacting Services and Support How to Obtain Services and Support To contact Applied Biosystems Technical Support from North America by telephone call 1 800 899 5858 For the latest services and support information for all locations go to http www appliedbiosystems com then click the link for Services and Support At the Services and Support page you can Search through frequently asked questions FAQs Submit a question directly to Technical Support Order Applied Biosystems user documents MSDSs certificates of analysis and other related documents Download PDF documents Obtain information about customer training Download software updates and patches In addition the Services and Support page provides access to worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities Contacting Services and Support C 1 Limited Warranty Statement Computer Configuration Applied Biosystems supplies or recommends certain configurations of computer hardware software and peripherals for use with its instrumentation Applied Biosystems reserves the right to decline support for or impose extra charges for supporting nonstandard computer configur
26. TmCalc Enter user and method names or CANCEL You did not enter a user name and a method name before storing a method Specify the method name and choose a user to store a method FATAL Block shut off by hardware Block thermal runaway Call Technical Support FATAL Block thermal runway Fatal error Turn off system Call Technical Support FATAL Cover shut off by hardware Heated cover thermal runaway Call Technical Support FATAL Heat sink is too hot Ambient conditions may be too warm Call Technical Support FATAL Heat sink sensor failure System error Call Technical Support FATAL Heated cover thermal runaway Fatal error Turn off system Call Technical Support Troubleshooting 8 3 Table 8 1 Error Messages continued Message Description Recommended Action FATAL Sample block sensor failure Fatal error Turn off system Call Technical Support Fatal Stack Overflow A warning or error message that displays which task stack overflowed The warning message is issued when the stack has reached within 10 of overflowing Call Technical Support Field is full You tried to enter more data in a field than the field size allows Reenter data within the specifications of the field Heated cover sensor failure The heated cover sensor failed Call Technical Support
27. avoided may result in minor or moderate injury It may also be used to alert against unsafe practices UE Indicates a potentially hazardous situation which if not avoided could result in death or serious injury N BUda Indicates an imminently hazardous situation which if not avoided will result in death or serious injury This signal word is to be limited to the most extreme situations Introduction and Safety 1 3 Symbols on Instruments Electrical Symbols The following chart is an illustrated glossary of all electrical symbols that are used on Applied Biosystems instruments Whenever such symbols appear on instruments please observe appropriate safety procedures Indicates the On position of the main power switch Indicates the Off position of the main power switch Indicates the On Off position of a push push main power switch Indicates a terminal that may be connected to the signal ground reference of another instrument This is not a protected ground terminal Indicates a protective grounding terminal that must be connected to earth ground before any other electrical connections are made to the instrument Indicates a terminal that can receive or supply alternating current or voltage l A OO Indicates a terminal that can receive or supply an alternating or direct current or voltage ll Safety Symbols The following is an illustrated glossary of all nonelectrical safety ale
28. cee teen ene n ees 7 2 Changing FUSES cuesta eines ege RP Mahe ba a AER 7 3 8 Troubleshooting OVINA A Sas Sneed 8 1 About This Chapt r oies sarin iga A RUD ER veh ERE 8 1 In This Chapter venez a ne Ae epe GER ai dace e ey 8 1 It There Is a Power Failures naci AREA eis OE Eee ee eed 8 2 Introduction 2e pes oh we epe p A La CARES NODE RR DER DERE 8 2 During a Power Failure 2 0 ce e 8 2 Display Screen Error Messages cocco ea Re RR RRR RRR eee eee eens 8 3 Error Messages Table bo in Sara Saeed rU 8 3 Troubleshooting Information 000 0 eee cece een eee 8 6 Troubleshooting Table s 65 625 lid ie e UE gee ae ede e 8 6 A Instrument Specifications OVA tia A 1 About This Appendix ici a EORR a a cd A 1 In This Appendix noi a RR PAR ORI A 1 System Specifications as ia a RR Pe eta eee ter Bed PR Meee A 2 DIMENSIONS cti radar eger ra A EAD aa ale Data A 2 Power Configurations e g e E KeK R R cence eee R i a A 2 Electrical Requirements cos eek darte cade pe p RR CEN ER NE A 2 Control Panel Specifications uss suussnunr rnnr rr arrra r rererere rrer A 4 Display Screen uc A ie a ewe A es eg A 4 KO Si A E aud forged Sete C ER ERE ats A 4 Sample Temperature Information 0 0 0 eee ce eee A 4 Temperat te e socseqtbBAa e REE L ra Lee ee ae A 4 Printer Specifications ei a ae MEER ete A 4 Serial Interface Board Specifications 0 0 0 eee eee eee eee A 4 Cable Part NUMDGt zone ene RARO Kafe e E TE
29. dialog box appears 7 From the directory dialog box find and select the 9700 upgrade file and click OK A message at the bottom of the window indicates that the program is sending the file and a progress bar appears When the download is complete the GeneAmp PCR System 9700 automatically resets 8 When the download is complete from the File menu choose Save to save these parameters Instrument Setup 3 21 Upgrading Firmware from a PCMCIA Flash Memory Card 3 22 Instrument Setup The following procedure describes how to upgrade the firmware using a PCMCIA Flash Memory Card Note Contact your local Applied Biosystems representative to obtain a PCMCIA Flash Memory Card To upgrade using a PCMCIA Flash Memory Card Step Action 1 Insert a PCMCIA Flash Memory Card that contains the updated firmware into the slot at the rear of the right side of the instrument Note The label and arrow on the card face forward and toward the instrument PCMCIA Flash Memory Card 2 Press the card firmly to ensure the card is seated in the slot IMPORTANT Do not remove the card or turn off the instrument until the upgrade is completed 3 From the Diagnostics screen press Upgrade From the Diagnostics screen press PCcard 5 The Checksum screen appears while the instrument checks the inserted PCMCIA Flash Memory Card to ensure that it contains a valid firmware upgrade Checking PC card checksums
30. electrical shock disconnect the power supply to the instrument unplug the power cord and wait at least 1 minute before working on the instrument a p The fuses are located in the Power Entry Module Insert a small flat tip screwdriver into the slot in the upper portion of the power entry module and open the door Pull the fuse compartment out There are two fuses in the fuse compartment Pull out the fuse from the back of the fuse compartment and replace the blown fuse with one 8 amp Type T 250 V fuse Place the fuse compartment back into the Power Entry Module and close the door Press the door until it locks in place Connect the instrument power cord Routine Maintenance 7 3 Troubleshooting Overview About This Chapter This chapter describes instrument problems you may have the probable causes of these problems and any display screen messages you may encounter when using the GeneAmp PCR System 9700 In This Chapter The following topics are covered in this chapter Topic See page If There Is a Power Failure 8 2 Display Screen Error Messages 8 3 Troubleshooting Information 8 6 Troubleshooting 8 1 If There Is a Power Failure Introduction An automated restart function allows for power failures and safe continuation of a PCR run after resumption of power During a Power Failure 8 2 Troubleshooting The following table lists
31. field howto 2 3 specifications A 4 using the keys 2 3 counting cycles See cycles CPU board testing 3 15 Create Methods screen displaying 5 7 custom parameters setting 3 7 to 3 11 baud rate setting 3 10 date setting 3 8 Idle State Setpoint temperature setting 3 10 Pause Time Out setting 3 9 printer enabling disabling 3 8 screen contrast saver mode setting 3 11 time setting 3 8 custom parameters settings Configuration Screen displaying 3 7 run time beeper turning on off 3 9 cycles counting of 4 7 inserting 5 14 cycling modifying 5 11 to 5 17 AutoX function using 5 11 to 5 12 cycles inserting 5 14 deleting holds 5 14 holds inserting 5 13 ramp rates modifying 5 12 to 5 13 D damage reporting D 3 damaged items returning D 3 data bit serial board specifications 3 10 3 26 date last used sorting methods by 4 5 setting 3 8 deleting methods 5 18 to 5 21 user name 5 5 diagnostic tests running 3 13 to 3 16 CPU board testing 3 15 Diagnostic screen viewing 3 13 Display screen testing 3 15 electrical components testing 3 14 keypad testing 3 16 Diagnostic screen viewing 3 13 dimensions instrument A 2 display screen See diagnostic tests running Display softkey function of 3 14 DNA Thermal Cycler converting hold times 6 2 to 6 5 E editing methods 5 18 to 5 21 electrical components testing 3 14 electrical safety 1 3 to 1 10 End of Run screen when a run completes 4 12 environment 1 11 error me
32. increases with the number of cycles while the amount of available enzyme remains constant To automatically change temperature control parameters Step Action 1 From the Create screen use the Circular Key Pad to select a time or temperature parameter in the PCR segment 2 Press More The Modify screen appears 3 Press Modify The Select Modification screen appears 4 Press AutoX The AutoX screen appears 2 Pre PCR 3 Tmp 25 Cycles 2 Holds F1 F2 F3 F4 F5 Note If you have inserted a programmed pause the AutoX screen displays the pause but you cannot modify it from the AutoX screen 5 Select the PCR time or temperature parameter that you want modified when you run your method Note From the AutoX screen you cannot modify the number of parameters in each segment or the number of cycles Creating and Editing Methods 5 11 5 12 To automatically change temperature control parameters continued Step Action 6 You can take the following action If you want to Then press increase the value every cycle plus sign a plus sign displays in the current field decrease the value every cycle minus sign a minus sign displays in the current field An asterisk appears on method screens for parameters that have been modified Press Accept to accept all entries on the AutoX screen Modifying Ramp The ramp ti
33. media Applied Biosystems does not warrant that the operation of the instrument or its operating software will be uninterrupted or error free Any applicable warranty period under these sections begins on the earlier of the date of installation or ninety 90 days from the date of shipment for hardware and software installed by Applied Biosystems personnel For all hardware and software installed by the buyer or anyone other than Applied Biosystems and for all other products the applicable warranty period begins the date the product is delivered to the buyer Warranty claims must be made within the applicable warranty period or for chemicals or other consumable products within thirty 30 days after receipt by the buyer The above warranties do not apply to defects resulting from misuse neglect or accident including without limitation operation with incompatible solvents or samples in the system operation outside of the environmental or use specifications or not in conformance with the instructions for the instrument system software or accessories improper or inadequate maintenance by the user installation of software or interfacing or use in combination with software or products not supplied or authorized by Applied Biosystems and modification or repair of the product not authorized by Applied Biosystems THE FOREGOING PROVISIONS SET FORTH APPLIED BIOSYSTEMS SOLE AND EXCLUSIVE REPRESENTATIONS WARRANTIES AND OBLIGATIONS WI
34. parameter a Press Enter b Type in a hold time value between 00 00 and 98 59 minutes seconds 4 Enter information for the next pre PCR hold a Press Enter b Repeat step 2 and step 3 until you have hold time and temperature values for each of the pre PCR hold parameters you defined in step 1 The Tmp field on the Create screen defines the number of temperature control parameters in the PCR cycling segment of your method Three temperature PCR is the typical setting for many PCR amplifications Template denaturation Primer annealing Primer extension To define the PCR parameters Step Action 1 On the Create screen in the Tmp field type in the number of temperature control parameters 2 6 you want for the PCR segment of your method Note Specifying only the minimum number of PCR cycles required for analysis will minimize the chance that unwanted targets will amplify competitively 2 Enter the number of cycles you want the method to run a Press Enter to select the Cycles field b In the Cycles field type in the number of cycles from 2 99 Note Twenty five cycles is the default setting 3 Create the first temperature parameter a Press Enter b Type in a temperature value between 4 0 C and 99 9 C Creating and Editing Methods 5 9 To define the PCR parameters continued Step Action 4 Create the first hold time parameter a Press Enter
35. xx There was a power failure during a Report Power failed at hh mm ss am for hh mm ss specified point in a cycle R t hh mm UL TSUI Dads mo em The message for gt 18 indicates that the power was off for more than 18 hours Drift error in Cycle xx Setpt xx Repxx Temperature Block drift error Report al The block has drifted 2 C from set point during the hold segment of a run Cover error in Cycle xx Setpt xx Repxx Heated cover drift error Report rented E The cover has drifted 5 C from 105 C anytime during the run Sensor error in Cycle xx Setpt xx Repxx Block sensor failure Fatal error Block sensor failure Call for service Sensor error in Cycle xx Setpt xx Repxx Cover sensor failure Heated cover sensor failure Fatal error Call for service Setpt error in Cycle xx Setpt xx Repxx Could not reach xx x in hh mm ss This setpoint error is only logged for setpoints above 15 C The limit is 5 times the normal ramping time Fatal error Call for service Program pause in Cycle xx Setpt xx Rep xxx Method A programmed pause was Report paused at xx C for hh mm ss encountered Manual pause in Cycle xx Setpt xx Rep xxx Method You paused the run Report paused at xx C for hh mm ss Running PCR Samples 4 11 When a Run Completes End of Run Screen At completion of a run the instrument beeps and the End of Run screen appears From the End of Run screen you can perform
