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Applied Biosystems Veriti™ Thermal Cycler User Guide (PN 4375799)

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1. Veriti Thermal Cycler User Guide B 3 ChapterB Disposables Other Supplies for Sample Handling The following parts can simplify working with your samples and the Veriti Thermal Cycler Product Part Number MicroAmp 96 Well Base N8010531 MicroAmp Splash Free 96 Well Base 4312063 MicroAmp Cap Installing Tool Handle 4330015 MicroAmp Multi Removal Tool 4313950 MicroAmp Adhesive Film Applicator 4333183 MicroAmp Centrifuge Adapter N8013822 B 4 Veriti Thermal Cycler User Guide Predefined Run Methods C This appendix covers Predefined Run Methods 0 cece eee ee eee ete eee eens Veriti Thermal Cycler User Guide ChapterC Predefined Run Methods Predefined Run Methods The following run methods are supplied with the Veriti Thermal Cycler and are stored in the Shared folder These run methods are based on recommended protocols from Applied Biosystems and should be considered as starting points for the different applications Your results may vary between instrument models so some optimization may be needed Please note that the ramp rates of these methods are 100 AmpliCycle Seq Run Method AmpliTag Gold DNA Polymerase Run Method BigDye Fast Run Method BigDye Standard Run Method Fast PCR Run Method General PCR Run Method LMS2 Run Method Time Release Run Method Touchdown PCR Run Method XL PCR Run Method These run methods may
2. Applied Biosystems Veriti Thermal Cycler User Guide Applied Biosystems Copyright 2007 Applied Biosystems All rights reserved General Laboratory Use 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 LABEL LICENSE The Veriti Thermal Cycler is covered by one or more of US Patents Nos 5 038 852 5 333 675 5 656 493 5 475 610 5 602 756 6 703 236 5 552 580 and corresponding claims in their non US counterparts owned by Applera Corporation 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 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 Applera
3. Nem CHEMICAL HAZARD Formamide Exposure causes eye skin and respiratory tract irritation Itis a possible developmental and birth defect hazard Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves JN DNIe ELECTRICAL HAZARD Failure to ground the instrument properly can lead to an electrical shock Ground the instrument according to the provided instructions Veriti Thermal Cycler User Guide Safety and EMC Compliance Information Symbols on Instruments Electrical The following table describes the electrical symbols that may be displayed on Symbols on Applied Biosystems instruments Instruments Symbol Description Indicates the On position of the main power switch Indicates the Off position of the main power switch Indicates a standby switch by which the instrument is Switched on to the Standby condition Hazardous voltage may be present if this switch is on standby 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 IOA OCO Indicates a
4. Applied Biosystems AB Design ABI PRISM AmpliCycle BigDye GeneAmp and MicroAmp are registered trademarks and VeriFlex and Veriti are trademarks of Applera Corporation or its subsidiaries in the U S and or certain other countries AmpliTaq Gold is a registered trademark of Roche Molecular Systems Inc All other trademarks are the sole property of their respective owners Part Number 4375799 Rev A 3 2007 Contents Preface POW TOUSE TNS GUE og seu ee dir a en ble dee eee ald ae on doe ely ae ai vii How to Obtain More Information 0 0 00 ee eee eens viii HOWTO ODN SUDDO sereisas oc neta auth E bs oie eee Ao a a ees viii Safety and EMC Compliance Information Chapter 1 Chapter 2 Safety Conventions Used in This Document 0 0 0 es xii Symbols on Instruments nanana aaaea xiii Safety Labels on Instruments 0 eaaa XIV General Instrument Safety 0 ccc dareena aaa XVI Chemical ale lt i kan a oe a iies oe ee aoe Ce Re ee hee ea ae wae XVI Chemical Waste Safety cc eee eee eet t etnies XVII BICC UIC also Oly a ig ach oh ord ts ne ahi Se ee i a eh eae ae RS xviii PhysicalHazard Safely neries vs neds ews ec arenes ee EEA xviii Safety and Electromagnetic Compatibility EMC Standards xviii System Overview Introducing the Veriti Thermal Cycler 0 0 ccc cece eee ees 1 2 Using the Touchscreen 4 darn iard Vek Se iia aio aly eine Ae ae wae 1 3 MCR USO VET VICW b
5. Viewing and Printing the Run Report At the end of arun the Run Report screen is displayed below If the last stage of the run method is an infinite hold you must touch Stop then OK in the message box before the Run Report is displayed You can also see the Run Report by touching View Last Run in the Tools Menu Date amp Time 2007 02 14 10 07 11 PM Instrument Mame 123545670901 23545670901 234 Initiating Hub 123545670901 2345670901 234 Run Method Lhe Run ID 200702140936 User Name gregor Reaction Yolumeuly 10 Cover Tenperature Degree Cy 105 0 Run Started 2007 02 14 09 37 35 PM Run Completed 2007 02 14 10 07 11 PM Motes This is a quick test for Joe s samples with a 3 minute vortex step Run Status Note The run report is saved only until the next run is finished 3 20 Veriti Thermal Cycler User Guide Chapter 3 Performing a Run e To print the run report in the Run Report screen touch Print If any errors occurred during the run the error information is also printed e To save the run report to the USB drive touch Save Removing the Samples from the Instrument Grasp the sample tray retainer assembly or reaction plate firmly with both hands and gently rock it back and forth until the tubes or plate are free N oF Vege Sample caps may pop off if the cover is opened when the sample block temperature is above 27 C Veriti Thermal Cycler User Guide 3 21 Chapter 3 Perform
6. http www appliedbiosystems com then click the link for Support At the Support page you can e Search through frequently asked questions FAQs e Submit a question directly to Technical Support e Order Applied Biosystems user documents MSDSs certificates of analysis and other related documents e Download PDF documents e Obtain information about customer training e Download software updates and patches e Contact technical services by clicking the Care Center link In addition the Support page provides access to worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities Veriti Thermal Cycler User Guide Preface TVK Support To send the temperature verification kit equipment for recalibration 1 Use the address or Fax information below to request a quote from Alpha Technics for a recalibration order e Mail Alpha Technics 17151 Gillette Avenue Irvine Ca 92614 5602 e Fax 949 271 2300 2 Ensure that the probe assembly has been decontaminated see Decontaminating the Probe Assembly on page 4 11 3 Pack the digital thermometer and the probe assembly in the black case 4 Create a shipping package with e Black case containing the digital thermometer and probe assembly e Decontamination certificate see Appendix D e Payment for shipping handling in one of the following forms Purchase order Company letterhead with the words verbal purchase ord
