GeneAmp® PCR System 9700 Auto-Lid Dual 384 Sample Block
Contents
1. The combined weight of the base module and sample block module exceed 18 kg 41 Ib Lifting or moving the assembled unit should be done with caution When lifting or moving a heavy object Step Action 1 Assess the load and pathway of the lift and carry Ensure that the instrument can be gripped comfortably and securely Bring the load as close to the body as possible Keep the head and shoulders up and the upper body erect as the lift begins Q AJ OJN Lift with the legs by bending and straightening the knees y Wez La ale If a direction change is necessary don t twist and lift Instead move the feet pivot Don t jerk Lift and move smoothly and slowly If two or more individuals are involved in the lift communicate your moves and intentions Set the object down smoothly again using your legs to support the weight Make sure fingers and other appendages are free of the objects weight as it is put down Pollution Category 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 nonconductive pollutants only Instrument Storage 1 6 Safety Information The system 9700 must be stored at a temperature between 20 C and 60 C 4 F and 140 F at altitudes ranging from 0 12 000 meters above sea lev2. 650 638 5884 06 2010 amp Applied KS Biosystems Part Number 4310838 Rev D
3. S or Canada dial 1 800 487 6809 or from outside the U S and Canada dial 1 858 712 0317 2 Follow the voice instructions to order documents for delivery by fax Note There is a limit of five documents per fax request Obtaining Documents Through the Web Site To view download or order documents through the Applied Biosystems web site Step Action 1 Go to http www appliedbiosystems com 2 Click SERVICES amp SUPPORT at the top of the page then click Documents on Demand 3 In the search form enter and select search criteria then click Search at the bottom of the page 4 In the results screen do any of the following Click the pdf icon to view a PDF version of the document Right click the pdf icon then select Save Target As to download a copy of the PDF file Select the Fax check box then click Deliver Selected Documents Now to have the document faxed to you Select the Email check box then click Deliver Selected Documents Now to have the document PDF format e mailed to you Note There is a limit of five documents per fax request but no limit on the number of documents per e mail request To obtain Applied Biosystems training information Step Action 1 Go to http www appliedbiosystems com 2 Click SERVICES amp SUPPORT at the top of the page then click Training Getting Help A 7 Index Numerics 20 uL Probe Assembly setting up Calibra
4. Support on page A 2 Testing the Sample Block Module 4 7 Running the Temperature Non Uniformity Test Overview Use this test to verify the temperature uniformity of the GeneAmp PCR System 9700 Auto Lid Sample Block Module The Temperature Non Uniformity Test consists of several subprocedures which must be done in order Subprocedure See Page Setting Up the 20 uL Probe Assembly 4 9 Configuring the System 9700 4 10 Running the Test 4 11 Evaluating the Results 4 14 PNG Me PHYSICAL INJURY HAZARD Hot Surface Use care when working around the heated cover and sample block to avoid being burned by hot components Equipment Required This test requires the Dual 384 Well Sample Block Module Temperature Verification Kit P N 4308354 Note This kit is also used for the Auto Lid Sample Block Module Your kit includes Light mineral oil Two 384 Well Temperature Verification Plates 20 uL Probe Assembly Digital thermometer with 9V battery installed 4 8 Testing the Sample Block Module Setting Up the 20 uL To set up the 20 uL Probe Assembly Probe Assembly Step Action 1 Make sure the heated cover is in the rear position If it is not press and release the red button to automatically move the heated cover to the rear position 2 Place both 384 Well Temperature Verification Plates on the sample blocks The plate labeled L1 L6 is for the left sa
5. System 9 700 Auto Lid Sample Block Module The Calibration Verification Test consists of several subprocedures which must be done in order Subprocedure See Page Setting Up the 20 uL Probe Assembly 4 3 Configuring the System 9700 4 4 Running the Test 4 5 Evaluating the Results 4 7 PNG ej PHYSICAL INJURY HAZARD Hot Surface Use care when working around the heated cover and sample block to avoid being burned by hot components Equipment Required This test requires the Dual 384 Well Sample Block Module Temperature Verification Kit P N 4308354 Note This kit is also used for the Auto Lid Sample Block Module Your kit includes Light mineral oil Two 384 Well Temperature Verification Plates 20 uL Probe Assembly Digital thermometer with 9V battery installed 4 2 Testing the Sample Block Module Setting Up the 20 uL To set up the 20 uL Probe Assembly Probe Assembly Step Action 1 Make sure the heated cover is in the rear position If it is not press and release the red button to automatically move the heated cover to the rear position Place both 384 Well Temperature Verification Plates on the sample blocks The plate labeled L1 L6 is for the left sample block The plate labeled R1 R6 is for the right sample block Position the plates so the angled corners face away from you Note The plates are used as a guide to help you locate the probes within the samp
6. back the adhesive film This will help keep sample at the bottom of the wells If the reaction plate is tilted or jostled the sample may have to be centrifuged 3 6 Using Maintaining the Sample Block Module Cleaning the Sample Block Module Overview The following procedures describe how to Put the heated cover into the cleaning position Clean the heated cover Clean the sample block wells IMPORTANT Before using any cleaning or decontamination method except those recommended in this manual check with Applied Biosystems to ensure that the proposed method will not damage the equipment Cleaning Position To clean the Auto Lid Sample Block Module you must first put the heated cover into the cleaning position Follow the steps below To put the heated cover into the cleaning position Step Action 1 Make sure the heated cover is in the rear position If it is not press and release the red button to automatically move the heated cover to the rear position 2 The heated cover is now in the correct position 3 Lift the front of the heated cover The cleaning position is shown below Using Maintaining the Sample Block Module 3 7 Cleaning the Heated Clean the heated cover once a month or more frequently if needed Cover During instrument operation the temperature of the heated cover can be as high as 108 C and the temperature of the sample block module can be as high as 100 C Before performing
7. be placed and removed manually Modules Accessories and Disposables Overview The modules listed below are available for the GeneAmp PCR System 9700 Base Module The accessories and disposables are for use with the Auto Lid Sample Block Module number See the tables below Ordering Order modules accessories and disposables from Applied Biosystems by part Modules Part Number 96 Well Sample Block Module N805 0251 96 Well Gold Sample Block Module 4314443 96 Well Aluminum Sample Block Module 4314445 Dual 384 Well Sample Block Module N805 0400 Auto Lid Dual 384 Sample Block Module 4312904 0 5 mL 60 Well Sample Block Module 4309131 Accessories Part Number Tool 384 Well Plate Extraction T 6273 Dual 384 Well Sample Block Module Temperature Verification Kit Note This kit is also used for the Auto Lid Sample Block Module 4308354 Disposables Part Number MicroAmp 384 Well Reaction Plates Box of 50 4305505 MicroAmp Clear Adhesive Films Pack of 100 4306311 2 4 Sample Block Module Overview Using Maintaining the Sample Block Module Overview About This Chapter This chapter describes how to use and maintain the Auto Lid Sample Block Module In This Chapter The following topics are covered in this chapter Topic See Page Installing the Auto Lid Sample Block Module 3 2 Using Reaction Plates with the Sample Block Module 3 4 Cleanin