36. 0 30 7 00 0 30 es Start Store Print More F1 F2 F3 F4 F5 2 From the Create screen you can take the following action If you want to Then start running the default method press Start store the method under a user s name press Store print a record of the method parameters press Print enter temperature control parameters enter the information on the create screen and create a new method display more functions for modifying methods press More Note The More function only displays when you select a time or temperature parameter For detailed information on using the More function to modify cycles see Modifying Cycling on page 5 11 return to the previous screen press Cancel Creating and Editing Methods 5 7 Entering When you enter temperature control parameters you define values for parameters in Temperature each of the three segments of a method pre PCR PCR and post PCR Control Parameters To enter temperature control parameters Step Action 1 On the Create screen select a field When you first display the Create screen the Hld field is highlighted 2 Use the numeric keys to enter values Press Enter to accept a value The next field is then selected in the order shown in Figure 5 1 Pre PCR segment PCR segment Post PCR segment Figure 5 1 Order of advancement of the highlig
37. 3 16 EC 230 10 50 60 Hz 1 3 14 UK pre 1992 240 6 10 50 60 Hz 1 3 12 Australia 240 6 10 50 60 Hz 1 3 12 a Acceptable AC line voltage tolerances 100 120 220 230 1096 240 VAC 6 10 50 60 Hz 1 Note The Volt Amp number for this instrument is 725Volt Amps Instrument Specifications A 3 Control Panel Specifications Display Screen The display screen is a 7 x 40 character display with a graphics mode of 60 x 240 pixel resolution Keys The instrument control panel consists of a display screen and 22 keys The keys are 4 9 9 Sample Temperatu Function keys Arrow keys Stop key Enter key 10 number keypad re Information Temperature The following table lists sample temperature information Note Sample temperatures are displayed in degrees Celsius to the nearest 0 1 C Sample Temperature Range 4 0 to 99 9 C Temperature Calibration Traceable to National Institute of Standards and Technology NIST Printer Specifications Serial Interface The instrument can use any printer with a serial RS 232C interface board with the Board Specifications following parameters Baud Rate 9600 Parity NONE Data Bits 8 Stop Bits 1 Cable Part Number Connect the printer to the Instrument port with printer cable part number N805 1326 A A Instrument Specifications Supplied Methods Overview About this Appendix This ap
38. 3 FA 1 Weissenbach J et al 1992 A second generation linkage map of the human genome Nature 359 794 801 2 Gyapay G et al 1994 G n thon Human Genetic Linkage Map Nature Genet 7 246 339 3 Dib C et al 1996 Nature 380 152 154 B 4 Supplied Methods Touchdown PCR XL PCR When the optimal annealing temperature is unknown one strategy touchdown PCR incrementally decreases the annealing temperature in early cycles in order to maximize the yield of specific products 2 Tmp x 20 2 Tmp x 10 94 0 94 0 0 15 N 65 0 0 15 PET 55 0 De 0 30 Method Touchdown PCR F1 F2 F3 FA F5 This supplied method has an initial annealing temperature 65 C that incrementally decreases by an additional 0 5 C in each of the first 20 cycles followed by 10 cycles at 55 C XL PCR is the protocol specified for amplification of 5 kb 40 kb PCR products using rTth DNA Polymerase XL and unique reaction conditions 1 Hld 2 Tmp X 16 2 Tmp X 12 2 Holds 94 0 94 0 l Method XL PCR This protocol uses two temperature cycling 94 C for 15 seconds 68 C for 10 minutes and invokes a 15 second AutoX automatic segment extension for the anneal extend step in the last 12 cycles By providing longer templates XL PCR complements technologies for rapid long range PCR More complete genes can be amplified in one reaction from known expressed sequences thus more introns can be crossed You can use XL
39. 5 deleting username 5 5 protecting methods 5 3 to 5 4 copying using PCMCIA card 3 24 to 3 25 creating 5 6 to 5 10 basic parameters to create method 5 6 Create Methods screen displaying 5 7 default method about 5 6 PCR holds defining 5 9 to 5 10 post PCR holds defining 5 10 pre PCR holds defining 5 9 temperature control parameters entering 5 8 editing or deleting methods 5 18 to 5 21 modifying cycling 5 11 to 5 17 AutoX function using 5 11 to 5 12 cycles inserting 5 14 deleting holds 5 14 naming and storing methods 5 16 to 5 17 programmed pauses 5 14 5 16 ramp rates modifying 5 12 to 5 13 printing a method 5 17 reviewing history of run 4 10 to 4 11 history file records 4 11 history formats 4 10 procedure 4 10 running 4 6 to 4 9 method information viewing 4 8 pausingarun 4 8 Run Time screen about 4 7 starting a run 4 6 to 4 7 stopping run before completion 4 9 selecting 4 2 to 4 4 method defined 4 2 method parameters viewing 4 4 methods searching for 4 4 methods sorting 4 5 predefined methods list of 4 2 procedure 4 3 supplied B 2 to B 5 AmpliCycle Sequencing B 2 AmpliTaq Gold B 2 BigDye B 1 B 3 BigDye B 1 LMS2 B 1 Touchdown PCR B 5 XLPCR B 5 transferring or storing about 2 4 when a run completes 4 12 MSDSs 1 7 N naming methods 5 16 to 5 17 numeric keys definition of 2 3 O operating precautions 1 11 P parameters Hold Time 2 3 temperature control 5 11 temperature
40. 5 ise e ge e Reed ge rg RR de 5 2 Protecting Methods ie RR ere P RENS e ru eer eruere 5 3 Changing a User Names compra t eb P PEEL tle DSUES Dee 5 5 De letinga User Name s ose eV eei edis UR e a 5 5 Creating Methods ion BGA Bt bre PIRA Ee ee T 5 6 About the Default Method s sss s ag eee eens 5 6 Basic P ramet rS ut b RRRIS ye Rete setae da cats Mee GSE es 5 6 Displaying the Create Methods Screen neeru e rarere 5 7 Entering Temperature Control Parameters 0 00 eee 5 8 Defining Pre PCR Holds eda R R E dR ARRE cee eee 5 9 Defining PCR Parameters d K A a TT cc NR A NT EH T 5 9 Defining Post PCR Holds 0 0 0 taa oi a RE RR eee 5 10 Modifying Cycling eese sem Ged a EE EE Meat 5 11 IntrodUctionc ceno ess dele hoes de Pe tad macGUei ao ees teed ENS 5 11 Changing Temperature Control Parameters 0 0 e eee eee eee 5 11 Modifying Ramp Rates 5 12 Inserting Holds essct aie eh ena et pe pos ei 5 13 Deleting Holds sive Sos ri ELLE IER ERR RE DA ERES 5 14 Inserting Cycles 23 occ fea als aude dai 5 14 Inserting Programmed Pauses 00 0 eee ee eee 5 14 Editing Programmed Pauses 0 0 0 cee eee nee 5 16 Naming and Storing Methods 0 00 0 2 eee eee ee eee 5 16 Printing a Method tale Fes Secs A ne See UE 5 17 Introduction boi ii ee Ee Se hie Re hee ED Hehe 5 17 Printing Method scssi es ae a REI Rer RACE RR DR Y 5 17 Editing or Deleting Methods 0 0
41. C Card is detected in the Card slot you will get a choice of deleting a method on the PC Card or the instrument The top line of the display continuously cycles between the following three lines Methods on Inst User Size Stored or Last Used or on PC card Used Mem xxx methods xxx segments Free Mem xxx methods xxx segments The following table describes these fields Field Description Units for Based on a calculation of the complexity and length of the Size field a method relative to a maximum size of 1102 size segments for the storage capacity of the instrument Used Mem Field Displays the number of segments used by all stored methods Free Mem Field Displays the number of segments available to store created methods Select one of the methods displayed on the screen or select another method as follows If you want to Then press view method parameters the View key Refer to Viewing Method Information on page 4 8 sort methods by different criteria Refer to Sorting Methods the Sort key on page 4 5 Press Delete The Delete Confirmation screen appears If the method is protected enter a four digit PIN and press Accept when the number is correct 5 20 Creating and Editing Methods To delete a method continued Step Action 4 Press Yes to confirm the deletion This deletes the method and returns you to the Delete screen
42. Entry Module Diagram E GR0961 Compartment door Jumper clip Fuse compartment Instrument Setup 3 5 Turning On the Instrument Turning On the To turn on the instrument Instrument 3 6 Instrument Setup Step Action 1 Plug the power cord into the side of the instrument and into an outlet 2 Press the power switch to the ON position The cooling fan powers up and the Start up screens appear APPLIED BIOSYSTEMS www appliedbiosystems com Applied Biosystems GeneAmp PCR System 9700 Copyright 1996 F1 F2 F3 FA F5 3 After several seconds the Main menu appears You can use any of the functions displayed above the soft keys 08 00 AM 4 25 01 GeneAmp PCR System 9700 Name tc001 User lt lt pe gt gt Run Create Edit Util F1 F2 F3 FA F5 Note The Main menu should appear within a few seconds If any permanent patterns of lines or bars display on the screen contact Applied Biosystems Technical Support Setting Custom Parameters Overview The instrument is shipped with default configuration values The following procedure describes how to set customized values as well as how to enable or disable optional features Displaying the To display the Configuration Screen Configuration Screen Step Action 1 From the Main menu press Util The Utilities screen appears Utilities Diag I
43. GeneAmp PCR System 9700 User s Manual Y Applied hA Biosystems GeneAmp PCR System 9700 Base Module User s Manual KS Sped ns Copyright 2003 2010 Applied Biosystems All rights reserved Information in this document is subject to change without notice Applied Biosystems assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication In no event shall Applied Biosystems be liable for incidental special multiple or consequential damages in connection with or arising from the use of this document NOTICE TO PURCHASER LABEL LICENSE The GeneAmp PCR System 9700 thermal cycler is covered by US patent claims and corresponding claims in their non US counterparts No right is conveyed expressly by implication or by estoppel under any other patent claim such as claims to apparatus reagents kits or methods such as 5 nuclease methods Further in formation on purchasing licenses may be obtained by contacting the Director of Licensing Applied Biosystems 850 Lincoln Centre Drive Foster City CA 94404 USA ABI Prism Applied Biosystems and BigDye are registered trademarks of Applied Biosystems or its subsidiaries in the U S and or certain other countries AB Design and Applera are trademarks of Applied Biosystems or its subsidiaries in the U S and or certain other countries AmpliCyle AmpliTaq AmpliTaq Gold and GeneAmp ar
44. O NOT TURN OFF THE INSTRUMENT OR REMOVE SERIAL CABLE Upgrading over the serial port will take approximately 10 minutes Instrument will re boot when complete F1 F2 F3 FA F5 Take the following action If you are using See Microsoft Windows Downloading Firmware Using Windows 95 or 95 or Microsoft Windows NT on page 3 20 Windows NT9 Microsoft Windows9 Downloading Firmware Using Windows 3 1 on 3 1 page 3 21 Instrument Setup 3 19 Downloading Firmware Using Windows 95 or Windows NT 3 20 Instrument Setup To download the system firmware using Windows 95 or Windows NT Step Action 1 Click Start gt Programs gt Accessories gt HyperTerminal 2 Click the HyperTerminal icon The Connection Description dialog box appears 3 In the Connection Description dialog box enter the following information and click OK The Connect Using dialog box appears In this field Take this action Name Enter a name for example TEC Icon Choose one of the icons 4 In the Connect Using dialog box connect using either Direct to Com 1 or Direct to Com 2 depending on the port to which the cable is attached Note For Windows NT applications this dialog box is titled Connect To and the fields are COM1and COM2 5 Depending on whether you chose Com 1 or Com 2 in the pre
45. PCR System 9700 Labels and Warnings 1 9 Laboratory Environmental Requirements 1 11 Introduction and Safety 1 1 About This Manual Overview This manual describes how to use the GeneAmp PCR System 9700 It includes the following chapters and appendixes Chapter 1 Introduction and Safety contains safety information Chapter 2 Product Overview describes the instrument its components and requirements for installation Chapter 3 Instrument Setup provides information on how to set up the instrument and place it correctly in the laboratory how to configure the instrument and how to connect and configure a printer Chapter 4 Running PCR Samples provides information on selecting a method starting and stopping a run reviewing the history of a run and what to do when the run is completed Chapter 5 Creating and Editing Methods describes how to create and edit PCR methods and how to work with stored methods Chapter 6 Converting Hold Times provides information about setting hold times for the GeneAmp PCR System 9700 compared to the DNA Thermal Cycler or DNA Thermal Cycler 480 Chapter 7 Routine Maintenance provides procedures for routine maintenance on the instrument Chapter 8 Troubleshooting lists error messages and suggestions for dealing with other problems you may encounter Appendix A Instrument Specifications describes the dimensions pow
46. TANT Do not remove the card or turn off the instrument until the upgrade is completed From the Utilities screen press More and from this secondary utility screen press Copy The Copy Method dialog box appears Copy Method ToInst Copy a method to the instrument ToCard Copy a method to the PC card ToInst ToCard 3 24 Instrument Setup To copy a method continued Step Action 4 In the Copy Method dialog box you can take the following action Press To Tolnst Transfer a method from a Methods Transportability card to the instrument ToCard Transfer a method from the instrument to a Methods Transportability card A screen appears with a list of the methods on the instrument or the Methods Transportability card depending on whether you selected Tolnst or ToCard Methods on Inst User Size Stored XL PCR lt lt pe gt gt 11 9 9 96 Touchdown PCR lt lt pe gt gt 9 9 96 AmpliTaq Gold lt lt pe gt gt 9 9 96 AmpliCycle Seq lt lt pe gt gt 9 9 96 Copy J View User Sort F1 F2 F3 FA F5 5 Use the Circular Key Pad to select a method and press Copy Confirmation appears when the method has been successfully copied Copy Method Method XXXXX was successfully copied to the PC card Copy another method Yes Instrument Setup 3 25 Connecting and Configuring a Printer Connecting a Printer f you connect an