7. 12 Cap Strip Assorted Colors X X N8010834 8 Well Strips MicroAmp Fast 8 Tube Strip 0 1 mL X 4358293 MicroAmp 8 Tube Strip 0 2 mL X N8010580 MicroAmp 8 Tube Strip Assorted Colors 0 2 mL X N8010838 MicroAmp Optical 8 Tube Strip 0 2 mL X 4316567 MicroAmp 8 Cap Strip X X N8010535 X X N8011535 MicroAmp 8 Cap Strip Assorted Colors X X N8010835 MicroAmp Optical 8 Cap Strip X X 4323032 Single Tubes MicroAmp Fast Reaction Tube with Cap 0 1 mL X 4358297 Veriti Thermal Cycler User Guide Chapter B Disposables Table B 1 Disposables for the Veriti Thermal Cycler continued relouescnpeol Orme Oa ma Number MicroAmp Reaction Tube with Cap 0 2 mL X N8010540 X N8011540 MicroAmp Reaction Tube with Cap Assorted X N8010840 Colors 0 2 mL MicroAmp Reaction Tube with Cap Autoclaved X N8010612 0 2 mL MicroAmp Reaction Tube without Cap 0 2 mL X N8010533 X N8011533 MicroAmp Reaction Tube without Cap Assorted X N8010833 Colors 0 2 mL MicroAmp Optical Tube without Cap 0 2 mL X N8010933 Seals amp Covers MicroAmp Clear Adhesive Film X X 4306311 MicroAmp Optical Adhesive Film X X 4360954 X X 4311971 MicroAmp Optical Adhesive Film Kit X X 4313663 Reaction Trays MicroAmp 96 Well Tray for VeriFlex Blocks X X 4379983 MicroAmp 96 Well Tray Retainer Set for Veriti X 4381850 Systems
8. 14 saving 3 7 scrolling to left and right 3 18 Run Monitor screen 3 17 run parameters entering 3 15 viewing during arun 3 18 run report printing 3 21 saving 3 21 viewing most recent 3 20 S safety before operating the instrument xvi chemical xvi chemical waste xvii conventions xii electrical xviii guidelines xvii Veriti Thermal Cycler User Guide instrument operation xvi moving and lifting instrument xvi moving parts xviii moving lifting xvi physical hazard xviii standards xviii safety labels on instruments xiv safety standards xviii safety symbols on instruments xiii sample block Statistics 4 7 temperature when idle 2 14 sample wells cleaning 6 2 decontaminating 6 3 samples loading 3 4 unloading 3 21 Sanger sequencing C 3 C 4 saving run methods 3 7 run report 3 21 test results 4 9 4 10 4 11 serial port A 2 Settings Menu screen 1 7 shortcuts creating 2 15 SKIP button 3 18 stages adding 3 8 cycling 3 8 deleting 3 14 holding 3 8 standards EMC xviii safety xviii statistics instrument 4 7 steps adding 3 9 deleting 3 14 skipping during a run 3 18 STOP button 3 18 symbols safety xiii T Technical Support contacting viii Temperature Nonuniformity Test 4 11 temperature verification kit contents 4 9 decontaminating 4 11 instructions for shipping 1x recalibrating 4 11 user guide 4 9 Temperature Verification Test 4 10 temperature editing 3 10 Veriti Thermal Cycl
9. Ensure that the installation site is maintained under the following conditions Condition Acceptable Range Temperature 15 to 30 C 59 to 86 F Humidity 20 to 80 relative humidity noncondensing Avoid placing the instrument adjacent to heaters cooling ducts or in direct sunlight Fluctuations between day and night temperatures can cause system instability Place away from any equipment that vibrates such as a refrigerator or centrifuge The Veriti Thermal Cycler has a Pollution Degree rating of 2 It may be installed in an environment that has nonconductive pollutants only such as dust particles or wood chips Typical environments with a Pollution Degree II rating are laboratories and sales and commercial areas The safety of Veriti Thermal Cycler use was tested for altitudes up to 2000 ft e Scissors pocket knife or box cutter e Compressed air e Protective hardware as appropriate see below Applied Biosystems supports the use of the following devices to protect the Veriti System from damage resulting from electrical hazards and the resultant loss of data Before installing the system decide what additional hardware if any you want to install e Power line regulator 1 5 k VA e Surge protector line conditioner 10 kVA e Uninterruptible power supply 1 5 kVA Unpacking the Veriti System IMPORTANT Save the packing materials and box in case you need to ship the instrument to Applied Biosystems
10. Heating of Materials Canadian EMC This instrument has been tested to and complies with ICES 001 Issue 3 Industrial Standard Scientific and Medical Radio Frequency Generators European Safety Safety bs b on This instrument meets European requirements for safety Low Voltage Directive tanaards 73 23 EEC This instrument has been tested to and complies with standards C EN 61010 1 2001 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements EN 61010 2 010 Particular Requirements for Laboratory Equipment for the Heating of Materials EN 61010 2 081 Particular Requirements for Automatic and Semi Automatic Laboratory Equipment for Analysis and Other Purposes 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 Australian EMC This instrument has been tested to and complies with standard AS NZS 2064 Standards Limits and Methods Measurement of Electromagnetic Disturbance Characteristics of Industrial Scientific and Medical ISM Radio frequency Equipment Veriti Thermal Cycler User Guide X X Safety and EMC Compliance Information XX Veriti Thermal Cycler User Guide System Overview
11. Internet go to www appliedbiosystems com b Click Support then Software Downloads c Select Veriti Thermal Cycler in the list then click Updates amp Patches d Find the appropriate file If the version number 1s e The same as the current version from step 1 you do not need to upgrade the firmware e Different from the current version from step 1 follow the steps below to download and upgrade the firmware 3 Download the new firmware to a USB drive a Insert the USB drive into the USB port on the computer b Click the link in the Software column to download the file Select the USB drive as the location for the saved file c Remove the USB drive from the computer when the download is complete To upgrade the instrument with the new firmware 1 Follow the instructions in Backing Up Run Methods and Other Settings on page 1 13 to save your run methods and settings from the Veriti Thermal Cycler 2 Insert the USB drive with the new firmware in the USB port on the front of the Veriti Thermal Cycler Log in as a user with Administrator access In the Main Menu screen touch Settings Menu In the Settings Menu screen touch Admin Menu at es E i In the Admin Menu screen touch Upgrade Firmware The Firmware Upgrade screen opens n Firmware Upgrade x Please select source file for firmware upgrade Source File Current Version 0 20 0 4 39696 3 1 6S Insert a USB drive wit