8. run the Rate Test Step Action 1 Turn on the system 9700 The main menu appears Press F4 Util The Utilities screen appears Press F1 Diag The Diagnostics screen appears 2 3 4 Press F2 System The System Performance screen appears System Performance Rate Cool and Heat Rate Tes Cycle Cycle Performance Test Rate Cycle ET F2 F3 F4 F5 Press F1 Rate from the System Performance screen A Warning message appears WARNING Install the Appropriate Empty Consumables into the Sample Block Refer to System Performance Section of Block User Manual Fl F2 F3 F4 E5 Note You will install the MicroAmp 384 Well Reaction Plates Note Make sure the reaction plates are sealed with the adhesive film Place empty MicroAmp 384 Well Reaction Plates in the sample blocks Press and release the red button to automatically close the heated cover After you have installed the reaction plates press F1 Cont The instrument runs through a series of tests in which the sample blocks are stabilized at 35 C 94 C and 4 C Testing the Sample Block Module 4 15 To run the Rate Test continued Step Action 8 View the test results At the conclusion of the test the Cool and Heat Rate Test screen appears The screen displays the test results and indicates whether the test passed or failed Cool and Heat Rate Test Heating rate
9. sample well formats as well as throughput capacity IMPORTANT Interchanging sample block modules may require a firmware change If the sample block module is placed on a base module running an earlier software version the instrument will not operate correctly To upgrade the base module software use the PCMCIA Personal Computer Memory Card International Association interface card that is shipped with the Auto Lid Sample Block Module For instructions on upgrading the software see the GeneAmp PCR System 9700 Base Module User s Manual P N 0993 6247 or see To Reach Technical Support Through the Applied Biosystems Web Site on page A 6 Auto Lid Sample Block Module Heated cover Sample blocks System 9700 Base Module 2 2 Sample Block Module Overview Sample Blocks There are two sample blocks in the Auto Lid Sample Block Module Each holds one 384 well reaction plate IMPORTANT The right sample block is the primary control block the left is a slave lf you are using only one reaction plate Place the reaction plate you are using in the right sample block Place an empty reaction plate in the left sample block GR1761 GR1760 w Lo Using reaction plates in both sides Using one reaction plate in right si
10. this procedure wait until the heated cover and sample block module reach room temperature To clean the heated cover Step Action 1 Put the heated cover into the cleaning position See Cleaning Position on page 3 7 Turn off the instrument Wait 20 30 minutes for the heated cover to cool down Soak a cotton swab or clean cloth with pure isopropanol and gently wipe the bottom of the heated cover CHEMICAL HAZARD Isopropanol is a flammable liquid and vapor It may cause eye skin and upper respiratory tract irritation Prolonged or repeated contact may dry skin and cause irritation It may cause central nervous system effects such as drowsiness dizziness and headache etc Please read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Remove any remaining isopropanol from the heated cover with a clean cloth and return the cover to its normal position If the heated cover becomes contaminated with amplified DNA a Wipe the heated cover with a clean cloth or cotton swab soaked in 10 bleach b Wipe with a clean damp cloth NUNNA CHEMICAL HAZARD Sodium hypochlorite bleach is a liquid disinfectant that can be corrosive to the skin and can cause skin depigmentation Please read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Cleaning the Sample Clean the sample block w
11. trademark of Applied Biosystems or its subsidiaries in the U S and or certain other countries AmpErase AmpliTaq AmpliTaq Gold EnviroAmp GeneAmp and TaqMan are registered trademarks of Roche Molecular Systems Inc Microsoft Windows and Windows NT are trademarks of Microsoft Corporation All other trademarks are the sole property of their respective owners Part Number 4310838 Rev D 06 2010 Contents Safety Information OVERVIEW arae i a a e ee Sh ee Se ee ee ae a a 1 1 Symbols and Instrument Labels kk kk kk kK KK KK KK KK KK KK KK KK KK KK KK KK kk 1 2 Operating Precautions sinoi odin eke o die oad ar Elk A dP SOR W A KN A Ak 4 1 4 ST Haa rh gg gmmagggggga 1 8 Sample Block Module Overview OVEDVIEW apea cai bead pais Reed N MD MMDM M M I M IMMUMMMNMNNNHNHNHnHnEunHHD ZH NMMME E2P 2 1 About the Auto Lid Sample Block Module 0 2 0 0 cee KK KK KK KK KK KK KK KK KK KK 2 2 Modules Accessories and Disposables LL kK KK KK KK KK KK KK KK KK KK KK KK KK KK KK 2 4 Using Maintaining the Sample Block Module OVERVIEW ite alee ot to eae alee ee es rr hes ee cae 3 1 Installing the Auto Lid Sample Block Module KK KK KK KK KK KK KK KK KK KK KK 3 2 Using Reaction Plates with the Sample Block Module 0 0 eee KK KK 3 4 Cleaning the Sample Block Module kk kK KK KK KK KK KK KK KK KK KK KK KK KK eens 3 7 DMME ME NSS DD DD rrr Mie asec hae Ma EEE eez 3 9 Test
12. wells Note The sample volume range is 5 20 jL Seal the reaction plates with adhesive films See Sealing the Reaction Plates below Note Do not use mineral oil or glycerine in the sample blocks or as a vapor barrier over the samples in the wells The adhesive films prevent evaporation or contamination In addition the Auto Lid Sample Block Module s heated cover prevents condensation Sealing the Reaction Seal the reaction plates for the Auto Lid Sample Block Module with MicroAmp Clear Plates Adhesive Films Note Do not use mineral oil or glycerine in the sample blocks or as a vapor barrier over the samples in the wells The adhesive films prevent evaporation or contamination In addition the Auto Lid Sample Block Module s heated cover prevents condensation To seal the reaction plate Step Action 1 Remove the paper backing from the adhesive film 2 Place the adhesive side of the film onto the reaction plate 3 Smooth down the adhesive film working from the center of the reaction plate toward the edges After the reaction plates have been sealed place them into the sample blocks 3 4 Using Maintaining the Sample Block Module Placing the Reaction Placing the Reaction Plates Into the Sample Blocks Plates Removing the Reaction Plates IMPORTANT The right sample block is the primary control block and the left is a slave If you are using only one reactio
13. x xx C s Cooling rate x xx C s Fl F2 F3 F4 F5 Check your Rate Test results against the passing ranges listed below Heating Rate gt 1 0 C second Cooling Rate gt 1 4 C second 10 If the test fails repeat the procedure once If the test fails again contact Applied Biosystems Technical Support See Technical Support on page A 2 4 16 Testing the Sample Block Module Running the Cycle Use the Cycle Test to verify that the PCR cycling function operates properly This test Test takes approximately 15 minutes to run To run the Cycle Test Step Action 1 Turn on the system 9700 The main menu appears Press F4 Util The Utilities screen appears Press F1 Diag The Diagnostics screen appears 2 3 4 Press F2 System The System Performance screen appears System Performance Rate Cool and Heat Rate Tes Cycle Cycle Performance Test Rate Cycle Press F2 Cycle from the System Performance screen A Warning message appears WARNING Install the Appropriate Empty Consumables into the Sample Block F1 F2 F3 F4 F5 Note You will install the MicroAmp 384 Well Reaction Plates Place empty MicroAmp 384 Well Reaction Plates in the sample blocks Press and release the red button to automatically close the heated cover After you have installed the reaction plates press F1 Cont The C