47. TH RESPECT TO ITS PRODUCTS AND APPLIED BIOSYSTEMS MAKES NO OTHER WARRANTY OF ANY KIND WHATSOEVER EXPRESSED OR IMPLIED INCLUDING WITHOUT LIMITATION WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE WHETHER ARISING FROM A STATUTE OR OTHERWISE IN LAW OR FROM A COURSE OF DEALING OR USAGE OF TRADE ALL OF WHICH ARE EXPRESSLY DISCLAIMED THE REMEDIES PROVIDED HEREIN ARE THE BUYER S SOLE AND EXCLUSIVE REMEDIES WITHOUT LIMITING THE GENERALITY OF THE FOREGOING IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE WHETHER IN CONTRACT TORT WARRANTY OR UNDER ANY STATUTE INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT OR ON ANY OTHER BASIS FOR DIRECT INDIRECT PUNITIVE INCIDENTAL MULTIPLE CONSEQUENTIAL OR SPECIAL DAMAGES SUSTAINED BY THE BUYER OR ANY OTHER PERSON OR ENTITY WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES INCLUDING WITHOUT LIMITATION DAMAGES ARISING FROM OR RELATED TO LOSS OF USE LOSS OF DATA FAILURE OR INTERRUPTION IN THE OPERATION OF ANY EQUIPMENT OR SOFTWARE DELAY IN REPAIR OR REPLACEMENT OR FOR LOSS OF REVENUE OR PROFITS LOSS OF GOOD WILL LOSS OF BUSINESS OR OTHER FINANCIAL LOSS OR PERSONAL INJURY OR PROPERTY DAMAGE NO AGENT EMPLOYEE OR REPRESENTATIVE OF APPLIED BIOSYSTEMS HAS ANY AUTHORITY TO MODIFY THE TERMS OF THIS LIMITED WARRANTY STATEMENT OR TO BIND APPLIED BIOSYSTEMS
48. TO ANY AFFIRMATION REPRESENTATION OR WARRANTY CONCERNING THE PRODUCT THAT IS NOT CONTAINED IN THIS LIMITED WARRANTY STATEMENT AND ANY SUCH MODIFICATION AFFIRMATION REPRESENTATION OR WARRANTY MADE BY ANY AGENT EMPLOYEE OR REPRESENTATIVE OF APPLIED BIOSYSTEMS WILL NOT BE BINDING ON APPLIED BIOSYSTEMS UNLESS IN A WRITING SIGNED BY AN EXECUTIVE OFFICER OF APPLIED BIOSYSTEMS THIS WARRANTY IS LIMITED TO THE BUYER OF THE PRODUCT FROM APPLIED BIOSYSTEMS AND IS NOT TRANSFERABLE Some countries or jurisdictions limit the scope of or preclude limitations or exclusion of warranties of liability such as liability for gross negligence or wilful misconduct or of remedies or damages as or to the extent set forth above In such countries and jurisdictions the limitation or exclusion of warranties liability remedies or damages set forth above shall apply to the fullest extent permitted by law and shall not apply to the extent prohibited by law Damages Claims and Returns Damages Claims Returns If shipping damage to the product is discovered contact the shipping carrier and request inspection by a local agent Secure a written report of the findings to support any claim Do not return damaged goods to Applied Biosystems without first securing an inspection report and contacting Applied Biosystems Technical Support for a Return Authorization RA number After a damage inspection report is received by Applied Biosystems Applied Bio
49. Your Printer Port 0 00 0 00000000 3 10 Configuring the Contrast and Screen Saver Options 20005 3 11 Setting the IP Address 0 0 oe eee eee eh 3 11 Running Instrument Diagnostics 0 ee eee eens 3 13 COVETVICW e 0 5 ae PS CAA A Ae Qc ede Be ee e dg 3 13 Viewing the Diagnostic Screen rerun erreneren 3 13 Testing the Electrical Components 0 00 cece eee eee 3 14 Testing the Display Screen 0 r cee eee 3 15 Testing the Keypad edi o Decade di mRCPM 3 16 Using the Te Calculator ide 3 17 How to Use the Tp Calculator esses 3 17 Upgrading the System Firmware 0 00 cece ec cee eee 3 18 Introduction cuida ee Bop ed ERREUR ee a le ERE at 3 18 Upgrading Through the Serial Port renun r rarene 3 18 Downloading Firmware Using Windows 95 or Windows NT 3 20 Downloading Firmware Using Windows 3 1 0 0 00 c eee eee eee 3 21 Upgrading Firmware from a PCMCIA Flash Memory Card 3 22 Copying Methods p da dia RR TRE aes 3 24 How to Copy Methods an a e a cence eee 3 24 Connecting and Configuring a Printer 2 20 0 eee eee 3 26 Connecting Printer ir di hese pedi ees ee en 3 26 Configuring the Printer 0 2 0 ee cee eee eee 3 26 4 Running PCR Samples OVerVvIew i3 ui ees dte egre em eee rp et Ge Eel ke Roe aoa a oh alae eda 4 1 About This Chapter a R 0 RR E uati sna Nd R eee E eae 4 1 Tn This Chapter vato d
50. aia A 4 B Supplied Methods OVerVIeW sebo enm re ttt t eoe tes utt ees B 1 About this Appendix ssie mss pole KTR R TNT T ET RT N A NTR AR hh B 1 In This Appendix ii ees ERR ees Ie A UR RE RE eee ESI B 1 About the Methods oc eee EIER Re E ROUEN oe P Een M VIE B 2 Introduction cals Sas ee e Cep SOS R abs CCP ARR ONE atacand aa EORR ae B 2 AmpliCycle Sequencing 2 0 eee I B 2 AmpliTaq Gold DNA Polymerase eA B 2 BigDye Terminators cc eR RE bade da bags eed B 3 General POR roo RIS EU E a Hare A ee ha ean ie eds B 3 EMS2 eh hi REA A OU SR IUE Peli ELE E ER e B 4 Time Release PCR oi EE Vb Eee iue ai ges B 4 Touchdown PCR ee ea ido Peg B 5 XL PRR Torsen oerna ae seas eal eee ak ide aga earl nas etal te saree Save boa ed B 5 C Contacting Services and Support D Limited Warranty Statement Computer Configuration steep ee ee ye oe bs Ro RRR ee NES D 1 Limited Product Warranty cee ene eee e m mn D 1 Damages Claims and Returns 0 cece eee eee een ences D 3 Damages aid Reais telesales AA D 3 Ci A A A VEA EN MR Ce e mte ae D 3 REI ra MSN E Eg etes inve entis D 3 Index Introduction and Safety Overview About This Chapter This chapter provides information to help you safely operate the GeneAmp PCR System 9700 In This Chapter The following topics are covered in this chapter Topics See Page About This Manual 1 2 Instrument Safety 1 3 Chemical Safety 1 6 GeneAmp
51. alibration reset to default System error Block data reset to defaults Call Technical Support Block isn t configured The instrument has defaulted to a 96 well configuration Call Technical Support Block initialized Block module has been re initialized Call Technical Support Block version unknown update firmware The calibration data in the block is not recognized by the firmware Upgrade the firmware Bus Error System error Call Technical Support Calibration battery RAM initialized Calibration lost Instrument may not perform to specification Call Technical Support Can only enter an infinity hold at end A method can only have a HOLD segment with an infinity hold as the last segment in a method This message occurs when you try to enter an infinity hold segment in the middle of a method Assign finite time segments to holds within a method Can t allocate timer System error Call Technical Support Delete your methods first User tried to delete a user name that has methods stored under it Delete or transfer the associated methods before deleting a user name Enter a name or CANCEL You did not enter at least one character on the User Name screen before pressing the Accept key Enter the user name to which the desired method is assigned Enter oligo sequence Incomplete TmCalc data Enter a value in the P1P2 fields of the
52. ameters of the method you selected 2 Hld 3 Tmp 25 Cycles 2 Holds 94 0 94 0 72 0 72 0 0 30 5 00 CO Method exp 001 F1 F2 F3 F4 F5 2 After reviewing PCR and post PCR parameters of a stored method you can Press Start to start the method Press Return and return to the Stored Methods screen Note You cannot edit parameters from the View Method screen Searching for You can find any method that has been stored under a user name Methods 4 4 Running PCR Samples To search for a method Step Action 1 From the Stored Methods screen press User Select which user s methods to view by taking the following action If you want to Then list all the methods currently stored on the instrument Press All display the methods stored under that user s name Press Accept Note You cannot add delete or modify a user name from this screen 2 Making a selection returns you to the Stored Methods screen which now displays the methods of the user you selected Sorting Methods If you have a large number of stored methods you can sort them by name date last used date stored and size To sort methods Step Action 1 From the Stored Methods screen press Sort The sorting criteria screen appears Sort Methods By Method name Date last used Date stored Method size F1 F2 F3 FA F5 Use the up and down Circular Key Pad to select the ty
53. ant to keep The Select User Name screen appears The new name you entered should now display on the screen Press Cancel to cancel your entry and return to the previous screen 5 4 Creating and Editing Methods Changing a User f you know the personal identification number for a user name you can use the Name Circular Key Pad to select that name and change it To change a user name Step Action 1 From the Main menu press User The Select User Name screen appears Use the Circular Key Pad to select the name you want to change Press Edit If a PIN has been previously entered the Security Check screen appears Type in the four digit PIN of the user name you selected Press Name to enter a new user name Press the CE key to clear the previous name Enter a new user name o NI O c0 A Press Accept The Security Code screen appears again Deleting a User If there aren t any methods stored under a user name you can delete that name from Name the Select User Name screen To delete a user name Step Action 1 Use the Circular Key Pad from the Select User Name screen to select a user name 2 Press Delete to delete the name This removes the name from the Select User Name screen and allows you to add a new name to the instrument Creating and Editing Methods 5 5 Creating Methods About the Default The GeneAmp PCR System 9700 comes with a def
54. ations or components that have not been supplied or recommended by Applied Biosystems Applied Biosystems also reserves the right to require that computer hardware and software be restored to the standard configuration prior to providing service or technical support For systems that have built in computers or processing units installing unauthorized hardware or software may void the Warranty or Service Plan Limited Product Warranty Limited Warranty Applied Biosystems warrants that all standard components of its GeneAmp9 PCR System 9700 Base Module will be free of defects in materials and workmanship for a period of one 1 year from the date the warranty period begins Applied Biosystems will repair or replace at its discretion all defective components during this warranty period After this warranty period repairs and replacement components may be purchased from Applied Biosystems at its published rates Applied Biosystems also provides service agreements for post warranty coverage Applied Biosystems reserves the right to use new repaired or refurbished instruments or components for warranty and post warranty service agreement replacements Repair or replacement of products or components that are under warranty does not extend the original warranty period Applied Biosystems warrants that all optional accessories supplied with its GeneAmp PCR System 9700 Base Module such as peripherals printers and special monitors will be free of defect
55. ault PCR thermal profile called a Method method The create screen displays this default method For information on displaying the create screen see Displaying the Create Methods Screen on page 5 7 You can run the default method shown above or use it as a template to create a customized method Number of PCR segment temperature control Will run 9 temperature parameters in the control parameters PCR segment in the post PCR segment Number of cds 1 Hid 3 Tmp 25 Cycles 2 Holds parameters 94 0 94 0 72 0 72 0 in the 55 0 0 30 7 00 pre PCR 0 30 y C Segment Start Store Print More Pre PCR segment PCR segment Post PCR segment Basic Parameters To create a method you need to define the following four basic parameters Temperature Control Parameters Pre PCR Holds PCR Parameters Post PCR Holds For detailed information about these parameters refer to the table below For information about See page Entering Temperature Control Parameters 5 8 Defining Pre PCR Holds 5 9 Defining PCR Parameters 5 9 Defining Post PCR Holds 5 10 5 6 Creating and Editing Methods Displaying the Follow the steps below to display the Create Methods screen Create Methods Screen To display the Create Methods screen Step Action 1 From the Main menu press Create The create screen appears 1 Hld 3 Tmp 25 Cycles 2 Holds 94 0 94 0 i 5 00 0 30 T2 Ori de E
56. ays the executing segment and the next segment to execute Temperature parameters are displayed above the graph HOT displays when the sample block exceeds 50 C Post PCR segment Pre PCR segment PCR segment Hold times are displayed below the graph Calculated sample temperature Ramps flash when system is updated as run progresses approaching next temperature value Use the Run Time screen for For more information see page Viewing Method Information 4 8 Pausing a Run 4 8 Stopping a Run Before It Completes 4 9 Running PCR Samples 4 7 Viewing Method You can view the Method Information screen during a run by pressing Info Press Information Pausing a Run 4 8 Running PCR Samples Return to return to the Run Time screen 02 32 PM Information 55 29C User lisa Method XL PCR Run started at 01 32 30 PM 01 01 00 Run will end at 06 35 30 PM 01 01 00 Reaction vol 50 uL Ramp Speed 9600 You can manually pause a run for a ten minute period of time during a run by pressing Pause Figure 4 1 If you want to specify a different period of time for a pause see Setting the Pause Time Out on page 3 9 Press Resume to resume running a method before a pause expires Note You can pause a run in order to add a reagent Do not to touch the sample block or the bottom of the heated cover during a pause Sample 56 7 Cycle 1 of 25 94 0 94 0 72 0 72 0 Resume Paused Will re
57. ble lists the two levels of protection If a Then other users cannot user has entered a PIN edit that user s name without knowing the PIN method is locked delete overwrite the method Creating and Editing Methods 5 3 Follow the procedure below to protect a method To protect a method Step Action 1 Press PIN The New PIN Number screen appears Create a PIN Number Your PIN number protects the access to your user name and protection level Enter a PIN number New PIN XXXX F1 F2 F3 FA F5 2 In the New PIN field use the numeric keys and type in a four digit PIN 3 Press Enter The PIN Confirmation screen appears Confirm PIN Number Your PIN number protects the access to your user name and protection level Enter a PIN number again PIN XXXX Press Accept to confirm your PIN F1 F2 F3 FA F5 Confirm your PIN by typing your four digit PIN in the Confirm PIN field Press Enter The Protection Status screen appears Username hank PIN number XXXX Protection Unlocked Press PIN to create a Then you set protection to Locked to prevent methods from being overwritten or deleted Accept Name PIN Lock F1 F2 F3 FA F5 6 Press Lock to lock your method This toggles between a Locked and Unlocked state The Protection field displays the status of the method 7 Press Accept when you have entered a PIN you w