12. Polymerase FS and the cycle sequencing reagents supplied with the BigDye Terminator kits Fast PCR Run Method Use this run method for use with the GeneAmp Fast PCR Master Mix For more information on how to convert your standard methods to Fast methods refer to the product literature for Fast PCR Master Mix available from www appliedbioystems com C 4 Veriti Thermal Cycler User Guide ChapterC Predefined Run Methods General PCR Run Method Use this run method for standard PCR use This method is set as the default run method for the Veriti Thermal Cycler LMS2 Run Method Use this run method for ABI PRISM Linkage Mapping Set Version 2 5 LMS2 thermal cycling Linkage Mapping Set Version 2 uses over 400 fluorescently labeled PCR primer pairs for analysis of select microsatellite loci from the G n thon human linkage map Veriti Thermal Cycler User Guide C 5 ChapterC Predefined Run Methods Time Release Run Method Use this run method for use with AmpliTaq Gold DNA Polymerase This method minimizes the pre PCR activation step and adds a minimum of 10 additional cycles allowing for slow activation of the enzyme during cycling This provides a simple method where polymerase activity increases more slowly as product accumulates improving specificity Touchdown PCR Run Method Use this run method if the optimal annealing temperature is not known This method incrementally decreases the annealing t
13. Power off the Veriti Thermal Cycler then remove the power cord 2 Allow the instrument to cool until the heated cover and sample block reach room temperature Cleaning the Clean the touchscreen with any commercially available LCD cleaning product Be Touchscreen careful not to scratch the screen Cleaning the If you use any cleaning or decontamination method except those recommended in Sample Wells the manual you risk damaging the equipment Clean the sample wells once a month or as needed Nem Always wear protective glasses and gloves when servicing the instrument Also make sure you disconnect the instrument from AC line power before you begin any service procedure AN or Vogue During instrument operation the temperature of the heated cover can be as high as 108 C and the temperature of the sample block can be as high as 100 C Before performing the procedure keep hands away until the heated cover and sample block reach room temperature To clean the sample wells 1 Follow the steps in Preparation above 2 Open the heated cover 3 Remove the sample tray from the sample block and set it aside 4 Use a cotton swab soaked in pure isopropanol to clean the sample wells thoroughly Make certain that the isopropanol has evaporated completely before reloading a sample tray 6 2 Veriti Thermal Cycler User Guide Chapter6 Maintenance Decontaminating Ifthe sample wells become contaminated with any biological agen
14. Reaction Tube with Cap 0 2 mL 96 Well Tray for VeriF lex Blocks MicroAmp Fast Reaction Tube with Cap 0 1 mL or MicroAmp Reaction Tube with Cap 0 2 mL MicroAmp 96 Well Tray for VeriFlex Blocks MicroAmp Splash Free 96 Well Base MicroAmp 8 Tube Strip 0 2 mL or MicroAmp Reaction Tube MicroAmp 8 Cap Strip and MicroAmp 96 Well Tray Retainer Set for MicroAmp 8 Cap Strip MicroAmp 96 Well without Cap 0 2 mL Veriti Systems Retainer MicroAmp 8 Tube Strip AES 0 2 mL L ERN or EE MicroAmp Reaction Tube E 9 without Cap 0 2 mL Ss P MicroAmp 96 Well Tray for Veriti Systems GR2003 MicroAmp Splash Free 96 Well Base Veriti Thermal Cycler User Guide 3 3 Chapter 3 Performing a Run Loading Samples into the Instrument Loading Tubes with Attached Caps Loading the Reaction Plate Loading Tubes Without Caps Placing the Sample Tray or Plate onto the Sample Block 3 4 This section describes how to load samples in e Tubes with attached caps e 96 well reaction plates e 96 well tray retainer assemblies There is no need to use mineral oil or glycerine in the sample block wells or as a vapor barrier over the PCR reaction mixture in the tubes The MicroAmp Reaction Tubes fit tightly in the wells and the heated cover exerts an even pressure on all tubes
15. Thermal Cycler User Guide 2 9 Chapter 2 Getting Started e Yes to restart the instrument so the changes take effect immediately You cannot restart the instrument if a run is in progress Follow the instructions in Adding Yourself as a User on page 2 10 after you restart Or e Noto have the changes take effect the next time the instrument is restarted using the power switch on the back of the instrument Adding Users Access Levels Fach user is assigned an access level that determines how he or she can interact with the instrument There are three access levels e Limited User Can perform runs view and print run methods and run tests Cannot edit or create run methods manage users or set instrument preferences e User Can perform runs create view edit delete save and print run methods and run tests Cannot manage users or set instrument preferences e Administrator Can access all instrument functions including setting security managing users and settings instrument preferences Adding Yourself If you set the instrument to require login you need to use the default administrator as a User user name and password until you create your own user To add yourself as a user 1 In the opening screen touch On then Log In Log In aa IGE PREBLE BEET 2 In the Log In screen touch a The User field then enter admin b The Password field then enter password c Log In 3 In the M
16. YES are the radioactivity survey results at or below local background level YES d NO O Attach the results to this form Or in the US only for service work excluding any transportation at levels designated to be clean or safe as stated in the Customer s regulatory approved Site Radioactive Materials License 3 Hazardous Chemicals Has this instrument been exposed to chemicals that are very toxic in quantities harmful to human contact carcinogenic mutagenic toxic for reproduction sensitizing and or which have not yet been fully tested YES O NO O If YES please identify the hazardous chemicals If YES please describe the procedures used to decontaminate the instrument Veriti Thermal Cycler User Guide ChapterD Certificate of Decontamination Applied Biosystems an Applera Corporation Business Examples of Instrument Decontamination Procedures 1 Biological Agents The following procedures are based on widely used industry standards for instrument or part hereinafter referred to as instrument decontamination but the Customer must assess the suitability of these methods for the biological agents concerned Some instruments may require decontamination by an outside service refer to your User Manual or Applied Biosystems Representative for further information Hazard Group 1 or 2 Instruments exposed to biological agents in Hazard Group 1 or 2 situated in a Biosafety Level Containment Level 1 or 2 laboratory or