14. 00 completes the Temperature Non Uniformity Test the TNU Results Performance screen appears See the table below to evaluate the results If the Then Temperature of the sample block wells is uniform Pass appears after each setpoint temperature TNU Performance TNU at 94 C is xx xx Pass TNU at 37 C is xx xx Pass F1 F2 E3 F4 F5 Temperature variation of the sample block wells exceeds performance specifications Fail appears after the setpoint temperature s for which the test failed TNU Performance TNU at 94 C is xx xx Fail TNU at 37 C is xx xx Fail Fl F2 F3 F4 F5 Ifthe test fails repeat the procedure to make sure the meter was not misread and that errors were not made entering data Ifthe test fails again contact Applied Biosystems Technical Support See Technical Support on page A 2 4 14 Testing the Sample Block Module Running System Performance Diagnostics Overview Equipment Required Running the Rate Test After you have configured the GeneAmp PCR System 9700 conduct the System Performance Diagnostics to verify the integrity of the cooling and heating system There are two System Performance Diagnostics Rate Test Cycle Test These diagnostics require Two MicroAmp 384 Well Reaction Plates Use the Rate Test to verify that the Peltier units are operating correctly The test takes approximately 10 minutes to run To
15. Amperage A Nominal Japan 100 10 50 60 Hz 1 3 16 USA Canada 120 10 50 60 Hz 1 4 20 EC 230 10 50 60 Hz 1 3 14 Maximum power is 860 VA Line voltage must be within 10 of the nominal value High or low voltages may have adverse effects on the electronic components of the instrument In areas where the supplied power is subject to fluctuations exceeding these limits a power line regulator may be required Voltage Spikes Short duration high voltage spikes often cause random failures in microprocessor controlled instrumentation These spikes can be caused by other devices using the same power source refrigerators air conditioners and centrifuges or by outside influences such as lightning A dedicated line and ground between the instrument and building main electrical service are necessary to prevent such problems If your environment contains devices that are electrically noisy or you are in an area with frequent electrical storms a line conditioner with a recommended capacity of 2 0 VA will enhance the reliability of your system This may be lower depending on the conditioner or power supply design Safety Information 1 5 Physical Specifications Lifting the Instrument Weight Sample Block Module 10 kg 22 Ib Base Module 8 6 kg 19 Ib Dimensions footprint with sample block installed Height 26 0 cm 10 in Width 28 0 cm 11 in Depth 46 5 cm 19 5 in
16. GeneAmp PCR System 9700 Auto Lid Dual 384 Sample Block Module User s Manual lt gt Applied KS Biosystems Copyright 2006 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 APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE WHETHER IN CONTRACT TORT WARRANTY OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL INCIDENTAL INDIRECT PUNITIVE MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING BUT NOT LIMITED TO THE USE THEREOF NOTICE TO PURCHASER LIMITED LICENSE The combination of the GeneAmp PCR System 9700 Sample Block Module with a GeneAmp PCR System 9700 Base Unit is licensed under US patents for thermal cycler apparatus and counterpart patent claims in other countries No other rights are conveyed expressly by implication or by estoppel Further information on purchasing licenses may be obtained by contacting the Director of Licensing Applied Biosystems 850 Lincoln Centre Drive Foster City California 94404 USA TRADEMARKS AB Design Applied Biosystems and MicroAmp are registered trademarks Applera Celera Genomics and BigDye is a
17. Scoresby Victoria 61 3 9730 8600 61 3 9730 8799 China Beijing 86 10 64106608 or 86 10 64106617 86 800 8100497 Hong Kong 852 2756 6928 852 2756 6968 India New Delhi 91 11 653 3743 3744 91 11 653 3138 Korea Seoul 82 2 593 6470 6471 82 2 593 6472 Malaysia Petaling Jaya 60 3 79588268 60 3 79549043 Singapore 65 896 2168 65 896 2147 Taiwan Taipei Hsien 886 2 2358 2838 886 2 2358 2839 Thailand Bangkok 66 2 719 6405 66 2 319 9788 Europe Austria Wien 43 0 1 867 35 75 0 43 0 1 867 35 75 11 Belgium 32 0 2 532 4484 32 0 2 582 1886 Denmark Naerum 45 45 58 60 00 45 45 58 60 01 Finland Espoo 358 0 9 251 24 250 358 0 9 251 24 243 France Paris 33 0 1 69 59 85 85 33 0 1 69 59 85 00 Germany Weiterstadt 49 0 6150 101 0 49 0 6150 101 101 Italy Milano 39 0 39 83891 39 0 39 838 9492 Region Telephone Fax Norway Oslo 47 23 12 06 05 47 23 12 05 75 Portugal Lisboa 351 0 22 605 33 14 351 0 22 605 33 15 Spain Tres Cantos 34 0 91 806 1210 34 0 91 806 12 06 Sweden Stockholm 46 0 8 619 4400 46 0 8 619 4401 Switzerland Rotkreuz 41 0 41 799 7777 41 0 41 790 0676 The Netherlands Nieuwerkerk a d IJssel 31 0 180 392400 31 0 180 392409 or 31 0 180 392499 United Kingdom Warrington Cheshire 44 0 1925 825650 44 0 1925 282502 Eu
18. ase see the section To Obtain Technical Documents following the telephone information below To Contact Technical You can contact Applied Biosystems Technical Support by e mail for help in the Support by E Mail following product areas A 2 Getting Help Product Product Area E mail address Genetic Analysis DNA Sequencing galab appliedbiosystems com Sequence Detection Systems Real Time pcrlab appliedbiosystems com PCR and PCR Protein Sequencing Peptide and DNA corelab appliedbiosystems com Synthesis Biochromatography BioCAD tsupport appliedbiosystems com SPRINT VISION and INTEGRAL Workstations and POROS Perfusion Chromatography Products Expedite 8900 Nucleic Acid Synthesis Systems MassGenotyping Solution 1 MGS1 Systems PNA Custom and Synthesis Pioneer Peptide Synthesizers Proteomics Solution 1 PS1 Systems ICAT Reagent FMAT 8100 HTS Systems Mariner ESI TOF Mass Spectrometry Workstations Voyager MALDI TOF Biospectrometry Workstations CytoFluor 4000 Fluorescence Plate gt e Reader LC MS support sciex com Applied Biosystems MDS Sciex Chemiluminescence Tropix tropix appliedbiosystems com To Contact Technical To contact Applied Biosystems Technical Support in North America use the telephone Support by Telephone or Fax North America or fax numbers in the table below Note To schedule a servic
19. ation 2 3 I installing the sample block module 3 3 instrument labels 1 3 interchangeability sample block modules 2 2 Internet address customer training information A 7 Documents on Demand A 6 J jams fixing 3 9 L loading samples 3 4 M maintenance routine 1 7 MicroAmp 384 Well Reaction Plates partnumber 2 4 MicroAmp Clear Adhesive Films partnumber 2 4 MSDSs_ 1 9 N non electrical symbols 1 2 O operating precautions 1 4 to 1 7 ordering parts 2 4 P parts ordering modules accessories and disposables 2 4 Index 1 PCR cycling function testing 4 17 to 4 18 Peltier unit heating cooling unit 2 3 verifying running correctly 4 15 performance tests 4 15 to 4 18 Cycle Test running 4 17 to 4 18 Rate Test running 4 15 to 4 16 placing the reaction plates 3 5 pollution category 1 6 R Rate Test running 4 15 to 4 16 reaction plates loading samples into 3 4 manually loading into the sample blocks 3 5 manually removing from the sample blocks 3 5 part number 2 4 removing adhesive films from 3 6 sealing 3 4 using with the sample block module 3 4 3 6 S safety 1 1 to 1 10 sample block modules interchanging 2 2 sample blocks about 2 3 cleaning the wells 3 8 DNA contamination in wells 3 9 manually loading reaction plates into 3 5 manually removing reaction plates from 3 5 verifying calibration 4 2 to 4 7 verifying temperature uniformity 4 8 to 4 14 samples loading into the reaction plates 3 4 seali