58. ct the Date field 2 The three fields to set in the Date field are the Days field Month field Year field Press the D M Y or Y M D soft keys until the format you want for the current date displays in the Date field Use the numeric keys and type in a number for each of the three fields The order of these three fields depends on the format you chose in step 3 Enabling or Enabling the printer allows you to print method parameters or records of run time Disabling a Printer events directly from the display screen The default value for the optional printer is Off Note For connection and configuration see Connecting and Configuring a Printer on page 3 26 To enable or disable the optional printer Step Action 1 Select the Run Time Printer field This changes the functions of the soft keys 2 You can take the following action If you want to Then enable the printer Press ON disable the printer Press Off Press Enter to accept your entry Press Cancel to cancel all entries and return to the previous screen 3 8 Instrument Setup Turning the When turned on the run time beeper beeps during a pause and once at the Run Time Beeper completion of a run The default value is Off On or Off To turn the Run Time Beeper on or off Step Action 1 Select the Run Time Beep field This changes the valu
59. ction will not display on the Insert screen if the highlighted segment already has a pre programmed pause or if highlight box is not on a PCR segment parameter Press Hold to insert a hold of 4 0 C for 30 seconds to the left of the parameter you selected in step 1 Type in a value for the hold temperature Type in a value for the hold time Press More to return to the Create screen Your modified method now appears Creating and Editing Methods 5 13 Deleting Holds Follow the procedure below to delete holds To delete holds From the Edit screen select a hold parameter and press More Use the Circular Key Pad to a select a time or temperature hold parameter 2 Pre PCR 3 Tmp 25 Cycles 2 Holds 94 0 94 0 Insert Delete More Press Delete Inserting Cycles Follow the procedure below to insert cycles To insert cycles Step Action 1 From the Create screen use the Circular Key Pad to select a time or temperature parameter to the right of where you want to insert a cycle Press More Depending on the parameter you select in step 1 one of three screens displays from which you can access the insert function Press Insert The Insert screen appears 2 Pre PCR 3 Tmp 25 Cycles 2 Holds 72 0 72 0 55 0 10 00 0 30 2 00 F1 F2 F3 FA F5 Press Cycle to insert a cycle to the left of the segment you selecte
60. d in step 2 Note You can delete a cycle by entering O in the Tmp field Inserting Follow the procedure below to insert a programmed pause Programmed Pauses To insert a programmed pause Step Action 1 From the Create screen use the Circular Key Pad to select a PCR segment time or temperature parameter where you want to insert a programmed pause Press More Press Insert The Insert screen appears 5 14 Creating and Editing Methods To insert a programmed pause continued Step Action 4 From the Insert screen press Pause The Programmed Pause screen appears Define Programmed Pause Start first pause at cycle 1 of 25 Pause every 25 cycles for 00 30 Beep during the pause No F1 F2 F3 F4 F5 5 In the Start first Pause at Cycle field type in the cycle number where you want the method to first pause 6 In the Pause Every field type in the pause frequency in cycles The pause frequency specifies the number of cycles that will run between each pause 7 In the Cycles For field type in the length of the pause in minutes seconds 00 01 98 59 format In the Beep During The Pause field press Yes or No 9 Press Accept to accept the pause information on the screen The word Pause now displays to the right of the incubation step where you programmed the pause Note You can only insert one pause in each cycle Creating a
61. d that lasts indefinitely You can enter an x hold time by typing a hold time value of 99 00 or greater Press Enter This selects the next temperature parameter Repeat step 4 through step 7 until you have time and temperature values for each of the post PCR hold parameters you defined in step 2 5 10 Creating and Editing Methods Modifying Cycling Introduction Changing Temperature Control Parameters In addition to customizing values for PCR temperature control parameters you can use the More function on the create screen and access cycle modification functions that allow you to Auto increment decrement time and temperature parameters Modify up ramp and down ramp rates in the cycling segment of a method Insert holds cycles and programmed pauses Delete temperature control parameters The time or temperature parameter you select on the create screen determines which modification function you can access when you press More Different modification functions are available depending on whether you select a temperature control parameter in the pre PCR segment the PCR segment or the post PCR segment of a method Using the AutoX function you can automatically increase or decrease the value for any PCR segment parameter by a fixed amount every cycle Note This feature is particularly useful towards the end of the amplification process since the amount of PCR product available to be extended
62. e bench or other heat generating equipment Locations subject to wide temperature fluctuation such as direct sunlight or air drafts Damp areas Environments where there is an oil mist Do not block the circulation of air to the vents located on the sides and bottom of the instrument NN LJ i E aN C i Note When operating multiple 9700 instruments provide at least 8 in of space in between the instruments Instrument Setup 3 3 Fuse Service Configuration Input Voltage Interchangeable Sample Block Modules 3 4 Instrument Setup The instrument is shipped with double line service configuration N D Neli ELECTRICAL SHOCK HAZARD To protect yourself against shock hazards use a properly wired three terminal outlet Do not use an adapter to a two terminal outlet Ner FIRE HAZARD Improper fuses can damage the wiring system and cause a fire Before turning on the instrument verify that the fuses are properly installed IMPORTANT You must be able to disconnect the main power supply to the instrument immediately if necessary The following table specifies the electrical operating range for the instrument in various parts of the world Select the appropriate fuse configuration based on the voltage used Location Voltage VAC Frequency Amperage A Nominal Japan 100 10 50 60 Hz 1 3 16 USA Canada 120 10 50 60 Hz 1 4 20 EC
63. e history file The instrument stores the history file until it is overwritten by the next method used To review the history Step Action 1 To display the History File screen From the End of Run screen press Hist History of method exp002 Run started at 02 30 45 PM O Run aborted at 02 50 42 PM O Length of run 00 19 57 Ramp speed 9600 4 From the Utilities screen press More and then press Hist User lisa Reaction volume 50 pL 01 00 01 00 F1 F2 F3 FA No exceptions PageDn Print Return F5 Press PageUp to move up through the record or PageDn to move down 3 Press Print to print the record History Formats The following table lists the history line formats Pre PCR hold Exception in Pre PCR xx Setpt xx PCR segment Exception in Cycle xx Setpt xx Repxx Any other hold Exception in Hold xx Setpt xx 4 10 Running PCR Samples History File Records The following table lists the history file records Record Description Type History of method xxxxxxxXxXXXXXXX This header record is always created Report User xxxxxx Reaction volume xxx uL Run started at hh mm ss am mm dd yy Note If you stopped a method before it completed running then the Run ended at hh mm ss am mm dd yy message Run ended at will be Run Length of run hh mm ss RampSpeed 9600 aborted at Power failure in Cycle xx at Setpt
64. e in the temperature required to reach the next target temperature Table 6 1 on page 6 3 a down ramp on the starting temperature of the ramp and the change in temperature required to reach the next temperature Table 6 2 on page 6 5 Setting Up Ramps The following table lists the process of setting the up ramp temperature Thermal Cycler or the DNA Thermal Cycler 480 Step Action 1 Determine the change in temperature required to reach the next target temperature and round this value off to the closest value found in Table 6 1 2 Subtract the number of seconds indicated from the hold time used for the DNA The result is the hold time to use for the GeneAmp PCR System 9700 Note The typical hold time is 10 to 15 seconds for denaturation Table of Conversions The following table lists the times for converting up ramp hold times greater than one minute from the DNA Thermal Cycler and the DNA Thermal Cycler 480 to the GeneAmp PCR System 9700 Table 6 1 Converting up ramp hold times Seconds to subtract from DNA Thermal Cycler or A Temp C DNA Thermal Cycler 480 hold times gt 1 min 10 38 sec 15 45 sec 20 49 sec 30 54 sec 40 55 sec 50 57 sec 60 57 sec Converting Hold Times 6 3 Up Ramp Example n this example the temperature was increased by 17 C This value was rounded to 15 C According to Table 6 1 subtract 45 sec
65. e of the soft keys 2 You can take the following action If you want to Then turn the beeper on Press ON turn the beeper off Press Off 3 Press Enter to accept your entry Setting the Pause The Pause Time Out field sets the time in minutes seconds format for the length of a Time Out pause when you use the Pause soft key to pause a run from the Run Time screen For more information on Pausing a Run see Pausing a Run on page 4 8 To set the pause time out Step Action 1 Select More to display the second configuration screen Instrument Configuration Pause Time Out 10 00 00 01 99 59 Idle State Setpoint 25 0 C 4 0 99 9 Baud Rate 9600 FI F2 F3 F4 F5 2 Set the Pause Time Out field by using the numeric keys to enter a time in minutes and seconds From this screen you can also define the 4 Idle state setpoint temperature 4 Baud rate for your printer port 3 Press Accept when all information on this screen is correct Note CE clears an entry Instrument Setup 3 9 Defining the Idle State Setpoint Temperature Defining the Baud Rate for Your Printer Port 3 10 Instrument Setup The Idle State Set Point temperature is the temperature at which the instrument will remain when powered up but idle IMPORTANT After a run is completed or terminated there is approximately a 30 second delay before the instrument attains the specified idle state temperature T
66. e recommended in the manual you may risk damaging the equipment Maintain your instrument in good working order In the event that the instrument has been subjected to adverse environmental conditions such as fire flood earthquake etc contact your local sales office for advice Introduction and Safety 1 11 Safety and Electromagnetic Compatibility EMC Standards U S and Canadian Safety Standards c UL us Canadian EMC Standard European Safety and EMC Standards CE Australian EMC Standards This section provides information on U S and Canadian Safety Standards Canadian EMC Standard European Safety and EMC Standards Australian EMC Standards This instrument has been tested to and complies with standard UL 3101 1 Safety Requirements for Electrical Equipment for Laboratory Use Part 1 General Requirements This instrument has been tested to and complies with standard CSA 1010 1 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements This instrument has been tested to and complies with ICES 001 Issue 3 Industrial Scientific and Medical Radio Frequency Generators Safety This instrument meets European requirements for safety Low Voltage Directive 73 23 EEC This instrument has been tested to and complies with standards EN 61010 1 2001 Safety Requirements for Electrical Equipment for Measurement Contro
67. e registered trademarks of Roche Molecular Systems Inc All other trademarks are the sole property of their respective owners 06 2010 Part Number 4303481 Rev H Contents 1 Introduction and Safety uu TEL 1 1 About This Chapter te ve enc hele Sse te ee PEU PS i E QI 1 1 In Thus Chapter A A PU A Eee eun 1 1 About This Manual ag Rg tege RR Ep Rede nee In ee mes 1 2 OVERVIEW essit umm ten eer E Pete pp bts E ROREM RR ERE 1 2 Instrument S tety iii ii e ERES ue PIENE Eve eee e ees 1 3 Before Operating the Instrument errr rrr arruer rrer 1 3 Documentation User Attention Words eee 1 3 Symbols on Instruments e e e e e e e K e I eae 1 4 Electrical Symbols seino ia rl ER RG eG Oo eae Tae eee ES 1 4 Safety Symbols A ii 1 4 Safety Labels on Instruments ee eee eee eae 1 5 Chemical Safety e ERA as soca casei Goede We aah CETUR RU ias 1 6 Chemical Hazard Warning 0 0 0 cece cee eee eee 1 6 Chemical Waste Hazard Warning eee ee 1 6 About MSDS Sii ees dee rp Re nea tala RR ia 1 7 Ordering MSDSS Lorem ee eee PLE Ep E EAT EE REN 1 7 About Waste Disposal oleis a wel a UR MER ede he e RT N 1 8 GeneAmp PCR System 9700 Labels and Warnings 0 000 000 een 1 9 Instrument Safety Labels e 1 9 Instrument Warnings Diagram rererere rreren 1 9 DangerofBurbs isis idad tbi b RI ACRI E Selb RE Sad 1 10 Grounding and Electrical Safety 1 10 nr 2L 1 10 Laboratory Environmental Requirements
68. ed otherwise the protection provided by this instrument may be impaired IMPORTANT This instrument is designed for indoor use IMPORTANT Do not operate in a Cold Room or a refrigerated area The system 9700 will operate safely when the ambient temperature is 5 C to 40 C 41 F to 104 F and will meet performance specifications when the ambient temperature is 15 C to 30 C and the ambient relative humidity is 20 to 80 These specifications have been calculated for altitudes between 0 and 2 000 meters Norm FIRE HAZARD This instrument is not designed for operation in an explosive environment Do not place the instrument close to potentially explosive materials or objects IMPORTANT The instrument should be stored between 20 C and 60 C 4 F and 140 F at altitudes between 0 and 12 000 meters Note This instrument is able to withstand transient overvoltage according to Installation Category Il as defined in IEC 1010 1 The installation category overvoltage category for this instrument is Il and it is classified as portable equipment The instrument has a pollution degree rating of 2 and may be installed in an environment that has non conductive pollutants only For our European customers any product marked with the CE label meets the European EMC directive 89 336 EEC and the Low Voltage Directive 72 23 EEC This product meets Class B emission limits If you use any cleaning or decontamination method except thos