17. eliminating condensation on the tubes Set the 96 well tray on a splash free 96 well base Place the reaction tubes in the tray Pipette the samples into the reaction tubes Cap the tubes eS eS See Placing the Sample Tray or Plate onto the Sample Block on page 3 4 _ Place the reaction plate on a splash free 96 well base 2 Pipette the samples into the sample wells 3 Cap the plates using the MicroAmp 8 Cap Strips or cover the plates the with MicroAmp Clear Adhesive Film 4 See Placing the Sample Tray or Plate onto the Sample Block on page 3 4 To load the 96 well tray retainer 1 Place the tray on the splash free 96 well base Load tubes onto the tray using either single tubes or the 8 tube strips Place the retainer over the tubes 2 3 4 Pipette the sample into the tubes 5 Cap the tubes using a MicroAmp 8 Cap Strip 6 See Placing the Sample Tray or Plate onto the Sample Block on page 3 4 The steps for placing the sample tray in the sample block are the same for e A sample tray retainer e A sample tray without a retainer e A 96 well plate 1 Lift the sample tray from the splash free 96 well base and place it in the sample block 2 Place the MicroAmp Tray or Plate onto the sample block so that well A1 is at the upper left corner of the tray as shown below Veriti Thermal Cycler User Guide Chapter 3 Performing a Run 00 HD 1 DODO O0 OO0O0000O O
18. exposed to any human source material or cell culture including clinical samples a Follow Universal Precautions and wear all applicable personal protective equipment Place the instrument in a well ventilated area b Apply a freshly made solution of 1 10 v v dilution of 5 25 sodium hypochlorite e g Clorox bleach with water to accessible product surfaces A spray dispenser may help to ensure complete coverage c Keep surfaces wet for at least 15 minutes then wipe dry d Repeat steps b and c e Clean all decontaminated surfaces with water to remove residual bleach and wipe dry If an alternative to 1 10 v v dilution of bleach is used for instrument decontamination please provide details in written form and attached to the Certificate of Instrument Decontamination Hazard Group 3 or 4 Instruments situated in Biosafety Level Containment Level 3 or 4 laboratories must be decontaminated by the customer using an internationally approved sterilization procedure The customer must then move the instrument to either a Containment Level 1 or 2 laboratory for service Applied Biosystems employees are not permitted to enter Biosafety Level Containment Level 3 or 4 laboratories It may not be possible for Applied Biosystems to service or transport these instruments 2 Radioactive Materials Apply an industry standard radioactivity decontaminant e g Radiacwash Rad Con or equivalent to the instrument and wipe surfaces as direc
19. or more run methods In the list of run methods touch each run method to Select it then touch Copy See Copying a Run Method on page 1 11 Print a run method In the list of run methods touch a run method to Select it then touch Print see Printing a Run Method on page 1 12 Delete one or more run methods In the list of methods touch each run method to Select it then touch Delete see Deleting a Run Method on page 1 12 Designate a run method as the See Designating a Run Method as the Default on default page 1 12 Back up run methods See Backing Up Run Methods and Other Settings on page 1 13 Restore run methods that you See Restoring Run Methods and Other Settings on previously backed up page 1 14 Copying a Run Note If your instrument requires login you must have User or Administrator level Method permissions to copy a run method To copy a run method 1 Log in as a user with User or Administrator access 2 Inthe Browse Run Methods screen find the run method or methods you want to COpy 3 Touch each run method to select it then touch Copy 4 In the Save Method screen a If you are copying one method touch Name then rename the method and or touch Folder to save the run method to a different folder or If you are copying more than one method touch Folder to save the run methods to a different folder b As needed touch Reaction Volume Cover Temper
20. x 30 10 60 3 When you finish touch Done to return to the Tools Menu screen Calibrating the Touchscreen Use this test to verity that all pixels on the touchscreen are visible and respond to touch 1 In the Main Menu screen touch Tools Menu 2 In the Tools Menu screen touch Calibrate Touch Screen Veriti Thermal Cycler User Guide 4 7 Chapter 4 Utilities 3 Follow the instructions on the screen touching the center of the sign at each location where it appears on the screen PLEASE TOUCH THE CROSSHAIR TO CALIBRATE 4 Atthe end of the test the following screen appears Touch Next to complete the calibration and view the Tools Menu screen Touch the yellow button Next on the bottom right If there is no response the touchscreen has not been calibrated accurately enough Please touch this button to redo the calibration If this button cannot be activated you need to restart the system Running the Cycle Performance Test Use this test to verify that the sample block is heating and cooling properly and that the PCR cycling function operates properly Required The appropriate sample plate for your instrument Materials 4 8 e Veriti 96 Well Fast Thermal Cycler MicroAmp Fast Optical 96 Well Reaction Plate with Barcode PN 4346906 Veriti Thermal Cycler User Guide Chapter 4 Utilities e Veriti 96 Well Thermal Cycler MicroAmp Optical 96 Well Reaction Plate PN N8010560 Procedure Th
21. 2 Veriti Thermal Cycler User Guide Chapter1 System Overview Using the Touchscreen You interact with the Veriti Thermal Cycler using a touchscreen Table 1 describes several buttons common to many of the touchscreens Table 1 Buttons in the Veriti Thermal Cycler touchscreen Button Function Returns to the Main Menu screen B B Returns to the previous screen When a run is in progress displays the Status Report to view any errors that occurred during the run When a run is in progress displays the Run Monitor screen to view the run g E 4 i Scrolls up and down through a list of items Displays the run method folders Indicates that a USB drive is connected to the instrument s USB port o ai 2 Veriti Thermal Cycler User Guide Opens the Help system 1 3 Chapter1 System Overview Entering Text When you touch a field that requires the input of text the text editor opens Figure 1 2 Figure 1 2 The Veriti Thermal Cycler text editor To Enter a lowercase letter Touch A letter button Enter an uppercase letter a Caps then the letter s d When you are done touch Caps again Enter punctuation or other symbols Symbols then the symbol s When you are done touch Symbols again Remove the contents of the entire field Delete the last letter Close the editor 1 4 Veriti The