20. de Heated Cover The heated cover slides over the sample blocks and performs two functions It raises the temperature of the upper part of the tube the part above the sample blocks above the temperature of the reaction mixture This eliminates condensation which may have a negative effect on your chemistry It puts pressure on the reaction plates to seat them firmly and precisely in the sample blocks This is important for proper heat transfer Peltier Heating The internal Peltier heating cooling unit is housed in the sample block module The Cooling Unit sample block module is made of aluminum to provide the optimal thermal transfer rate Platinum sensors in the sample block module provide Wide temperature range 4 99 9 C Accuracy 0 25 C from 35 100 C Uniformity of each sample block 0 5 C measured after 30 sec at 95 C Uniformity of combined sample blocks 0 75 C measured after 30 sec at 95 C Long term stability and high reliability Sample Block Module Overview 2 3 Auto Lid The auto lid automatically closes the heated cover over the reaction plates at the start of a PCR run and then opens the heated cover when the run is completed If you have access to an automatic arm the auto lid can also be programmed to Place the reaction plates on the sample block Remove the reaction plates from the sample block If you do not have access to an automatic tick arm the reaction plates can
21. e Frequently Asked Questions section 1 to display a list of FAQs for your area of interest Search the Solution Database To search for solutions to problems using the Solution Database Step Action Go to http www appliedbiosystems com Click SERVICES amp SUPPORT at the top of the page then click Frequently Asked Questions Follow the instructions under the Search the Solution Database section 2 to find a solution to your problem Submit a Question To submit a question directly to Technical Support Go to http www appliedbiosystems com Click SERVICES amp SUPPORT at the top of the page then click Frequently Asked Questions In the Personal Assistance E Mail Support section 8 click Ask Us RIGHT NOW In the displayed form enter the requested information and your question then click Ask Us RIGHT NOW Within 24 to 48 hours you will receive an e mail reply to your question from an Applied Biosystems technical expert To Obtain Technical You can obtain technical documents such as Applied Biosystems user documents Documents MSDSs certificates of analysis and other related documents for free 24 hours a day You can obtain documents By telephone Through the Applied Biosystems web site A 6 Getting Help To Obtain Customer Training Information Ordering Documents by Telephone To order documents by telephone 1 From the U
22. e Temperature Verification screen appears Verification Temperatur Temp Calibration Verification TNU Temperature Non Uniformity Temp J _INU_ F1 F2 F3 F4 F5 Press F2 TNU to automatically configure the system 9700 for the Temperature Non Uniformity Test The TNU Performance screen appears TNU Performance Sample temp xx x C Cover temp xxx C Place Probe in well Ll Press Run Run 4 10 Testing the Sample Block Module Running the Test The Temperature Non Uniformity Test uses the 20 uL Probe Assembly to test the temperature uniformity of six different wells in each sample block Note If necessary press F5 Cancel to exit the test To run the Temperature Non Uniformity Test Step Action 1 Press F1 Run This starts the Temperature Non Uniformity Test The TNU Performance screen appears with the setpoint value displayed TNU Performance Sample temp xx x C Cover temp xxx C Setpoint is 94 C Sample must be within 1 0 C of setpoint Fl F2 F3 F4 F5 Note The sample blocks must be within 1 0 C of the setpoint In addition the cover must be within 1 C of 105 C It may take several minutes for the system 9700 to ramp up Take a temperature reading a The TNU Performance screen counts down the time until the setpoint is stabilized TNU Performance Sample temp xx x C Cover temp xxx C Stabilizing at setpoi
23. e call for other support needs or in case of an emergency dial 1 800 831 6844 then press 1 Product Product Area Telephone Fax ABI Prism 3700 DNA Analyzer 1 800 831 6844 then press 8a 1 650 638 5981 DNA Synthesis 1 800 831 6844 press 2 then press 1a 1 650 638 5981 Fluorescent DNA Sequencing 1 800 831 6844 press 2 then press 22 1 650 638 5981 Fluorescent Fragment Analysis including GeneScan applications 1 800 831 6844 press 2 then press 3a 1 650 638 5981 Integrated Thermal Cyclers ABI PRISM 877 and Catalyst 800 instruments 1 800 831 6844 press 2 then press 44 1 650 638 5981 ABI Prism 3100 Genetic Analyzer 1 800 831 6844 press 2 then press 6a 1 650 638 5981 Peptide Synthesis 433 and 43x Systems 1 800 831 6844 press 3 then press 1a 1 650 638 5981 Protein Sequencing Procise Protein Sequencing Systems 1 800 831 6844 press 3 then press 2a 1 650 638 5981 Sequence Detection Systems Real Time PCR and PCR 1 800 762 4001 then press 1 for PCRa 2 for TaqMan applications and Sequence Detection Systems including ABI Prism 7700 7900 and 57004 6 for the 6700 Automated Sample Prep Systema or 1 800 831 6844 then press 5a 1 240 453 4613 Mariner ESI TOF Mass Spectrometry Workstations Voyager MALDI TOF Biospectrometry Workstations MassGenotyping Solution 1 MGS1 Sy
24. e safety procedures 1 2 Safety Information Electrical Symbols This symbol indicates the on position of the main power switch This symbol indicates the off position of the main power switch This symbol indicates the on off position of a push push main power switch This symbol indicates that a terminal may be connected to another instrument s signal ground reference This is not a protected ground terminal This symbol indicates that this is a protected ground terminal that must be connected to earth ground before any other electrical connections are made to the instrument This symbol indicates that this terminal either receives or delivers alternating current or voltage This symbol indicates that this terminal either receives or delivers alternating and direct current or voltage This symbol indicates the presence of high voltage and warns the user to proceed with caution PP a O This symbol alerts you to consult the manual for further information and to proceed with caution Non electrical Symbols AN This symbol illustrates a heater hazard Proceed with caution when working around these areas to avoid being burned by hot components Instrument Labels The following instrument labels are on the system 9700 with the Auto Lid Sample Block Module installed NTUN Disconnect supply cord before opening Grounding circuit continuity is vital for sa
25. el IMPORTANT The system 9700 is guaranteed to meet performance specifications only when the ambient temperature is 15 30 C and the ambient relative humidity is 20 80 between altitudes of 0 and 2000 meters Communautes Europeennes CE Compliance Routine Maintenance for Safe Operation 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 A emission limits Before using any cleaning or decontamination method except those recommended in the manual the user should check with Applied Biosystems to ensure that the proposed method will not damage 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 a service inspection of the instrument should be made to ensure safe operation Safety Information 1 7 Safety Documentation User Attention Words Chemical Hazard Warning Chemical Waste Hazard Warning 1 8 Safety Information 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 7 er Neg oli Cautions the use