69. er and electrical specifications of the GeneAmp PCR System 9700 system including the control panel sample temperature information and printer specifications Appendix B Supplied Methods contains information about the methods that are supplied with the instrument Appendix C Contacting Services and Support explains how to contact Applied Biosystems Technical Support staff Appendix D Limited Warranty Statement contains the instrument warranty statement 1 2 Introduction and Safety Instrument Safety Before Operating the Instrument Documentation User Attention Words Ensure that everyone involved with the operation of the instrument has Received instruction in general safety practices for laboratories Received instruction in specific safety practices for the instrument Read and understood all related MSDSs Tania Avoid using this instrument in a manner not specified by Applied Biosystems Although the instrument has been designed to protect the user this protection can be impaired if the instrument is used improperly Five user attention words appear in the text of all Applied Biosystems user documentation Each word implies a particular level of observation or action as described below Note Calls attention to useful information IMPORTANT Indicates information that is necessary for proper instrument operation N iz nile Indicates a potentially hazardous situation which if not
70. ess increase the ramp rate by 10 up to a maximum of 100 the Faster key decrease the ramp rate by 10 from 100 to 10 and by 5 the Slower key from 10 to 5 Note You can also use the numeric keys to enter a value that defines the percentage by which you want to decrease the ramp rate for each cycle of the method You can enter values between 5 and 95 or 100 For ramp rates less than 100 an asterisk appears next to modified ramps The asterisk remains beneath the modified temperature parameter to remind you that the method has been modified Note The following message appears if you enter a numeric value outside the range of acceptable values Valid range is 5 to 95 and 100 Press Accept to accept all entries and return to the previous screen Inserting Holds Use the Insert function to insert holds and cycles into your method and program pauses that the instrument automatically inserts into your method as it runs To insert holds Step Action 1 From the Create screen use the Circular Key Pad to select a time or temperature parameter to the right of where you want to insert a hold Press More Depending on the parameter you select in step 1 one of three screens displays from which you can access the insert function Press Insert The Insert screen appears 2 Pre PCR 3 Tmp 25 Cycles 2 Holds 72 0 72 0 Cycle Pause Note The Pause fun
71. ethods 4 2 Running PCR Samples After you have prepared your samples and loaded them in the sample block you can run a PCR amplification with a new or a stored method A method is a set of instructions in which you specify how the instrument should heat and cool your samples in a PCR thermal profile Methods are stored in the instrument software The GeneAmp PCR System 9700 supplies eight predefined methods that you can run AmpliCycle Sequencing AmpliTaq Gold DNA Polymerase BigDye Terminators General PCR LSM2 Time Release PCR Touchdown PCR XL PCR o 9 9 9 9 9 9 9 Each of these methods is stored under the user name lt lt pe gt gt You can edit these methods and store them under a different name a different user name or select any one and run it For a detailed description of each of these pre coded methods and how you can use them see Appendix B Supplied Methods Selecting a Method f the method you want to run has already been created and stored you can select it from a list If the method you want to run has not been created see Chapter 5 Creating and Editing Methods To select a method Step Action 1 From the Main menu press Run Note Ifa PC card is inserted choose whether to run the method from the PC card or the instrument The Stored Methods screen appears Methods on Inst User Size Stored exp001 lisa 10 06 23 96 exp002 lisa 15 06 25 96 Start Vie
72. his allows you to stop one method and start another before the instrument temperature changes To define the Idle State Set Point temperature Step Action 1 Select the Idle State Set Point field 2 Use the numeric keys and type in a temperature between 4 0 C and 99 9 C Note The default is 25 C 3 Press Enter to accept your entry The following section contains a table that lists serial board specifications and a procedure that describes how to define the printer port value in the Baud Rate field Serial Board Specifications You can connect the GeneAmp PCR System 9700 to any printer with a serial interface board and the following specifications Baud Rate 9600 Parity NONE Data Bits 8 Stop Bits 1 How to Set the Baud Rates To set baud rates Step Action 1 Select the Baud Rate field 2 You can take the following action If you want to Then increase the baud rate Press Up decrease the baud rate Press Down Note Available baud rates are 19200 9600 4800 1200 600 and 300 3 Press Enter to accept your entry Configuring the You can use the third Configuration screen to set Contrast and Screen 4 Screen contrast from 1 to 20 light to dark Saver Options Setting the IP Address Y Screen saver mode Displaying the Screen From the second Configuration screen choose More to display the third Configuration
73. hod Name exp001 stuvwxyz 2 7 Use ENTER key to select a character 5 16 Creating and Editing Methods To name and store methods continued Step Action 4 In the Method Name field follow these steps to enter a 1 16 character alphanumeric name Step Action a Use the Circular Key Pad to select a character in the list shown in the upper right portion of the screen b After selecting a character press Enter to place the character in the Method Name field c If you want to Then enter a number press the appropriate number key go back one space press the Backsp key clear the method name press the CE key Press Accept after you have entered a method name The Store screen appears again The method name you entered should now display in the Method Name field From the Store screen press Accept This stores the method under the name you entered Printing a Method Introduction If you have configured your instrument for a printer you can print a record of the parameters in a method For more information on configuring a printer see Setting Custom Parameters on page 3 8 Printing a Method To print a method Step Action 1 Access the Create or Edit screen From the Create or Edit screen you can print a copy of the parameters for the method displayed on the screen Press Print
74. ht box Number Description 1 Number of pre PCR holds 2 Pre PCR temperature parameter 3 Pre PCR hold time parameter 4 Number of PCR segment temperatures 5 Number of cycles for the PCR segment 6 PCR segment temperature parameter 7 PCR segment time parameter 8 PCR segment temperature parameter 9 PCR segment time parameter 10 PCR segment temperature parameter 11 PCR segment time parameter 12 Number of post PCR holds 13 Post PCR temperature parameter 14 Post PCR hold time parameter 15 Post PCR temperature parameter 16 Post PCR hold time parameter 5 8 Creating and Editing Methods Defining Pre PCR The Hid field on the Create screen defines the number of holds for the pre PCR Holds segment of your method One 1 is the typical setting for most PCR amplifications Defining PCR Parameters and is the default value for the Hld field Generally pre PCR holds define a temperature and hold time sufficient to denature any endonucleases or exonucleases that may contaminate your prepared samples To define pre PCR holds Step Action 1 On the Create screen in the Hld field type in the number of pre PCR holds for your method Note You can enter O in this field to delete the pre PCR hold segment from your method 2 Create the first temperature parameter a Press Enter b Type in a temperature value between 4 0 C and 99 9 C 3 Create the first hold time
75. i sine A A DES STE 4 1 Selecting Method ex A A A os boas 4 2 Introd ction 20000 AA A dee ber es 4 2 What Isa Method 4 step p a a RR Ee ERE 4 2 Predefined Methods cR s TT e aR RE ERER cc e 4 2 Selecting a Methodists oipdedd head a Aa te 4 3 Viewing Method Parameters 0 cece cee eee ee eens 4 4 Searching for Methods 4 4 Sorting Methods iu caia at pe EDU DR UE HUNE E 4 5 RunnmgaMethod opo E se ee ELEM RR ARE Sy ee Be eyed es 4 6 Starting a Run iioc sah gies repe eere ese theese ed eee pee acr en 4 6 About the Run Time Screen 9 66 E a 0 EE Rre Rr ce emen 4 7 Viewing Method Information 0 00 eee ects 4 8 Pausing Rut orcas 4 8 Stopping a Run Before It Completes 0 0 00 eee eee ee eee 4 9 Reviewing the History of a Run 0 cee eens 4 10 How to Review the History ofa Run 0 0 eee eee 4 10 History Formats s sehe soe pl Ep a RR UE Laas 4 10 History File Records aie ere RD EE SE e UR peser yb 4 11 When a Run Completes TR La eee m eens 4 12 End of Run Screen 4 za ii pga p gage epee es 4 12 Method Not Stored Screen ce eee 4 12 Creating and Editing Methods OVCEVIEW es stare vb e edt e bt aar ena decal ped bile m goo CR e LAE 5 1 About This Chapter 2 24 emm serm ta eed eee bad his weed ta 5 1 In This Chaptet ts cag dois ae v y ist dra ie 5 1 Adding or Changing Users 0 0 0 0 ee 5 2 Introduction 2c Reeve da eee Rer 5 2 Adding a New User Name
76. in Note You must provide sufficient space around the instrument for unrestricted air circulation Weight Base Module 8 6 kg 19 Ibs 96 Well Gold Aluminum Sample Block Modules 3 2 kg 7 Ibs Note See the sample block module user s manual for physical information on a module There is one version of the instrument The power requirements of the instrument under various power configurations are VAC 100 120 8 AMP T 5x20 mm or 50 60 Hz 8 AMP Slow Blow 3 AB Use 250 V fuses VAC 220 230 240 8 AMP T 5x20 mm Max Power 725 VA IMPORTANT You must be able to disconnect the main power supply to the instrument immediately if necessary In areas where the supplied power is subject to voltage fluctuations exceeding 10 of the nominal value a power line regulator may be required High or low voltages can have adverse effects on the electronic components of the instrument The following table specifies the electrical operating range for the instrument in various parts of the world Select appropriate fuse configuration based on the voltage used NITE In Japan the unit must have a dedicated 220 volt outlet The unit will not operate properly with a 100 volt outlet A 2 Instrument Specifications Amperage A Location Voltage VAC a Frequency Nominal Japan 220 10 50 60 Hz 1 3 16 USA Canada 120 10 50 60 Hz 1 4 20 Europe pre 1992 220 10 50 60 Hz 1
77. l and Laboratory Use Part 1 General Requirements and EN 61010 2 010 Particular Requirements for Laboratory Equipment for the Heating of Materials EMC This instrument meets European requirements for emission and immunity EMC Directive 89 336 EEC This instrument has been tested to and complies with standard EN 61326 Group 1 Class B Electrical Equipment for Measurement Control and Laboratory Use EMC Requirements This instrument has been tested to and complies with standard AS NZS 2064 Limits and Methods Measurement of Electromagnetic Disturbance Characteristics of Industrial Scientific and Medical ISM Radio frequency Equipment 1 12 Introduction and Safety Product Overview Overview About This Chapter This chapter describes the GeneAmp PCR System 9700 its components and requirements for installation In This Chapter The following topics are contained in this chapter Topic See page About the GeneAmp PCR System 9700 2 2 Product Overview 2 1 About the GeneAmp PCR System 9700 About the Instrument Control Panel Control Panel Diagram 2 2 Product Overview The GeneAmp PCR System 9700 is an automated instrument specifically designed for the amplification of nucleic acids using the Polymerase Chain Reaction PCR process The user interface consists of a control panel with a full numeric keypad soft keys and a graphical display screen that shows the time and tempe
78. me is the time it takes the instrument to change from one temperature to Rates another Using functions accessible from the Modify screen you can modify the up ramp and down ramp rates of the instrument by defining it as a percentage of the temperature s maximum rate of increase The default maximum up ramp and down ramp rates is 100 To modify ramp rates Step Action 1 Press Modify from the Modify screen The Select Modification screen appears 2 Press Ramp The Ramp Rate Modification screen appears 2 Pre PCR 3 Tmp 25 Cycles 2 Holds 94 0 Accept Faster Slower F1 F2 F3 F4 F5 In this example you can modify the rate at which the instrument ramps up from 72 0 C to 94 0 C down from 94 0 C to 55 0 C or up from 55 0 C to 72 0 C Use the Circular Key Pad to select a ramp that you want to modify Move the highlight box to the third temperature in the cycling segment of the default method to modify the highlighted ramp rate The third ramp rate defines the rate at which the instrument increases from 55 0 C to 72 0 C each time the method cycles 2 Pre PCR 3 Tmp 25 Cycles 2 Holds 94 0 Accept Faster Slower Creating and Editing Methods To modify ramp rates continued Step Action 5 Modify the up ramp and down ramp rates you selected by defining them as a percentage of the maximum of 100 If you want to Then pr
79. method is a basic one and can be easily modified with both pre and post PCR holds 1 Hld 3 Tmp 35 Cycles 2 Holds 55 0 72 0 72 0 Supplied Methods B 3 LMS2 The GeneAmp PCR System 9700 software includes a pre coded LMS2 method for ABI PRISM Linkage Mapping Set Version 2 LMS2 thermal cycling Linkage Mapping Set 2 employs over 400 fluorescent labeled PCR primer pairs for analysis of select microsatalite loci from the G n thon human linkage map 1 23 The following figures illustrate the thermal cycling profile for the LMS2 method 1 Hld 3 Tmp 10 Cycles 3 Tmp 20 Cycles 95 0 94 0 Method LMS2 3 Tmp x 10 3 Tmp 20 Cycles 2 Holds 89 0 72 0 72 0 72 0 0 30 10 00 0 15 0 15 a x Method LMS2 F1 F2 F3 FA F5 This supplied method consists of an initial hold at 95 0 C two sets of three temperature cycles followed by two additional holds at 72 0 C and 4 0 C See the ABI PRISM Linkage Mapping Set Version 2 User s Manual P N 904999 for comprehensive information on PCR amplification conditions electrophoresis conditions detection and data analysis Time Release PCR The Time Release PCR method is designed for use with AmpliTaq Gold DNA Polymerase The enzyme is activated more slowly than with the AmpliTaq Gold method Here the pre PCR hold is only 1 minute and the number of cycles is increased to 40 1 Hld 3 Tmp 40 Cycles 2 Holds 95 0 95 0 D oo Method Time Release PCR Fl F5 F2 F