22. 85 with 0 2 mL 0 2 mL Temperature Verification Kit 437 669 Sample wells For More See the Temperature Verification Kit 0 1 mL and 0 2 mL VeriFlex 96 Well Sample Information Blocks User Guide PN 4376864 Veriti Thermal Cycler User Guide 4 9 Chapter 4 Utilities Running the Heated Cover Verification Required Materials Procedure Use this test to verify that the heated cover is within 3 C of the 105 C set point The appropriate Temperature Verification Kit for your Veriti Thermal Cycler model see table above This test takes 10 to 15 minutes to complete AS erence PHYSICAL INJURY HAZARD Hot Surface Use care when working around the heated cover and sample block to avoid being burned 1 In the Main Menu screen touch Tools Menu 2 Inthe Tools Menu screen touch Run Heated Cover Verification 3 To save the test results to the USB drive insert the drive now Otherwise the test results are not saved but are displayed when the test is complete 4 Follow the instructions on the screen to perform the test The results are saved to the file heatedCover txt if the USB drive is present 5 If the test fails repeat the procedure Make sure that e The probe plate is in the correct location Probe should be in well A5 during this test e Cables are securely seated in the digital thermometer and in the instrument e The heated cover is closed 6 If the test fails again contact Applied
23. Biosystems Technical Support Running the Temperature Verification 4 10 Required Materials Procedure Use this test to verify that the average temperature for the sample block is within 0 25 C of the set point temperature The appropriate Temperature Verification Kit for your Veriti Thermal Cycler model see table above This test takes 25 to 30 minutes to complete but you can cancel before it is complete ANETTE PHYSICAL INJURY HAZARD Hot Surface Use care when working around the heated cover and sample block to avoid being burned 1 In the Main Menu screen touch Tools Menu 2 In the Tools Menu screen touch Run Temperature Verification 3 To save the test results to the USB drive insert the drive now Otherwise the test results are not saved but are displayed when the test is complete 4 Follow the instructions on the screen to perform the test The results are saved to the file bcalevents txt if the USB drive is present 5 If the test fails repeat the procedure Make sure that Veriti Thermal Cycler User Guide Chapter 4 Utilities e The probe is placed in the correct wells during the test e A drop of mineral oil is in each of the test wells e You save or print the results 6 If the test fails again contact Applied Biosystems Technical Support Running the Temperature Nonuniformity Test Use this test to verify that the sample well temperatures are within the threshold temperature ran
24. OD OOOO VOU ODIO QOD OOOO DODO 26 0 6 e986 1e OOOO0000 6163S 216 6 1016 OO 6 6 618 6 YOOQOQOOO0O CeO ee OOOO UU See ee eee s 6 6 222 tee ed Cie 2 eee Se 3 5 MicroAmp Optical 96 Well Reaction Plate 0 2 mL IMPORTANT Do not place the base in the sample block MicroAmp Fast Optical 96 Well Reaction Plate 0 1 mL 3 Close the heated cover Veriti Thermal Cycler User Guide Chapter 3 Performing a Run Creating a New Run Method 1 In the Main Menu screen touch Browse New Methods 2 Inthe Browse Run Methods screen touch New The default run method is displayed in the Edit Run Method screen For instructions on setting the default run method see Designating a Run Method as the Default on page 1 12 Edit Run Method LMS2 amp sages Run Add Delete Options Save Touch a stage or a step to insert a stage or step Touch a time or temperature to edit it Touch Options to create AutoDelta or VeriFlex steps to show ramp rates or to add a pause 3 Edit the default run method as needed e Insert a stage see Adding a Stage on page 3 8 e Insert a step see Adding a Step on page 3 9 e Add a step to program different temperatures on the VeriFlex Block see Creating a Step for the VeriFlex Block on page 3 11 e Add an AutoDelta step see Creating an AutoDelta Step on page 3 12 e Add a pause see Adding a P
25. Options menu touch VeriF lex step The Create a VeriFlex Step screen opens Edit Run Method mu yd EJ EJ EJ EJ EJ 3 Touch a temperature field then enter the desired temperature Temperatures for neighboring zones can be the same but 1f they are not the same they must be at least 0 1 C apart but no more than 5 0 C apart The maximum temperature is 99 9 C Veriti Thermal Cycler User Guide 3 11 Chapter 3 Performing a Run 4 Repeat step 3 for each of the six zones then touch Done Note To set each field to the same temperature touch the desired temperature field then touch Apply Selected to All 5 Depending on your instrument configuration enter either a duration or a ramp rate e Touch Time enter the duration in minutes and seconds then touch Done or e Touch Ramp Rate enter the ramp rate as a percentage value then touch Done Creating an An AutoDelta step allows you to increase or decrease the temperature and or change AutoDelta Step the duration of the cycle during a cycling stage One use for an AutoDelta step is for touchdown PCR a method in which the earliest cycles have a high annealing temperature followed by cycles where the annealing temperature decreases slightly for each cycle Touchdown PCR increases the specificity of the PCR products The high initial temperature favors more specific annealing between the primer and the template Because these fragments are further amplified dur
26. Rhee SEE Chass eet Gi ge jects EEE A a ners erence ere Veriti Thermal Cycler User Guide A 1 ChapterA Instrument Specifications System Specifications Physical Dimensions and Electrical Specifications Power and Communication Connections A 2 Physical Dimensions Width 23 7 cm 9 3 in Height 24 5 cm 9 6 in Depth 48 5 cm 19 1 in Weight 10 2 kg 22 5 Ibs Electrical Input Voltage 100 to 240 VAC 50 60 Hz Max Power 10 A AC Line Voltage Tolerances 100 120 220 230 10 240 VAC 6 10 50 60 Hz 1 Table 1 Power and Communication Port Description 800 VA power cable 10 100 fast Ethernet port for a network connection v USB v1 0 port for a connection to an external USB drive RS232 serial communication port for connecting the probe for the Temperature IOIOI Verification Kit Figure A 1 Connections for power and communications on the Veriti Thermal Cycler hh ah ah a ah ah a rah a 0 020 of at ater nla af ee 080 998 ate o n o o Oa e a a fat ater nn nt eve 0 a e8 eee ete eX oe a Veriti Thermal Cycler User Guide Chapter A Instrument Specifications Sample e Sample temperature range 4 to 99 9 C Temperature e Temperature calibration accuracy Traceable to National Institute of Standards Range and Technology NIST Touchscreen 640 x 480 pixel LCD color display with full VGA resolution Specification