26. ells once a month or more frequently if needed Block Wells To clean the sample block wells Step Action 1 Let the system 9700 cool to the idle setpoint 25 C 2 Put the heated cover into the cleaning position See Cleaning Position on page 3 7 Turn off the instrument Remove the reaction plates from the sample block module and set them aside Soak a cotton swab in pure isopropanol and clean the sample block wells thoroughly CHEMICAL HAZARD Isopropanol is a flammable liquid and vapor It may cause eye skin and upper respiratory tract irritation Prolonged or repeated contact may dry skin and cause irritation It may cause central nervous system effects such as drowsiness dizziness and headache etc Please read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves 3 8 Using Maintaining the Sample Block Module To clean the sample block wells continued Step Action 6 Remove any remaining isopropanol from the heated cover before reloading the reaction plates 7 If the sample block wells become contaminated with amplified DNA a Clean the wells thoroughly with a cotton swab soaked in 10 bleach b Wipe with a clean damp cloth NUNNA CHEMICAL HAZARD Sodium hypochlorite bleach is a liquid disinfectant that can be corrosive to the skin and can cause skin depigmentation Please read the MSDS and
27. fe operation of equipment Never operate equipment with grounding conductor disconnected AVERTISSEMENT Debrancher le cordon d alimentation avant d ouvrir la continuite des masses est essentielle Pour un fonctionnement sans danger Ne jamais utiliser equipment si le fil de terre n est pas raccorde NEURIR HOT SURFACE Use care when working around this area to avoid being burned by hot components Attention Surface chaude Safety Information 1 3 Operating Precautions Overview General Use Environment Humidity and Temperature Sample Block Module 1 4 Safety Information The following precautions should be taken whenever you operate the system 9700 with the Auto Lid Sample Block Module installed F NOTA The instrument should be used according to the instructions provided in this manual If used otherwise the protection provided by this instrument may be impaired PNIA This instrument is designed for indoor use and for altitudes not exceeding 2000 meters 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 The system 9700 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 2000 meters 7 Mer NE Ele This instrument is not designed for operatio
28. fication screen appears Calibration Verification Block temp xx x C Cover temp xxx C Place probe in well R3 Press Run Run 4 4 Testing the Sample Block Module Running the Test Use the digital thermometer to take temperature readings of the sample well connected to the 20 uL Probe Assembly You will take a reading at two different setpoint temperatures Note If necessary press F5 Cancel to exit the test To run the Calibration Verification Test Step Action 1 Press F1 Run This starts the Calibration Verification Test The Calibration Verification screen appears with a setpoint value displayed Calibration Verification Block temp xx x C Cover temp xxx C Setpoint is 85 C Cover must be within 1 C of 105 C Fl F2 F3 F4 F5 Note The cover must be within 1 C of 105 C It may take several minutes for the system 9700 to ramp up During calibration a The Calibration Verification screen counts down the time until the setpoint is reached Calibration Verification Block temp xx x C Cover temp xxx C Stabilizing at setpoint x xx Fl F2 F3 F4 F5 b When the Stabilizing at setpoint value decrements to 0 read the digital thermometer Note Refer to the instructions included with your Temperature Verification Kit for a detailed description on operating the digital thermometer Testing the Sample Block Module 4 5 To run the Calibration Verif
29. follow the handling instructions Wear appropriate protective eyewear clothing and gloves Fixing a Jam About Jams The following table describes how to fix a jam that is causing the auto lid to stop If the auto lid jams Then while closing the auto lid will automatically retract to the open position Find the jam and clear it Press the red button and hold for 1 sec The heated cover returns to the open position and the instrument is reset while opening the auto lid will stop moving and remain in place Try to find the jam and clear it Press the red button and hold for 1 sec The heated cover returns to the open position and the instrument is reset Using Maintaining the Sample Block Module 3 9 Testing the Sample Block Module Overview About This Chapter This chapter describes how to perform tests that verify that your Auto Lid Sample Block Module is functioning properly In This Chapter The following topics are covered in this chapter Topic See Page Running the Calibration Verification Test 4 2 Running the Temperature Non Uniformity Test 4 8 Running System Performance Diagnostics 4 15 Data Sheet Calibration Verification Test 4 19 Data Sheet Temperature Non Uniformity Test 4 20 Testing the Sample Block Module 4 1 Running the Calibration Verification Test Overview Use this test to verify the temperature calibration of your GeneAmp PCR
30. g the Sample Block Module 3 7 Fixing a Jam 3 9 Using Maintaining the Sample Block Module 3 1 Installing the Auto Lid Sample Block Module Diagrams A lever behind the sample block module releases it from the GeneAmp PCR System 9700 Base Module The top and bottom of the Auto Lid Sample Block Module are shown below GR1760 Top view Auto Lid Sample Block Module Lever M Bottom view Auto Lid Sample Block Module 3 2 Using Maintaining the Sample Block Module Installing the Sample To install the sample block module into the GeneAmp PCR System 9700 Base Block Module Module Step Action 1 Pull the lever out from the sample block module 2 Place the sample block module onto the base module then push the sample block module back to seat the electrical connections 3 Push the lever into the base module to secure the sample block module Note If the sample block module is not seated correctly the instrument cannot be turned on Installing the To install the communication card and cable into the GeneAmp PCR System 9700 Communication Base Module Card and Cable Step Action 1 Insert the communication card into the slot at the rear of the right
31. ication Test continued Step Action 3 Using the numeric keys type the value displayed on the digital thermometer in the Enter actual block temperature field Calibration Verification Block temp xx x C Cover temp xxx C Enter actual block temperature xx x Fl F2 F3 F4 F5 Note The digital thermometer displays a four digit value round this off to three digits before typing it in the Calibration Verification screen Note To keep a permanent record of the test record this value on the Calibration Verification Test Data Sheet page 4 19 Press Enter The system 9700 automatically begins the second reading 45 C setpoint The Calibration Verification screen appears with the setpoint value displayed Calibration Verification Block temp xx x C Cover temp xxx C Setpoint is 45 C Cover must be within 1 C of 105 C Fl F2 F3 F4 F5 Note The cover must be within 1 C of 105 C Repeat step 2 and step 3 for the second reading The system 9700 evaluates the calibration of the sample block temperature for the setpoint values you entered and displays the results A summary screen appears at the conclusion of the test Calibration Verification Actual temperature at 85 C Actual temperature at 45 C Fl F2 F3 F4 F5 If you entered values on the Calibration Verification Test Data Sheet compare those values with the actual test results Press F1 Accept To interp