80. module not installed correctly Is power switch ON Is power cord connected Check fuses Printer fails 4 Incorrect printer configuration 4 Incorrect printer cable Check printer settings baud rate 9600 no parity one stop bit eight data bits Purchase Applied Biosystems printer cable Instrument cooling fan does not make whirring sound Fuse blown Not connected to power source Interchangeable module not installed correctly Is power switch ON Is power cord connected Check fuses 8 6 Troubleshooting Instrument Specifications Overview About This Appendix In This Appendix This appendix describes the dimensions power and electrical specifications for the GeneAmp PCR System 9700 system including the control panel sample temperature information and printer specifications The following topics are covered in this appendix Topic See page System Specifications A 2 Control Panel Specifications A 4 Sample Temperature Information A 4 Printer Specifications A 4 Instrument Specifications A 1 System Specifications Dimensions Power Configurations Electrical Requirements The following tables list the footprint and the weight of the instrument with the 96 Well or 60 Well sample block module Footprint With Sample Block Module Installed Height 26 cm 10 in Width 28 cm 11 in Depth 41 cm 16
81. nd Editing Methods 5 15 Editing f you have inserted a programmed pause in your method you can edit the Programmed Pauses parameters for the pause at any time To edit programmed pauses Step Action 1 From the Create screen use the Circular Key Pad to highlight the word Pause The Edit soft key appears Press Edit to access the programmed pause screen From this screen you can Change any of the pause parameters or Use the Circular Key Pad to select the pause time parameter on the screen and edit it by entering a different time After you have entered all modifications to the customized method you are creating you should store the method before running it see Naming and Storing Methods below Naming and Storing Naming and storing completes the creation of the method Methods To name and store methods Step Action 1 From the Create screen press Store 2 You can take the following action If you want to Then store the method under the name displayed in the user field press the and name the method the default name displayed in the Accept key method field The default method name is expxxx where xxx a number from 0 to 999 rename the method go to step 3 From the Store screen press Method The Method Name screen appears Note The blank space after the letter Z is used to insert blank spaces abcdefghi jklmnopaqrj Met
82. nger includes individual setpoint time and temperature information An automated restart or incubate function is available for use after a power outage Product Overview 2 5 Instrument Setup Overview About This Chapter In This Chapter This chapter provides information on how to set up the GeneAmp PCR System 9700 and place it correctly in the laboratory how to configure the instrument and how to connect and configure a printer The following topics are covered in this chapter Topic See page Unpacking the Instrument 3 2 Setting Up your Laboratory 3 3 Double Line Fuse 3 5 Turning On the Instrument 3 6 Setting Custom Parameters 3 7 Running Instrument Diagnostics 3 13 Using the T Calculator 3 17 Upgrading the System Firmware 3 18 Copying Methods 3 24 Connecting and Configuring a Printer 3 26 Instrument Setup 3 1 Unpacking the Instrument Inspecting the Inspect the GeneAmp PCR System 9700 and all other supplied parts for any Instrument damage that may have occurred during shipment If there has been any damage during transit notify the carrier and Applied Biosystems immediately Note Save the shipping container and all packing materials in case it becomes necessary to reship the instrument To order additional instruments or supplies contact one of the regional offices listed in Appendix C Contacting Services and Support Additional Part You can order modules
83. nostics Hard Hardware Diagnostics System System Performance Tests TmpVer Temperature Verification Upgrad Firmware Upgrade Hard System TmpVer Upgrad F1 F2 F3 F4 F5 3 Press the soft key that accesses the diagnostic utility you want to run Press this soft key To Hard Access hardware diagnostic utilities that allow you to test hardware and electrical components such as the Display screen and Keypad System Access the system performance tests You can run these two system tests to test the rate of system heating and cooling and the performance of PCR cycling TmpVer Access the temperature verification tests that allow you to verify sample block calibration and uniformity These two tests are discussed in the users manual for the interchangeable sample block Upgrade Access a utility that allows you to update the 9700 instrument firmware through the RS485 serial port or using a PCMCIA Flash Memory card Instrument Setup 3 13 Testing the Use the hardware diagnostic utilities to test the electrical components of the 9700 instrument Electrical Components 3 14 Instrument Setup To test the electrical components Step Action 1 From the Diagnostics screen press Hard The Hardware Diagnostics appears Hardware Diagnostics Disp LCD Display Diagnostic Keypad Keypad Diagnostic Disp Keypad F1 F2 F3 FA F5 2 Use the corres
84. nstrument diagnostics TmCalc Calculates melting temp Config Instrument configuration Diag TmCalc Config More F1 F2 F3 FA F5 From the Utilities screen you can take the following action If you want to See page Delete a method 5 20 Run instrument diagnostics 3 13 Review the history of a run 4 10 Access the T calculator 3 17 Copy methods to or from a methods transportability card 3 24 2 Press Config The first Configuration screen appears Instrument Configuration Time 11 30 AM Date 01 25 00 M D Y Run Time Printer Off Run Time Beep Oft Accept 24Hr PM More Instrument Setup 3 7 Setting the Time In the first Configuration screen you can set the current time and date for file memory maintenance and run time displays You can also enable or disable the run time printer and the run time beep To set the time Step Action 1 Use the Circular Key Pad to select the Time field 2 Press the 24 Hr or PM AM soft keys until the format you want for the current time displays in the Time field Use the numeric keys to type in the hours followed by minutes Press Accept when your entries are complete Note CE clears an entry Setting the Date You must set the instrument to the correct date To set the date Step Action 1 Use the circular key to sele
85. nt panels are removed from the instrument There are no components inside the GeneAmp PCR System 9700 that you can safely service yourself If you suspect a problem contact an Applied Biosystems Technical Support Representative In This Chapter The following topics are covered in this chapter Topic See page Changing the External Fuses 7 2 Routine Maintenance 7 1 Changing the External Fuses Introduction T VEGANE FIRE HAZARD For continued protection against the risk of fire replace fuses only with Listed and Certified fuses of the same type and rating as those currently in the instrument All instruments have factory installed fuses However if you should ever need to change a fuse follow the instructions in Changing the External Fuses on page 7 2 Power Entry Module The Power Entry Module is located at the rear of the left side of the instrument Diagram 7 2 Routine Maintenance Fuse Compartment door Fuse compartment Changing Fuses Instruments have two 8 amp Type T 250 V 5x20 mm fuses P N 0999 1683 To change the fuses Step Action 1 Turn off the instrument and disconnect the power cord from the side of the instrument N Died ELECTRICAL SHOCK HAZARD Severe electrical shock which could cause physical injury or death can result from working on an instrument when the high voltage power supply is operating To avoid
86. ods When you attempt to store or create a new method which is larger than the available storage space Determine how much storage memory is available on the instrument or PC card Delete or store rarely used methods elsewhere Not implemented yet The feature is not implemented in the current firmware version Upgrade firmware when the new version is available from Applied Biosystems PC card and Flash do not verify The PC upgrade card and instrument memory do not match Firmware upgrade unsuccessful Call Technical Support PC card does not contain valid data The PC card being used to upgrade the instrument does not contain a valid program Call Technical Support 8 4 Troubleshooting Table 8 1 Error Messages continued Message Description Recommended Action Preferences battery RAM initialized User configuration has been reset due to software error Call Technical Support Printer not responding The printer has been disconnected or is off line Check printer connections and power switch Remove infinity hold first A method can have an infinity hold segment as the last segment in the method This message occurs when a user tries to add a segment after one which contains an infinity hold Add segments prior to the post PCR infinity hold Setpoint could not be reached 4 The instrument could not reach a temperature parame
87. ollows If you want to Then press view the parameters of a method before making a selection the View key Refer to Viewing Method Parameters on page 4 4 search for a method by user name the User key Refer to Searching for Methods on page 4 4 sort methods by different criteria the Sort key Refer to Sorting Methods on page 4 5 5 18 Creating and Editing Methods To edit a method continued Step Action 3 Press Edit after selecting a method The Edit screen appears 2 Pre PCR 3 Tmp 25 Cycles 2 Holds 55 0 10 00 0 30 72 0 TIRO 2 00 Hold Cycle Pause F1 F2 F3 F4 F5 Choose a temperature or time parameter within a PCR segment Edit temperature control or time parameters Note Editing parameters on the Create screen involves the same tasks and uses the same key combinations as you use when creating a method The same functions for modifying methods are also available From the Edit screen press Store to store the method Creating and Editing Methods 5 19 Deleting a Method The following procedure describes how to delete a method To delete a method Step Action 1 From the Utilities screen press More and then press Delete The Delete Method screen appears Delete Method Methods on Inst User Size Stored exp001 lisa 15 01 01 00 Press Yes to delete the method Yes F1 F2 F3 FA F5 Note Ifa P
88. onds from the hold time on the DNA Thermal Cycler or the DNA Thermal Cycler 480 resulting in a new hold time of 35 seconds see the figure below Note If methods developed on the GeneAmp PCR System 9700 will be used on the DNA Thermal Cycler or the DNA Thermal Cycler 480 you can also use Table 6 1 to convert the hold times Add the indicated times instead of subtracting them DNA Thermal Cycler GeneAmp PCR System 9700 Temp Temp C C 72 72 Hold 55 55 A temp 17 round to 15 a 80 sec 35 sec Time Time Setting Down Ramps The following table lists the process of setting the down ramp temperature Step Action 1 Determine the change in temperature required to reach the next target temperature and round this value off to the closest value found in Table 6 2 2 Based on the starting temperature of the ramp determine the number of seconds to subtract from the DNA Thermal Cycler or DNA Thermal Cycler 480 hold time to arrive at the new hold time Note The typical hold time is 10 to 15 seconds for annealing 6 4 Converting Hold Times Table of Conversions Down Ramp Example The following table lists the times for converting down ramp hold times greater than one minute from the DNA Thermal Cycler or the DNA Thermal Cycler 480 to the GeneAmp PCR System 9700 Table 6 2 Converting down ramp hold times Starting temperature of ramp C
89. optional printer to your 9700 instrument you can print out a hard copy of the time and temperature parameters for the PCR methods you create Connect one end of your printer cable N805 1326 to the RS 485 serial port on the side panel of the 9700 instrument and connect the other end to the RS 232C interface serial adapter on the rear panel of the printer Configuring the After you have connected the printer cable to the printer you must configure the Printer instrument for the printer You can connect the 9700 instrument to any printer with a serial board and the following specifications Baud Rate 9600 Parity NONE Data Bits 8 Stop Bits 1 See your printer manual for instructions on how to complete any other necessary installation steps 3 26 Instrument Setup Running PCR Samples Overview About This Chapter This chapter provides information on selecting a method starting and stopping a run reviewing the history of a run and what to do when the run is completed In This Chapter The following topics are covered in this chapter Topic See page Selecting a Method 4 2 Running a Method 4 6 Reviewing the History of a Run 4 10 When a Run Completes 4 12 Note For information on loading and unloading samples see the instructions accompanying your interchangeable sample block module Running PCR Samples 4 1 Selecting a Method Introduction What Is a Method Predefined M
90. parameters 2 3 See Also custom parameters setting parity bit 3 10 3 26 part numbers for ordering accessories 3 2 fuse part number 3 5 Pause Time Out setting 3 9 pauses programmed editing 5 16 inserting 5 14 PCMCIA card using to copy methods 3 24 to 3 25 using to upgrade firmware 3 22 3 23 PCR holds defining 5 9 to 5 10 PCR samples running methods running 4 6 to 4 9 selecting 4 2 to 4 4 PCR thermal profile method defined 4 2 PIN entering 5 4 pollution 1 11 post PCR holds defining 5 10 power configurations A 2 power failure whatto do 8 2 precautions operating 1 11 pre PCR holds defining 5 9 printer baud rate setting 3 10 connecting and configuring 3 26 enabling disabling 3 8 printer port defining See baud rate printing method 5 17 printer specifications A 4 programmed pauses editing 5 16 inserting 5 14 protecting methods 5 3 to 5 4 R RAnumber D 3 RA number See return authorization number ramp rates modifying 5 12 to 5 13 reaction volume entering 4 6 reporting damages D 3 return authorization RA number D 3 returning damaged items D 3 returns D 3 RS 232C serial interface board 3 26 Run softkey function of 3 15 run time beeper turning on off 3 9 S safety 1 1 to 1 8 sample temperature range A 4 Sanger sequencing B 2 screen contrast setting 3 11 screen saver mode setting 3 11 security code entering 5 4 selecting fields 2 3 serial interface board specifications 3 10 serial port upgrading fi