27. S Biosystems Veriti 96 Well Thermal Cycler colinux 2007 02 14 10 24 PM 2 1 Touch Power in the lower left corner of the screen to display the Main Menu screen 2 6 Veriti Thermal Cycler User Guide Chapter 2 Getting Started Setting Up the Veriti Thermal Cycler Recommended Instrument Settings Before performing a run be sure to set the following instrument settings e Instrument IP address page 2 7 e Instrument name page 2 8 e Current date and time page 2 8 e Printer information if you want to print run methods or the run report page 2 8 Optionally you can also change the settings for e User accounts and security page 2 9 e Idle state temperatures for the cover and the sample block page 2 14 e Durations for pauses and stand by page 2 15 e Shortcuts to other options displayed on the Main Menu page 2 15 Setting the IP Note If your instrument is not on a network you do not need to set the IP address Address The IP address can be assigned dynamically by a computer on the network using DHCP or set manually by entering a number in the IP Address screen Note Ask your system administrator if the IP address is assigned statically or dynamically For static addresses you need to know the IP address for the instrument the subnet mask and the default gateway 1 In the Main Menu screen touch Settings Menu 2 In the Settings Menu screen touch Admin Menu 3 Inthe Admin Me
28. The MSDS for any chemical supplied by Applied Biosystems is available to you free MSDSs_ 24 hours a day To obtain MSDSs 1 Go to https docs appliedbiosystems com msdssearch html 2 In the Search field of the MSDS Search page a Type in the chemical name part number or other information that you expect to appear in the MSDS of interest b Select the language of your choice c Click Search 3 To view download or print the document of interest a Right click the document title b Select e Open To view the document e Save Target As To download a PDF version of the document to a destination that you choose e Print Target To print the document 4 To have a copy of an MSDS sent by fax or e mail in the Search Results page a Select Fax or Email below the document title b Click RETRIEVE DOCUMENTS at the end of the document list c Enter the required information d Click View Deliver Selected Documents Now Note For the MSDSs of chemicals not distributed by Applied Biosystems contact the chemical manufacturer Chemical Safety To minimize the hazards of chemicals Guidelines e 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 See About MSDSs on page xvi e Minimize contact with chemicals Wear appropriate personal protective equipment when handling chemicals for exampl
29. This chapter covers Introducing the Veriti Thermal Cycler 0 00000 ccc e eee eee een 1 2 Re Te e s ee a oe 0 ee Oe ea oe eee ee eee ee 1 3 ho RO a o EEREN os a 440 ek EEEE es E 1 6 About NS 5 6 oe ee od Oe oo ESEE 1 8 PE op eet ee eae an ck E obbneehOseb04bG bE cawewnaan sees 1 15 Veriti Thermal Cycler User Guide 1 1 Chapter1 System Overview Introducing the Veriti Thermal Cycler Aboutthe There are two models of the Veriti Thermal Cycler Instrument Veriti Fast 96 Well Thermal Cycler PN 4375593 with 0 1 mL sample wells e Veriti 96 Well Thermal Cycler PN 4375785 with 0 2 mL sample wells The Veriti Thermal Cycler features the VeriFlex Sample Block with six independently regulated thermal areas to aid in designing a primer set and run method for optimal PCR conditions You control the Veriti Thermal Cycler using the touchscreen display and easy to use interface Up to twelve Veriti Thermal Cyclers can be connected in a satellite like format through a network switch With this connection you can transmit run methods from one Veriti thermal cycler to another and start multiple thermal cyclers at once This user guide provides information on how to maximize the capabilities of your new Veriti Thermal Cycler Figure 1 1 The Applied Biosystems Veriti Thermal Cycler Detailed specifications for the Veriti Thermal Cycler are found in Appendix A Instrument Specifications 1
30. Time Outs 2 In the Settings Menu screen touch Set Time outs n Set Time Outs f Default Standby Time Out 00 00 00 hh mm ss The standby time out is the duration the instrument is idle before it goes to standby mode The minimum time is 1 minute Set this value to 00 00 to disable standby mode Default Pause Duration 00 00 10 hh mm ss The pause duration is the duration of the instrument pause after you touch Pause during a run Touch the respective fields to edit the time out settings 2 3 Inthe Set Time Outs screen touch Time out then enter the duration e Default Standby Time Out sets the duration that the instrument is idle before the touchscreen is turned off Enter a duration of 00 00 if you do not want the instrument to turn off the touchscreen e Default Pause Duration sets the duration the instrument pauses after you touch Pause during a run 4 Touch Done then OK to save your changes and return to the Settings Menu screen Configuring Main You can add buttons to the Main Menu screen that allow you to go directly to various Menu Shortcuts instrument functions When login is required each user can configure his or her own shortcut buttons otherwise the shortcut buttons are displayed for all instrument users 1 In the Main Menu screen touch e Any button labeled Shortcut X where X is a number or e Settings Menu then Configure Shortcuts Veriti Thermal Cycler User Guide 2 15 Chap
31. Use this screen to access various tools and instrument tests Screen E 2007 02 14 8 22 PM User gregor 2 Figure 1 7 The Tools Menu screen available to all users For more information about the functions on the Tools Menu see Chapter 4 Utilities About Run Methods What Is a Run A run method is a set of instructions that specifies how the instrument should heat Method and cool your samples Run methods are stored in the instrument firmware Predefined The Veriti Thermal Cycler firmware has ten predefined run methods Methods ampliCycle Seq Run Method e AmpliTaq Gold DNA Polymerase Run Method e BigDye Standard Run Method e BigDye Fast Run Method e Fast PCR Run Method e General PCR Run Method e LMS2 Run Method e Time Release Run Method e Touchdown PCR Run Method e XL PCR Run Method Each method is stored in the Shared folder You can edit copy and run these predefined methods as you would any other run method but you cannot delete them For details on these methods see Appendix C Predefined Run Methods 1 8 Veriti Thermal Cycler User Guide Chapter1 System Overview Viewing a Run To view a run method Method 1 In the Browse Run Methods screen touch a run method to select it then touch View Edit The run method is displayed Edit Run Method LMS2 4 Delete Options Touch a stage or a step to insert a stage or step Touch atime or temperature to edit