32. ing the Sample Block Module DA mm mm E EE E Rs SUA aS 4 1 Running the Calibration Verification Test kK kK KK KK KK KK KK KK KK KK KK KK KK KK 4 2 Running the Temperature Non Uniformity Test 2 0 0 KK KK KK KK KK KK KK KK KK KK 4 8 Running System Performance Diagnostics 0 cece KK KK KK KK KK KK KK KK KK 4 15 Data Sheet Calibration Verification Test 0 0 0 cee cece KK KK KK KK KK KK KK 4 19 Data Sheet Temperature Non Uniformity Test 2 0 0 KK KK KK KK KK KK KK KK KK KK 4 20 Getting Help _ _ ac gt o gt oe eo o eo_wa nbbro eereb b b b b b p np n nm gt gt gt bbbeeomeomo n m mrrrreremeoeooa a a aN N A 1 Technical S pDDOT ky 5 13255 tote Qerh el ed ve a O D Seb ab o ek 5 Cek ir A 2 Index Safety Information Overview About This Chapter This chapter provides information to help you safely operate the GeneAmp PCR System 9700 and the Auto Lid Sample Block Module IMPORTANT Read this chapter before you install the system 9700 and the Auto Lid Sample Block Module In This Chapter The following topics are covered in this chapter Topic See Page Symbols and Instrument Labels 1 2 Operating Precautions 1 4 Safety 1 8 Safety Information 1 1 Symbols and Instrument Labels Symbols The following symbols are used on Applied Biosystems instruments Whenever such symbols appear on instruments please observe appropriat
33. int Value Well R3 Date Tested By Probe Serial No Serial No 85 C 45 C Testing the Sample Block Module 4 19 Data Sheet Temperature Non Uniformity Test Instructions When running the Temperature Non Uniformity Test record the setpoint values for wells L1 L6 and R1 R6 on this data sheet At the end of the Temperature Non Uniformity Test check the values displayed on the system 9700 against the values recorded here This will help you maintain accurate test records Note If desired you may photocopy this page Date Tested By Probe Serial No Thermometer Serial No Setpoint Value 94 C 37 C L1 L2 L3 L4 L5 L6 R1 R2 R3 R4 R5 R6 4 20 Testing the Sample Block Module Getfing Help Overview About this Appendix This appendix describes how to get technical help from Applied Biosystems Getting Help A 1 Technical Support Contacting You can contact Applied Biosystems for technical support Technical Support By e mail By telephone or fax Through the Applied Biosystems web site You can order Applied Biosystems user documents MSDSs certificates of analysis and other related documents 24 hours a day In addition you can download documents in PDF format from the Applied Biosystems web site Ple
34. ispose 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 NOAIN CHEMICAL HAZARD Be sure to familiarize yourself with the MSDSs before using reagents or solvents You can order free additional copies of MSDSs for chemicals manufactured or distributed by Applied Biosystems using the contact information below To order documents by automated telephone service 1 From the U S or Canada dial 1 800 487 6809 or from outside the U S and Canada dial 1 858 712 0317 2 Follow the voice instructions to order documents for delivery by fax Note There is a limit of five documents per fax request To order documents by telephone In the U S Dial 1 800 345 5224 and press 1 To order in English dial 1 800 668 6913 and press 1 then 2 then 1 In Canada To order in French dial 1 800 668 6913 and press 2 then 2 then 1 From any other See the specific region under To Contact Technical Support by country Telephone or Fax Outside North America To view download or order documents through the Applied Biosystems web site Step Action 1 Go to http www appliedbiosystems com 2 Click SERVICES amp SUPPORT at the top of the page click Documents on Demand then click MSDS 3 Click MSDS Index search through the list for the chemical of interest to you then click
35. le blocks Use the stick end of a cotton swab to coat well R3 with mineral oil Note The wells are too small for the swab end Place the 20 uL Probe Assembly into well R3 Thread the probe wire through the channels in the 384 Well Temperature Verification Plate to prevent damage to the probe and lead wires Make sure the probe is connected to the digital thermometer Press and release the red button to automatically close the heated cover IMPORTANT Seat the probe properly If the probe wire is crushed when the heated cover closes the probe may be damaged Turn on the digital thermometer Note Refer to the instructions included with your Temperature Verification Kit for a detailed description on operating the digital thermometer Testing the Sample Block Module 4 3 Configuring the To configure the system 9700 for the Calibration Verification Test System 9700 Step Action 1 Turn on the system 9700 The main menu appears Press F4 Util The Utilities screen appears Press F1 Diag The Diagnostics screen appears 2 3 4 Press F3 TmpVer The Temperature Verification screen appears Temperature Verification Temp Calibration Verification TNU Temperature Non Uniformity TNU F1 F2 F3 F4 F5 Temp J Press F1 Temp to automatically configure the system 9700 for the Calibration Verification Test The Calibration Veri
36. may apply 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 F NOTA 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 Sample Block Module Overview Overview About This Chapter This chapter provides an overview of the Auto Lid Sample Block Module In This Chapter The following topics are covered in this chapter Topic See Page About the Auto Lid Sample Block Module 2 2 Modules Accessories and Disposables 2 4 Sample Block Module Overview 2 1 About the Auto Lid Sample Block Module Overview Diagram The GeneAmp PCR System 9700 amplifies nucleic acids using the polymerase chain reaction PCR process The Auto Lid Sample Block Module attaches to the top of the GeneAmp PCR System 9700 Base Module and allows you to perform up to 768 reactions The Auto Lid Sample Block Module also adds automation to the system 9700 which can help increase throughput See Auto Lid on page 2 4 for more information You can remove the Auto Lid Sample Block Module and replace it with another sample block module as needed Interchangeability allows you to change
37. mple block The plate labeled R1 R6 is for the right sample block Position the plates so the angled corners face away from you Note The plates are used as a guide to help you locate the probes within the sample blocks 3 Use the stick end of a cotton swab to coat wells L1 L6 and R1 R6 with mineral oil Note The wells are too small for the swab end 4 Place the 20 uL Probe Assembly into well L1 Note As the test progresses you will move the 20 uL Probe Assembly to each of the test wells L1 L6 and R1 R6 5 Thread the probe wire through the channels in the 384 Well Temperature Verification Plate to prevent damage to the probe and lead wires 6 Make sure the probe is connected to the digital thermometer 7 Press and release the red button to automatically close the heated cover IMPORTANT Seat the probe properly If the probe wire is crushed when the heated cover closes the probe may be damaged 8 Turn on the digital thermometer Note Refer to the instructions included with your Temperature Verification Kit for a detailed description on operating the digital thermometer Testing the Sample Block Module 4 9 Configuring the To configure the system 9700 for the Temperature Non Uniformity Test System 9700 Step Action 1 Turn on the system 9700 The main menu appears Press F4 Util The Utilities screen appears Press F1 Diag The Diagnostics screen appears 2 3 4 Press F3 TmpVer Th