91. pe of sort The following table describes the sort methods Choose this item To sort Method name Methods alphabetically Date last used Methods chronologically in descending order by date of use The last method which ran or was stored is listed first Date stored Note Uses the most recent title and date between date last used and the data stored Methods chronologically by date stored The last method stored is listed first Method size Methods in increasing order by the amount of memory used to store each method The largest size method is listed first Press Accept to accept a selection This returns you to the Stored Methods screen where the displayed methods are sorted according to your selection in step 2 Running PCR Samples 4 5 Running a Method Starting a Run After choosing a method follow these steps to start a run 4 6 Running PCR Samples To start a run Step Action 1 From the Main menu press Run to display stored methods 2 Use the up and down Circular Key Pad to select the method 3 a Press Start The Select Method Options screen appears b Choose from the following options 96 Well Gold Select 9600 or MAX mode first and then select volume Sample Block Module Select Method Options Reaction Volume 50 uL Ramp speed 9600 Enter a value from 5 to 50 uL Start 9600
92. pendix provides information about the methods that are supplied with the GeneAmp PCR System 9700 In This Appendix The following topics are covered in this appendix Topic See page About the Methods B 2 AmpliCycle Sequencing B 2 AmpliTaq Gold DNA Polymerase B 2 BigDye Terminators B 3 General PCR B 3 LMS2 B 4 Time Release PCR B 4 Touchdown PCR B 5 XL PCR B 5 Supplied Methods B 1 About the Methods Introduction AmpliCycle Sequencing AmpliTaq Gold DNA Polymerase B 2 Supplied Methods The instrument supplies you with eight pre coded methods stored under the user name lt lt pe gt gt The eight pre coded methods are AmpliCycle Sequencing AmpliTaq Gold DNA Polymerase BigDye Terminators General PCR LSM2 Time Release PCR Touchdown PCR XL PCR o 9 9 9 94 9 9 9 See the following sections for detailed information about the methods Cycle sequencing has revolutionized Sanger sequencing of PCR products and other DNA templates The AmpliCycle Sequencing protocol is for 3 temperature cycling and for achieving clean sequence ladders from femtomole amounts of template 1 Hid 3 Tmp 25 Cycles 1 Hold 95 0 195 0 L0 72 0 1 00 10 30 HE2 EA 0 30 1 00 4 0 45 00 Method AmpliCycle Seq F1 F5 F2 F3 FA This cycle sequencing process and the benefits of AmpliTaq9 DNA Polymerase CS are described in the product insert for the AmpliCycle Sequencing Kit
93. ponding soft key to select the hardware component for which you want to perform one of the following tasks Press this soft key To Display Visually determine if the Liquid Crystal Display LCD screen is functioning properly Keypad Verify the operation of the keypad Testing the Display The Display diagnostic test allows you to visually determine if the display screen is Screen properly functioning by turning on and off all the LCD pixels To test the display screen Step Action 1 From the Hardware Diagnostics screen press Display The Display Diagnostic screen appears Display Diagnostics Read all instructions first Press Run to turn ON all pixels Press STOP to turn OFF all pixels Press STOP to exit F1 F2 F3 F4 F5 2 You can take the following action Press To Run Turn ON all pixels Check display Stop Turn OFF all pixels Check display Stop again Exit Instrument Setup 3 15 Testing the Keypad Use the Keypad diagnostic test to verify that all 22 keys on the control panel are functioning properly 3 16 Instrument Setup To test the keypad Step Action 1 From the Hardware Diagnostics screen press Keypad The Keypad Diagnostic screen appears Keypad Diagno
94. rature profile for each run The instrument control panel consists of a display screen and 22 keys The display screen shows a graphical representation of PCR events including pre PCR holds PCR cycling and post PCR holds You use the keys to enter information into fields on the display screen The following diagram shows the control panel La Soft keys F1 EA Numeric L C3 C3 CJ cJ En ce eJ mar SS a Power on off o Stop key Clear Entry key Enter key Circular Key Pad Using the Keys The following table describes the Control Panel keys in the previous figure Key Use to Soft keys F1 F5 Select the function specified above the key The function of each key is defined on the display screen above the key and is redefined as you view different screens Numeric keys Enter numbers from left to right into a field you highlight Stop key Stop a method while it is running Enter key Enter information typed into a field and advance the highlight box to the next field on a screen Clear Entry key CE Remove information from a field Circular Key Pad Move the highlight box to different fields on the display screen in the direction of the arrow Selecting a Field There are two ways to select a field If you want to Then move the highlight box in one of four directions
95. rmware 3 18 3 21 Size field definition of 5 20 soft keys definition of 2 3 Index 3 Sort function of 4 5 5 20 SRAM card using to copy methods 3 24 to 3 25 starting instrument 3 6 stop bit 3 10 3 26 Stop key definition of 2 3 storing methods 5 16 to 5 17 system firmware upgrading 3 18 to 3 23 through serial port 3 18 3 21 using PCMCIA card 3 22 3 23 System soft key function of 3 13 T technical support for computers with altered configuration D 1 temperature entering values 2 3 Idle State Setpoint setting 3 10 operating precautions 1 11 operating temperature 3 3 sample temperature information A 4 temperature control parameters entering 5 8 temperature control parameters entering 5 8 using AutoX function 5 11 to 5 12 Temperature Verification test partnumber 3 2 Time Release PCR 4 2 B 2 Time Release PCR about supplied method B 4 time setting 3 8 Ty calculator how to use 3 17 Tmp field using to define temperature control parameters 5 9 TmpVer soft key function of 3 13 ToCard softkey function of 3 25 Tolnst softkey function of 3 25 Touchdown PCR 4 2 B 2 about supplied method B 5 troubleshooting 8 1 to 8 6 display screen error messages 8 3 to 8 5 power failure what to do 8 2 table of information 8 6 turning on instrument 3 6 U unpacking the instrument 3 2 Upgrade soft key function of 3 13 User function of 4 4 users 5 2 to 5 5 adding users 5 2 to 5 3 changing user name 5 5 deleting username 5
96. roblems possible causes Table and recommended actions that you should take Table 8 2 Troubleshooting Information Problem Possible Causes Check and or Remedy Control panel not responding Keypad failure Run keypad diagnostic Call Technical Support Cooling rate too slow Ambient temperature is too warm Peltier failure Move instrument to well ventilated location 15 30 C Run rate test diagnostic Call Technical Support Cycling time too long Peltier failure Run cycle test diagnostic Displayed temperature does not match specified temperature Instrument may require calibration Run the Temperature Verification test Heated cover not responsive Heated cover failure Call Technical Support Heating rate too slow Peltier failure Run Rate Test diagnostic Call Applied Biosystems Technical Support Instrument can t reach high or low temperature range Ambient temperature is too warm Peltier failure 4 Run Rate Test diagnostic Run Cycle Test diagnostic Call Technical Support Instrument making too much noise Fan failure Check for sidevent obstructions No beep 4 Run time beeper disabled 4 Beeper failure Check Run Time Beep configuration Call Technical Support No screen display No response when you turn the instrument on Fuse blown Not connected to power source Interchangeable
97. rt symbols found on Applied Biosystems instruments Each symbol may appear by itself or in combination with text that explains the relevant hazard see Safety Labels on Instruments on page 1 5 These safety symbols may also appear next to DANGERS WARNINGS and CAUTIONS that occur in the text of this and other product support documents Symbol Description Indicates that you should consult the manual for further information and to proceed with appropriate caution Indicates the presence of an electrical shock hazard and to proceed with appropriate caution Indicates the presence of a hot surface or other high temperature hazard and to proceed with appropriate caution gt gt gt 1 4 Introduction and Safety Symbol Description Indicates the presence of a laser inside the instrument and to proceed with appropriate caution Indicates the presence of moving parts and to proceed with appropriate caution A A Safety Labels on Instruments The following CAUTION WARNING and DANGER statements may be displayed on Applied Biosystems instruments in combination with the safety symbols described in the preceding section English Francais CAUTION Hazardous chemicals Read the Material Safety Data Sheets MSDSs before handling ATTENTION Produits chimiques dangeureux Lire les fiches techniques de s ret de mat riels avant la manipulation des produits
98. s in materials and workmanship for a period of ninety 90 days from the date the warranty begins Applied Biosystems will repair or replace at its discretion defective accessories during this warranty period After this warranty period Applied Biosystems will pass on to the buyer to the extent that it is permitted to do so the warranty of the original manufacturer for such accessories With the exception of consumable and maintenance items replaceable products or components used on or in the instrument are themselves warranted to be free of defects in materials and workmanship for a period of ninety 90 days Applied Biosystems warrants that chemicals and other consumable products will be free of defects in materials and workmanship when received by the buyer but not thereafter unless otherwise specified in documentation accompanying the product Limited Warranty Statement D 1 Warranty Period Effective Date Warranty Claims Warranty Exceptions Warranty Limitations Applied Biosystems warrants that for a period of ninety 90 days from the date the warranty period begins the tapes diskettes or other media bearing the operating software of the product if any will be free of defects in materials and workmanship under normal use If there is a defect in the media covered by the above warranty and the media is returned to Applied Biosystems within the ninety 90 day warranty period Applied Biosystems will replace the defective
99. ssages display screen 8 3 to 8 5 F fields selecting 2 3 firmware upgrading 3 18 to 3 23 through serial port 3 18 3 21 using PCMCIA card 3 22 3 23 fuses changing for double line operation 7 3 converting from single to double line 3 5 to precautions about 1 10 service configuration 3 4 Index 1 G GeneAmp PCR System 9700 Control Panel about 2 2 specifications A 4 copying methods 3 24 to 3 25 custom parameters setting 3 7 to 3 11 baud rate setting 3 10 Configuration Screen displaying 3 7 date setting 3 8 Idle State Setpoint temperature setting 3 10 Pause Time Out setting 3 9 printer enabling disabling 3 8 run time beeper tuning on off 3 9 screen contrast saver mode setting 3 11 time setting 3 8 diagnostic tests running CPU board testing 3 15 Diagnostic screen viewing 3 13 Display screen testing 3 15 electrical components testing 3 14 keypad testing 3 16 fuses converting from single to double line fuse 3 5 to 22 laboratory setting up 3 3 to 3 4 air vents air circulation 3 3 choosing a location 3 3 fuse service configuration 3 4 input voltage table of 3 4 interchangeable block module about 3 4 operating temperature 3 3 what to avoid 3 3 overview 2 2 to 2 5 about the instrument 2 2 control panel keys using 2 3 control panel diagram 2 2 entering numeric values how to 2 3 how differs from 9600 System 2 5 methods transferring or storing 2 4 selecting a field howto 2 3 upgrading the firmware 2 4
100. ste Handle chemical wastes in a fume hood Minimize contact with chemicals Wear appropriate personal protective equipment when handling chemicals e g safety glasses gloves or protective clothing For additional safety guidelines consult the MSDS Minimize the inhalation of chemicals Do not leave chemical containers open Use only with adequate ventilation e g fume hood For additional safety guidelines consult the MSDS After emptying the waste container seal it with the cap provided Dispose of the contents of the waste tray and waste bottle in accordance with good laboratory practices and local state provincial or national environmental and health regulations About MSDSs Ordering MSDSs Some of the chemicals used with this instrument may be listed as hazardous by their manufacturer When hazards exist warnings are prominently displayed on the labels of all chemicals Chemical manufacturers supply a current MSDS before or with shipments of hazardous chemicals to new customers and with the first shipment of a hazardous chemical after an MSDS update MSDSs provide you with the safety information you need to store handle transport and dispose of the chemicals safely We strongly recommend that you replace the appropriate MSDS in your files each time you receive a new MSDS packaged with a hazardous chemical Tans CHEMICAL HAZARD Be sure to familiarize yourself with the MSDSs before using reagents or solvents
101. stic After pressing Run press the blinking key or press STOP twice to exit Run F1 F2 F3 F4 F5 2 Press Run The Control Panel screen appears F1 F2 F3 F4 F5 3 Press the indicated flashing key Using the T Calculator How to Use the Use the T Calculator to determine the annealing temperature of a primer set of T Calculator known sequence To use the T Calculator Step Action 1 From the Main menu press Util The Utilities screen opens as shown below Utilities Diag Instrument diagnostics TmCalc Calculates melting temp Config Instrument configuration Diag TmCalc Config More F1 F2 F3 FA F5 2 Press TmCalc The Tm Calculator appears Salt 50 mM Primer 0 20 uM Pies 5 P2 B Tm of Pl Tm of P2 Press ENT calculate Tm s 3 Enter the salt concentration Note The default is 50 Enter values 5 to 1000 4 Enter the primer concentration Note The default it 0 20 Enter values 0 01 to 10 00 5 Enter primer sequence in P1 6 Enter primer sequence in P2 and press Enter to calculate the T s The melting points are displayed Use this information to program a run For more information see Chapter 5 Creating and Editing Methods 7 Press Return to display the Utilities screen Instrument Setup 3 17 Upgrading the System Firmware Introduction You can update the GeneAmp PCR System 9700 firmware from a serial connection to