32. a Be Oh Rae wee 3 15 MONONA ERUN a 2 svuck tine mrna esate tate ead ak bt Ad da ee 3 17 Viewing and Printing the Run Report ce ee 3 20 Removing the Samples from the Instrument 0 0 0 eee eee 3 21 Chapter4 Utilities Using GeneAmp PCR System 9700 Run Methods ccc a 4 2 Upgrading System Firmware nanasa ccc et eee ete nees 4 4 Calculating Melting Temperatures 0 0 0 ccc ee ees 4 6 Viewing Instrument StatisticS 0 ee ee eee teens 4 7 Calibrating the Touchscreen 0c cee eee eee eens 4 7 Running the Cycle Performance Test 0c ccc eee eens 4 8 Tests Using the Temperature Verification Kit anaa aaa ee eee 4 9 Running the Heated Cover Verification 0 ccc ee 4 10 Running the Temperature Verification nanana aeaa 4 10 Running the Temperature Nonuniformity Test 00 eee eee 4 11 INK RECGIDTAUION 4 5 2058 og tte es ads ole awh de eens Be eae Gok es 4 11 Chapter5 Troubleshooting TOUDICSHOOUING i sista tectea dh ranima won ples aoe eed hai Aiea o ee e wg ae acne 5 2 Returning an Instrument for Service nuanua aaaea ea 5 2 Chapter6 Maintenance Scheduled Maintenance 0 eee eens 6 2 As Needed Maintenance cc eee een nena 6 2 Cleaning the Instrument 0 0c eee ee tee teens 6 2 iv Veriti Thermal Cycler User Guide REDIACING FUSES ard owes the ee eh eee ee erga oY Peet Se GI si N ohh chee E EE E Reda ar ae wean ae eee ae ee ee Appendix A In
33. activity use a commercially available decontaminant to remove the contamination If the block cannot be decontaminated the instrument cannot be returned to Applied Biosystems for service 3 Complete and sign a copy of the Certificate of Instrument Decontamination see Appendix D 4 Fax the Certificate of Instrument Decontamination to the customer care center 5 Pack the instrument in the provided packaging without any accessories or power cords Include a hard copy of the Certificate of Instrument Decontamination in the box Note Repairs for instruments without the Certificate of Instrument Decontamination are delayed 6 Affix the provided postage to the box then ship the instrument to the designated facility The repair process requires 2 to 3 weeks Veriti Thermal Cycler User Guide 5 3 Chapter5 Troubleshooting 5 4 Veriti Thermal Cycler User Guide Maintenance This chapter covers Scheduled Maintenance As Needed Maintenance 0c cece eee eee teen eee eee enna Parts List Veriti Thermal Cycler User Guide 6 1 Chapter6 Maintenance Scheduled Maintenance Run the following tests annually e Heated Cover Verification page 4 10 e Temperature Verification page 4 10 e Cycle Performance Test page 4 11 As Needed Maintenance Tests Run the Temperature Nonuniformity Test see page 4 11 Cleaning the Instrument Preparation Before cleaning the instrument 1
34. ain Menu screen touch Settings Menu 4 In the Settings Menu screen touch Admin Menu 2 10 Veriti Thermal Cycler User Guide Chapter 2 Getting Started 5 Follow the instructions in Adding Users to add yourself as a user Make sure you make yourself an Administrator Adding Users To add a user 1 Log in as a user with Administrator access 2 In the Main Menu screen touch Settings Menu 3 In the Settings Menu screen touch Admin Menu 4 Inthe Admin Menu screen touch Manage Users The Manage Users screen opens fi Manage Users f E Co oe admin 2006 12 07 Administrator myuser 2006 12 07 User myadmin 2006 12 07 Administrator ae Add User Edit User Delete User Touch a user name to select it then touch any of the buttons to perform an action Touch a column title to sort the table 5 Touch Add User The Create New User Account screen opens Create New User Account x d User Name PO Password PO Re enter Password PO Phone PO Email D Permission Level Last Update All information with is compulsory Please fill in the information accordingly 6 Enter information for the new user The required fields are User Name Password Re enter Password and Permission Level a User Name must be between 5 and 15 characters with no spaces Veriti Thermal Cycler User Guide 2 11 Chapter 2 Getting Started b Password must be at least 1 character with no spaces unless y
35. atible Instrumenti ID_001 Ready Disallowed lab1 ID_002 Running Ready Instrument2 ID_003 Ready Ready Number of hubs selected 2 ka Select the instruments for the run To run the method on the current instrument touch the button in the upper left corner 8 In the Select Instrument screen a Touch the check box corresponding to each instrument on which you want to perform the run Only instruments that are compatible with the run method are available Incompatible instruments are indicated by R If you want to perform the run on this instrument be sure to touch the check box in the upper left corner of the screen b Touch Start Run Now then OK The run method is sent to each selected instrument and if no problems are encountered the run begins After the run begins you must interact with any remote instruments directly if you want to make changes to the run method pause or stop the run When the runs are complete the Run Reports are displayed Veriti Thermal Cycler User Guide Chapter 3 Performing a Run Monitoring a Run The Run Monitor You can follow the status of a run using the Run Monitor screen below Screen a 95 0 C Method LMS2 Owner gregor C Stage 2 Stage 3 x 10 x 20 D 83 pias A 66 0 15 F Pause Run View Method Display Method SKIP STOP Information Time 5 aroa OESR A Table 4 Elements of the Run Monitor screen pocaron Element Description
36. ature and Notes to edit the values You can change any of these values when you perform a run with this run method c Touch Save amp Exit then OK Veriti Thermal Cycler User Guide 1 11 Chapter1 System Overview Printing a Run Deleting a Run Method Designating a Run Method as the Default Note Before you print a run method be sure your instrument is connected to a Method printer See Connecting to a Network Printer on page 2 5 l 2 In the Browse Run Methods screen locate the run method you want to print Touch the run method to select it then touch Print Note If your instrument requires log in you must have User or Administrator level permissions to delete a run method To delete a run method l Log in as a user with User or Administrator access In the Browse Run Methods screen find the run method you want to delete Touch the run method to select it then touch Delete 2 3 4 5 In the dialog box that opens verify the deletion Touch Yes in the message box The run method is deleted The run method that is designated as the default method is used as the starting point for all new methods The Veriti Thermal Cycler uses the General PCR run method shown on page C 5 as the default unless you change to another method IMPORTANT If your instrument requires login you must have User or Administrator level permissions to set the default run method Only a run met