38. n in an explosive environment Do not place the instrument close to potentially explosive materials or objects PNIA This instrument is not designed for operation with the heated cover retracted when running at 4 C If the heated cover is retracted and the instrument runs at 4 C water condensation may be excessive in the sample block area NUNI PHYSICAL INJURY HAZARD To protect yourself against burns do not open the heated cover or touch the sample block module when the word Hot displays on the screen This indicates a sample block temperature above 50 C The hot areas for the Auto Lid Sample Block Module are shown below FNAT To protect your samples and to guarantee the best temperature uniformity keep the heated cover closed at all times except when loading or unloading samples Grounding and Electrical Safety Power Requirements Voltage Quality The system 9700 must be grounded for protection against electrical shock AAIE Do not use an adapter to a two terminal outlet since this does not provide positive ground protection Refer to the GeneAmp PCR System 9700 Base Module User s Manual P N 0993 6247 for more information on electrical safety 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 Location Voltage VAC Frequency
39. n plate Place the reaction plate you are using in the right sample block Place an empty reaction plate in the left sample block To manually place the reaction plates in the sample blocks Step Action 1 Place a 384 well reaction plate into the right sample block Make sure the well numbered A1 points toward the upper right corner of the sample block module as shown below This orients the reaction plate for proper fit GR1761 aN If you are using a second reaction plate place it in the left sample block Make sure the well numbered A1 points toward the upper right corner of the sample block module This orients the reaction plate for proper fit Press the red button located near the right sample block to close the heated cover Process the samples as usual The 384 well plates can be removed by hand or with the assistance of the robotic arm The Plate Ejection system is a unique feature that allows for easy access by a robot arm to remove each 384 well plate from the sample block following cycling and opening of the lid Using Maintaining the Sample Block Module 3 5 Removing the To remove adhesive film Adhesive Film Step Action 1 Hold one corner of the adhesive film and pull it back across the reaction plate IMPORTANT Hold the reaction plate firmly down while pulling
40. ng the reaction plates 3 4 specifications physical 1 6 storing instrument 1 6 symbols Communautes Europeennes CE Compliance 1 7 electrical 1 2 non electrical 1 2 system performance tests Cycle Test running 4 17 to 4 18 Rate Test running 4 15 to 4 16 T technical support A 2 to A 7 e mail address A 2 Internet address A 6 regional sales offices A 4 to A 5 telephone fax North America A 3 A 4 Temperature Non Uniformity Test 4 8 to 4 14 data sheet 4 20 evaluating the results 4 14 required equipment 4 8 running the test 4 11 to 4 13 tests Index 2 Calibration Verification Test 4 2 to 4 7 Cycle Test 4 17 to 4 18 Rate Test 4 15 to 4 16 Temperature Non Uniformity Test 4 8 to 4 14 TmpVer softkey 4 4 4 10 Tool 384 Well Plate Extraction part number 2 4 training obtaining information A 7 y voltage quality 1 5 www appliedbiosystems com 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 Applied Biosystems is committed to providing the world s leading technology and information for life scientists 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
41. nt x xx F1 F2 F3 F4 F5 b When the Stabilizing at setpoint value decrements to zero read the digital thermometer Note Refer to the instructions included with your Temperature Verification Kit for a detailed description on operating the digital thermometer Testing the Sample Block Module 4 11 To run the Temperature Non Uniformity Test continued Step Action 3 Using the numeric keys type the value displayed on the digital thermometer in the Enter actual block temperature field TNU Performance Sample temp xx x C Cover temp xxx C Enter actual block temperature 00 0 F1 F2 F3 F4 F5 Note The digital thermometer displays a four digit value round this off to three digits before typing it in the TNU Performance screen Note To keep a permanent record of the test record this value on the Temperature Non Uniformity Test Data Sheet page 4 20 Press Enter The system 9700 automatically begins the second reading 37 C setpoint The TNU Performance screen appears with the setpoint value displayed TNU Performance Sample temp xx x C Cover temp xxx C Setpoint is 37 C Sample must be within 1 0 C of setpoint Fl F2 F3 F4 F5 Note The sample blocks must be within 1 0 C of the setpoint Repeat step 2 and step 3 for the second reading Press Enter The TNU Performance screen appears with the following prompt TNU Performance Sample temp xx x C Cover
42. on the MSDS document number for that chemical to open a pdf of the MSDS For chemicals not manufactured or distributed by Applied Biosystems call the chemical manufacturer Safety Information 1 9 Instrument Safety Labels About Waste Disposal Before Operating the Instrument 1 10 Safety Information Safety labels are located on the instrument Each safety label has three parts Asignal 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 See Symbols and Instrument Labels on page 1 2 for an explanation of all the safety alert symbols 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 your 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
43. pplied Biosystems instruments are potentially hazardous and can cause injury illness or death 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 waste 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 About MSDSs Ordering MSDSs 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 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 d
44. r that a potentially hazardous situation could occur causing injury to the user or damage to the instrument if this information is ignored INTONA Warns the user that serious physical injury or death to the user or other persons could result if these precautions are not taken OINA Indicates an imminently hazardous situation that if not avoided will result in death or serious injury NONIN CHEMICAL HAZARD Some of the chemicals used with Applied Biosystems instruments and protocols are potentially hazardous and can cause injury illness or death 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 NUNN CHEMICAL WASTE HAZARD Wastes produced by A
45. ret the results see Evaluating the Results on page 4 7 4 6 Testing the Sample Block Module To run the Calibration Verification Test continued Step Action 8 When you have completed all measurements be sure to Press F5 Exit Remove the 20 uL Probe Assembly from the sample blocks Turn off the digital thermometer and clean off the oil Remove the 384 Well Temperature Verification Plates from the sample blocks IMPORTANT Make sure the sample blocks are at room temperature 25 C before removing the reaction plates Evaluating the When the system 9700 completes the Calibration Verification Test one of two screens Results appears See the table below to evaluate the results If the sample block module Then the is properly calibrated Calibration Verification screen appears with the following message displayed Calibration Verification Calibration is good Fl F2 F3 F4 F5 does not pass the Calibration Verification Test Calibration Verification screen appears with the following message displayed Calibration Verification Instrument may require servic Contact Applied Biosystems Technical Support F1 F2 F3 F4 F5 Ifthe test fails repeat the procedure to make sure the meter was not misread and that errors were not made entering data If the test fails again contact Applied Biosystems Technical Support See Technical