102. sume in mm ss Figure 4 1 Pause screen Your samples remain at the temperature of the instrument when you pause the run The time remaining in a pause appears at the bottom of the screen in minutes seconds format It decrements to zero and the paused run resumes at the point where you paused it Stopping a Run The following procedure describes how to stop a run before it completes Before It Completes To stop a run before it completes Step Action 1 Press the Stop key The Stop confirmation screen appears Sample 50 1 Confirm Stop Press STOP to abort Press Resume to continue F1 F2 F3 F4 F5 The run pauses for a pre programmed period of time When the pause time expires the run aborts Press Resume to resume Note The stop and pause times are configured by setting the Pause Time Out See Setting the Pause Time Out on page 3 9 2 Press the Stop key again This stops the run and the End of Run screen appears 11 30 AM End of Run Method exp001 Run aborted at 11 30 05 AM 01 01 00 Length of run is 01 34 25 F1 F2 F3 F4 F5 If any errors occur during a run the following message appears Exception occurred check history file Press HIST to review the history file 3 Press Exit to return to the Main menu Running PCR Samples 4 9 Reviewing the History of a Run How to Review the You can read a record of the events and errors that occurred during a run by reviewing History of a Run th
103. systems will process the claim unless other instructions are provided Do not return any material without prior notification and authorization If for any reason it becomes necessary to return material to Applied Biosystems contact Applied Biosystems Technical Support or your nearest Applied Biosystems subsidiary or distributor for a return authorization RA number and forwarding address Place the RA number in a prominent location on the outside of the shipping container and return the material to the address designated by the Applied Biosystems representative Limited Warranty Statement D 3 Index Numerics 480 DNA Thermal Cycler converting hold times 6 2 to 6 5 A alphanumeric characters entering 5 3 AmpliCycle Sequencing 4 2 B 2 about supplied method B 1 B 2 B 3 AmpliTaq Gold 4 2 B 2 about supplied method B 2 AutoX function 5 11 to 5 12 B baud rate setting 3 10 beeper run time turning on off 3 9 BigDye 4 2 B 2 about supplied method B 3 C calculator Ty howto use 3 17 Changing 7 2 changing temperature control parameters 5 11 to 5 12 chemical hazard warning 1 6 chemical waste hazard warning 1 6 Circular Key Pad definition of 2 3 claims processing D 3 computer configuration requirement D 1 technical support for altered configuration D 1 Config function of 3 7 Configuration Screen displaying 3 7 Contacting Technical Support C 1 Control Panel diagram 2 2 entering numeric values how to 2 3 selecting a
104. t e e eens 3 2 Inspecting the Instrument lt a gR S ri Ea RN e RCR N RT RET ce eee eee 3 2 Additional Part Numbers 0 0 0 3 2 Setting Up your Laboratory 0 0 00 0 ce cence e 3 3 Choosing a Locations ose ste te REFERENT oie ee leat 3 3 Operating Temperature SRTR iea cee eens 3 3 What to AyOId e ssi eo eda tes veh cae ed ee Ee ee na ead ERA V CEPR ERREUR 3 3 Do Not Block Air Vents gg RR Rg ae K RR TR eh 3 3 Fuse Service Configuration oss isoeo e n cece cece eee 3 4 Input Voltage it cei ci tok NUR eee bee eas cite EE e 3 4 Interchangeable Sample Block Modules 0000 0 e eee eee eee ee 3 4 Double Fane FUSS cede a Sate ods dos eee Gos Be OVE P bala RR e ea 3 5 Introduction c iS RSE A A Dae ug ETag 3 5 Fuse Part Number is eis ood a sa 3 5 Power Entry Module Diagram 0 0 eee eee eee 3 5 Turning On the Instrument 0 00 cece eee 3 6 Turning On the Instrument e eee eee 3 6 Setting Custom Parameters s onorar E cence e 3 7 OVER IPSE 3 7 Displaying the Configuration Screen 0 0 0 0 cece eee eee 3 7 setting the Time lo nb heb XN A A ly cg IS 3 8 Setting the Date triste dettes Rela ev uel De ta rg tQ quera 3 8 Enabling or Disabling a Printer eee 3 8 Turning the Run Time Beeper On or OT 00 0000 0 eee eee eee 3 9 Setting the Pause Time Out 2 0 penenr ia cee eee 3 9 Defining the Idle State Setpoint Temperature 00 0000 00008 3 10 Defining the Baud Rate for
105. ter set by the user The unit has a Peltier or power amplifier failure Ambient conditions may be out of recommended range Call Technical Support SYSTEM ERROR invalid pointer System error Call Technical Support Tm temperature out of range Tm out of range Check input value and retry Call Technical Support User name already defined You entered a user name that already exists Do not duplicate user names WARNING Block version unknown Some data in the block is unrecognized Instrument operation will not be effected Upgrade firmware Watchdog timeout Software failure Call Technical Support Write to block failed Information written to the Interchangeable Sample Block Module has failed Call Technical Support Write to default block failed System error Write to memory in block failed Call Technical Support Write to default Xicor failed System error Write to memory in the block failed Call Technical Support Write to Xicor failed Information written to the Interchangeable Sample Block Module has failed Call Technical Support Valid range is You entered a number out of range The message include the valid range limits Reenter a value within the parameters of the field Troubleshooting 8 5 Troubleshooting Information Troubleshooting Refer to the following table for a description of potential p
106. the RS485 port or from a PCMCIA Flash Memory Card Contact your local Applied Biosystems representative to obtain a PCMCIA Flash Memory Card Upgrading Through The following procedure describes how to upgrade the firmware through the RS485 the Serial Port serial port 3 18 Instrument Setup To upgrade the firmware through the RS485 serial port Step Action 1 Connect the appropriate communication cable from a computer to the RS485 port on the 9700 instrument Base Module see the figure below You can use the following cables Communication cable Part number PC communication cable N805 1327 Macintosh communication cable N805 1328 For information on connecting the printer cable see page 3 26 gt 2 From the Diagnostics screen press Upgrade The Firmware Upgrade screen appears Firmware Upgrade PCcard Upgrade from PC card Serial Upgrade from serial port PCcard Serial To upgrade the firmware through the RS485 serial port continued Step Action 3 From the Firmware Upgrade screen press Serial Serial Port Firmware Upgrade Attach cable from RS485 port on 9700 to serial port on computer Press Update then begin download of file from the computer F1 F2 F3 FA F5 IMPORTANT Do not remove the cable or turn off the instrument until the upgrade is completed From the Serial Port Firmware Upgrade screen press Update D
107. the actions the instrument takes if the power is interrupted and the instrument turns off while you are operating it Note If the power is off for 15 seconds or longer and fails during execution of a cycle then the cycle currently running will restart If the power fails while executing a hold or approaching a hold then that hold temperature will restart from the beginning Note If the power failure lasts longer than 18 hours the Resume will not occur Do the following in a power failure Step Action 1 Restart or continue the PCR experiment The instrument determines what temperature was being approached or was holding Upon resumption of power it will go to that temperature and countdown the time remaining in the hold as soon as the temperature is within the specified clock start limits Incubate the samples until you can continue the experiment Enter a record for any power outage in the history file Display Screen Error Messages Error Messages Refer to the following table for a description of error messages and recommended Table actions that you should take Table 8 1 Error Messages Message Description Recommended Action Battery RAM version number lost This error is generated when the battery RAM has been lost and re initialized Call Technical Support Block Calibration initialized Software or hardware failure Call Technical Support Block C
108. the same functions as you can from the Stop Run screen 11 30 AM End of Run 25 19C Method XL PCR Run completed at 11 30 05 AM 01 01 00 Length of run is 01 34 25 F1 F2 F3 FA F5 If you have not yet stored the method you must store it before exiting or you will lose the settings The Store soft key appears if the method has not yet been stored Method Not Stored If you attempt to exit the End of Run screen before storing the method the Method Not Screen Stored screen displays Method Not Stored Press Store to save the method Press Exit to delete the method F1 F2 F3 F4 F5 The following table lists the actions you can take If you Then press want to store the method Store do not want to store the method Exit Note The Method Not Stored screen appears for a few seconds before the Exit key is recognized This prevents you from losing a newly created method You return to the top level screen and the method you created is not saved 4 12 Running PCR Samples Creating and Editing Methods Overview About This Chapter This chapter provides information about how to create and edit PCR methods and how to work with stored methods In This Chapter The following topics are covered in this chapter Topic See page Adding or Changing Users 5 2 Creating Methods 5 6 Modifying Cycling 5 11 Printing a Method 5 17 Editing or Deleting Methods 5 18
109. the target temperature Hold Time As shown in the figures below since the block reaches the target temperature before Differences the sample the programmed hold time on the DNA Thermal Cycler and the DNA Thermal Cycler 480 must include enough time for the samples to reach the target temperature A hold time of one minute or greater is required on the DNA Thermal Cycler and the DNA Thermal Cycler 480 for samples to reach the target temperature On the GeneAmp PCR System 9700 hold times of less than one minute are generally used DNA Thermal Cycler and DNA Thermal Cycler 480 HoldTime JA hs 22232 23222 2282255 cose A o A Temp Block Co Sample A 1 Time Clock starts 1 minute when block reaches target temperature GeneAmp PCR System 9700 Hold Time gaL u L O eee ss e Temp C Sample Time Clock starts when sample reaches target temperature 6 2 Converting Hold Times Guidelines for Converting Hold Times Introduction This section describes guidelines on how to convert hold times for the DNA Thermal Cycler or the DNA Thermal Cycler 480 to hold times for the GeneAmp PCR System 9700 when using the 9600 mode What to Base the New Hold Times On or down ramp The following table lists what to base the new hold time on if you are using an up ramp If you are using Then base the new hold time For more information see an up ramp on the chang
110. ur laboratory Ensure that the instrument waste is stored transferred transported and disposed of according to all local state provincial or national regulations Note Radioactive or biohazardous materials may require special handling and disposal limitations may apply GeneAmp PCR System 9700 Labels and Warnings Instrument Safety Safety labels are located on the instrument Each safety label has three parts Labels 4 A signal word panel which implies a particular level of observation or action e g CAUTION or WARNING If a safety label encompasses multiple hazards the signal word corresponding to the greatest hazard is used A message panel which explains the hazard and any user action required A safety alert symbol which indicates a potential personal safety hazard Instrument The following diagram shows the hazards and warnings labels located on the back of Warnings Diagram the GeneAmp PCR System 9700 instrument o l GR1069 A d A Applied ns GeneAmp PCR ae 9700 Part No N80502 IO Serial No 8505SYMMDD00 l n b Hn T MFG XXXXXXXXXX XXXX LISTED Laboratory Use Electrical Equipment 3277 EN61326 T TENGT328 Croup T Glass Class B CC O V229 Made in Singapore Electrical Rating 100 120 220 230 240 VAC 50 60 Hz Max Power 725 VA Fuse Rating 250 VAC 8A SB T Replace only with same TYPE and RATING FUSE DO NOT OPEN
111. vious step in the Properties dialog box enter the following In this field Enter Bits Per Second 9600 Data Bits 8 Parity None Stop Bits 1 Flow Control None When you have competed entering the information click OK 6 From the Transfer menu choose Send file The Send File dialog box appears 7 In the Send File dialog box enter the following and click Send In this field Take this action Filename Locate the upgrade file with the name under which you saved the file Protocol Enter Kermit A dialog box appears that displays the current packet number and the number remaining When the download is complete the GeneAmp PCR System 9700 automatically resets 8 From the File menu choose Save to save the parameters Downloading To download the system firmware using Windows 3 1 Firmware Using Windows 3 1 Step Action 1 From the Program Manager click the Terminal program icon 2 From the Settings menu choose Communication A dialog box appears 3 Enter the following information in the dialog box and click OK In this field Enter Baud Rate 9600 Data Bits 8 Stop Bits 1 Parity None Flow Control None Connector Com1 or Com2 depending on the port to which the cable is attached 4 From the Binary Transfers menu choose Settings A dialog box appears Select Kermit and click OK 6 From the Send Binary File menu choose Transfers A directory
112. w User Sort F1 F2 F3 F4 F5 Note Stored represents the date the method was last saved In the appropriate case this column designates the date last used 2 The units for the Size field are based on a calculation of the complexity and length of a method relative to a maximum size of 1102 size segments for the storage capacity of the instrument If you need help deciding which method to select you can View method parameters Sort methods by different categories Search for a method by user name 3 Select a method by using the Circular Key Pad to move the highlight box to a method listed on the Stored Methods screen Note You can use the up and down keys as repeat keys for quick scrolling 4 The top line of the display continuously cycles between the following three lines Methods on Inst User Size Stored Used Mem xxx methods xxx segments Note The Used Mem field displays the number of size segments used by all stored methods Free Mem xxx methods xxx segments Note The Free Mem field displays the number of size segments available to store created methods 5 Press Start and start running your samples see Running a Method on page 4 6 Running PCR Samples 4 3 Viewing Method To view parameters of a method before running Parameters Step Action 1 From the Stored Methods screen press View The View Method screen appears The screen shows all the par

GeneAmp PCR System 9700 Base Module

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