46. ropean Managed Territories EMT Africa English speaking Johannesburg South Africa 27 11 478 0411 27 11 478 0349 Africa French speaking Paris France 33 1 69 59 85 11 33 1 69 59 85 00 India New Delhi 91 11 653 3743 91 11 653 3744 91 11 653 3138 Poland Lithuania Latvia and Estonia 48 22 866 40 10 48 22 866 40 20 Warszawa For all other EMT countries not listed 44 1925 282481 44 1925 282509 Central and southeast Europe CIS Middle East and West Asia Japan Japan Hacchobori Chuo Ku Tokyo 81 3 5566 6230 81 3 5566 6507 Latin America Caribbean countries Mexico and 52 55 35 3610 52 55 66 2308 Central America Brazil 0 800 704 9004 or 55 11 5070 9694 95 55 11 5070 9654 Argentina 800 666 0096 55 11 5070 9694 95 Chile 1230 020 9102 55 11 5070 9694 95 Uruguay 0004 055 654 55 11 5070 9694 95 Getting Help A 5 To Reach Technical At the Applied Biosystems web site you can search through frequently asked Support Through questions FAQs or a solution database or you can submit a question directly to the Applied Technical Support Biosystems Web Site Search FAQs To search for FAQs Step Action Go to http www appliedbiosystems com Click SERVICES amp SUPPORT at the top of the page then click Frequently Asked Questions Click you geographic region for the product area of interest Follow the instructions under th
47. side of the instrument the label on the card face should be facing you Insert the connector end of the communication cable very short cable into the communication card Insert the other end of the cable plug type into the receptacle on the sample block module labeled I O Port Installing the Power To install the power line cords into the sample block module and the GeneAmp PCR Line Cords and System 9700 Base Module Powering Up Step Action 1 Plug one end of the power line cord into the sample block module receptacle and the other end into an outlet Plug the very short jumper cable into the sample block module and the other into the base module Flip the power switch located on the sample block module near the plug receptacle and press the power button located on the front of the instrument Using Maintaining the Sample Block Module 3 3 Using Reaction Plates with the Sample Block Module Overview The following procedures describe how to Load samples into the reaction plates Seal the reaction plates Place the reaction plates into the sample blocks both manual and automatic procedures Remove the reaction plates from the sample blocks both manual and automatic procedures Remove the adhesive films Loading Samples To load samples into the reaction plates into the Reaction Plates Step Action 1 Pipette the samples into the reaction plate
48. stems Proteomics Solution 1 PS1 Systems ICAT Reagent 1 800 899 5858 press 1 then press 3 1 508 383 7855 Getting Help A 3 Product Product Area Telephone Fax Biochromatography BioCAD SPRINT VISION and INTEGRAI Workstations and POROS Perfusion Chromatography Products 1 800 899 5858 press 1 then press 4 1 508 383 7855 Expedite 8900 Nucleic Acid Synthesis Systems 1 800 899 5858 press 1 then press 5 1 508 383 7855 Pioneer Peptide Synthesizers 1 800 899 5858 press 1 then press 5 1 508 383 7855 PNA Custom and Synthesis 1 800 899 5858 press 1 then press 5 1 508 383 7855 FMAT 8100 HTS Systems CytoFluor 4000 Fluorescence Plate Reader 1 800 899 5858 press 1 then press 6 1 508 383 7855 Chemiluminescence Tropix 1 800 542 2369 U S only or 1 781 271 0045 1 781 275 8581 LC MS Applied Biosystems MDS Sciex 1 800 952 4716 1 508 383 7899 a 5 30 AM to 5 00 PM Pacific time b 8 00 AM to 6 00 PM Eastern time c 9 00 AM to 5 00 PM Eastern time To Contact Technical To contact Applied Biosystems Technical Support or Field Service outside North Support by America use the telephone or fax numbers below Telephone or Fax Outside North America A 4 Getting Help Region Telephone Fax Eastern As ia China Oceania Australia
49. temp xxx C Place probe in well xx Press Run Run 4 12 Testing the Sample Block Module To run the Temperature Non Uniformity Test continued Step Action 7 Press and release the red button to automatically open the heated cover Repeat step 4 through step 7 of Setting Up the 20 uL Probe Assembly on page 4 9 and step 1 through step 6 of this procedure Complete these steps for all 12 wells to be tested Left Sample Block Right Sample Block L1 R1 L2 R2 L3 R3 L4 R4 L5 R5 L6 R6 8 The system 9700 evaluates the uniformity of the sample block temperature for the setpoint values you entered and displays the results A summary screen appears at the conclusion of the test F1 F2 F3 F4 F5 If you entered values on the Temperature Non Uniformity Test Data Sheet compare those values with the actual test results 9 Press F1 Accept To interpret the results see Evaluating the Results on page 4 14 10 When you have completed all measurements be sure to Press F5 Cancel Remove the 20 uL Probe Assembly from the sample blocks Turn off the digital thermometer and clean off the oil Remove the 384 Well Temperature Verification Plates from the sample blocks IMPORTANT Make sure the sample blocks are at room temperature 25 C before removing the reaction plates Testing the Sample Block Module 4 13 Evaluating the When the system 97
50. tion Verification Test 4 3 Temperature Non Uniformity Test 4 9 96 Well Sample Block Module part number 2 4 A adhesive films part number 2 4 removing 3 6 sealing the reactions plates with 3 4 C Calibration Verification Test 4 2 to 4 7 20 uL Probe Assembly setting up 4 3 datasheet 4 19 evaluating the results 4 7 required equipment 4 2 running the test 4 5 4 7 cleaning the sample block module 3 7 to 3 9 Communautes Europeennes CE Compliance 1 7 cooling information 2 3 verifying cooling system 4 15 customer support See technical support A 2 Cycle Test running 4 17 to 4 18 D data sheets Calibration Verification Test 4 19 Temperature Non Uniformity Test 4 20 diagnostics 4 15 to 4 18 Cycle Test running 4 17 to 4 18 Rate Test running 4 15 to 4 16 diagrams sample block module attached to 9700 Base Module 2 2 cleaning position 3 7 top and bottom views 3 2 digital thermometer 4 3 4 9 Calibration Verification Test 4 2 Temperature Non Uniformity Test 4 8 DNA contamination heated cover 3 8 sample block wells 3 9 Documents on Demand A 6 Dual 384 Well Sample Block Module part number 2 4 Dual 384 Well Sample Block Module Temperature Verification Kit part number 2 4 E electrical symbols 1 2 e mail address for technical support A 2 F Field Service in North America contacting A 3 G grounding and electrical safety 1 5 A heated cover about 2 3 cleaning 3 8 DNA contamination 3 8 heating and cooling inform
51. ycle Test executes a two temperature PCR cycling protocol then measures and reports the average cycle time and the cycle to cycle variation IMPORTANT Pressing Pause during the Cycle Test may generate false test results Rerun the Cycle Test if Pause was pressed during the test Testing the Sample Block Module 4 17 To run the Cycle Test continued Step Action 8 View the test results At the conclusion of the test the Cycle Performance screen appears The screen displays the test results and whether the test passed or failed Cycle Performance Pass Average Cycle Time xxx x sec Cycle Time STD X X SEC Fl F2 F3 F4 F5 Check your Cycle Test results against the passing ranges listed below Average Cycle Time lt 140 seconds Cycle Time STD lt 5 seconds If the test fails repeat the procedure once If the test fails again contact Applied Biosystems Technical Support See Technical Support on page A 2 4 18 Testing the Sample Block Module Data Sheet Calibration Verification Test Instructions When running the Calibration Verification Test record the setpoint values for well R3 on this data sheet At the end of the Calibration Verification Test check the values displayed on the system 9700 against the values recorded here This will help you maintain accurate test records Note If desired you may photocopy this page Thermometer Setpo
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