37. ault values for the Veriti Thermal Cycler See Option Default Value Page Idle temperatures for the cover and the sample Cover 105 C 2 14 Doc Sample block 25 C Durations for pause and standby time outs Pause 10 sec 2 15 Standby 1 min 30 sec Shortcuts to appear on the Main Menu screen None 2 15 Setting Idle 1 In the Main Menu screen touch Settings Menu Temperatures for the Block and Cover 2 In the Settings Menu screen touch Set Idle Temperatures i Idle State Temperatures Cover Idle Temperature 105 0 degrees C y Enabled S Disabled Block Idle Temperature 50 0 degrees C in Enabled y Disabled Idle state temperatures are the temperatures which the block or heated cover will go to when the instrument is idle Touch the respective fields to edit the idle state temperatures 3 In the Idle State Temperatures screen to set the temperatures for the sample block and the cover touch 2 14 Veriti Thermal Cycler User Guide Chapter 2 Getting Started a Enabled to turn the option on If this is disabled the temperature for the cover and or block are not maintained by the instrument and eventually come to room temperature b The Temperature field then enter the temperature The temperature for the cover must be between 4 and 99 C 4 Touch Done to save your changes and return to the Settings Menu screen Setting 1 Inthe Main Menu screen touch Settings Menu
38. ause on page 3 14 e Delete a step or stage see Deleting a Stage or Step on page 3 14 3 6 Veriti Thermal Cycler User Guide Chapter 3 Performing a Run 4 Touch Save amp Exit to display the Save Run Method screen Save Run Method E Run Method Lms2 Folder shared v Reaction Yolume hio Cover Temperature j105 0 Notes This method used for gene expression a ssay Enter a name reaction volume and choose a folder for this run method Notes can also be added When you are finished touch Save amp Exit 5 Touch Run Method to enter the name of the run method Names can be up to 48 characters with no spaces 6 Touch Folder to select a folder in which to save the run method e To save the run method so that all users have access to it touch Shared e To create a new folder for the run method touch New Folder at the bottom of the list enter a name of up to 12 characters no spaces for the new folder then touch Done e To save the run method to the USB drive touch USB available only when a USB drive is inserted in the instrument 7 Touch Reaction Volume to enter the reaction volume You can change this volume when you perform a run with this run method 8 Touch Cover Temperature to enter the cover temperature You can change this temperature when you perform a run with this run method 9 Touch Notes then enter any notes for the method 10 Touch Save amp Exit when
39. be edited and or deleted If you need to re create a run method the details are shown below AmpliCycle Seq Run Method Use this run method to achieve clean sequence ladders from femtomole quantities of template The cycle sequencing process and the benefits of AmpliTag DNA Polymerase CS are described in the product insert for the AmpliCycle Sequencing Kit PN N8080175 C 2 Veriti Thermal Cycler User Guide ChapterC Predefined Run Methods AmpliTaq Gold DNA Polymerase Run Method Use this run method for hot start PCR in place of labor intensive methods such as manual hot start or wax bead mediated hot start techniques The hot start technique helps to minimize the formation of primer dimers or nonspecific products thereby increasing specificity and sensitivity of PCR This run method specifies a pre PCR heat step for activation of AmpliTaq Gold DNA Polymerase BigDye Fast Run Method Use this run method for cycle sequencing of dideoxy Sanger terminator sequencing using ABI PRISM BigDye Terminator Cycle Sequence Ready Reaction Kits Veriti Thermal Cycler User Guide C 3 ChapterC Predefined Run Methods BigDye Standard Run Method Use this run method which consists of cycle sequencing parameters for dideoxy Sanger terminator sequencing with ABI PRISM BigDye Terminator Cycle Sequencing Ready Reaction Kits The pre coded conditions in the BigDye method are optimized for AmpliTaq DNA
40. cal municipal waste ordinances for ny proper disposal provisions to reduce the environmental WEEE l impact of waste electrical and electronic equipment European Union customers Call your local Applied Biosystems Customer Service office for equipment pick up and recycling See http www appliedbiosystems com for a list of customer Service offices in the European Union Safety Labels on Instruments XIV 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 CAUTION Hazardous waste Refer to MSDS s and local regulations for handling and disposal ATTENTION D chets dangereux Lire les fiches techniques de suret de mat riels et la r gulation locale associ es a la manipulation et l limination des d chets WARNING Hot lamp AVERTISSEMENT Lampe br lante Veriti Thermal Cycler User Guide Safety and EMC Compliance Information English Francais WARNING Hot Replace lamp with an Applied Biosystems lamp AVERTISSEMENT Composants brilants Remplacer la lampe par une lampe Applied Bios
41. e safety glasses gloves or protective clothing For additional safety guidelines consult the MSDS e Minimize the inhalation of chemicals Do not leave chemical containers open Use only with adequate ventilation for example fume hood For additional safety guidelines consult the MSDS e Check regularly for chemical leaks or spills If a leak or spill occurs follow the manufacturer s cleanup procedures as recommended in the MSDS e Comply with all local state provincial or national laws and regulations related to chemical storage handling and disposal Chemical Waste Safety Chemical Waste N UON HAZARDOUS WASTE Refer to Material Safety Data Sheets Hazard and local regulations for handling and disposal Veriti Thermal Cycler User Guide XVII Safety and EMC Compliance Information Electrical Safety JN aleis ELECTRICAL SHOCK HAZARD Severe electrical shock can result from operating the Veriti Thermal Cycler without its instrument panels in place Do not remove instrument panels High voltage contacts are exposed when instrument panels are removed from the instrument Fuses ASN Ge FIRE 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 gt VUONO FIRE HAZARD For continued protection against the risk of f
42. e same type and rating as those currently in the instrument JN Pieiaad ELECTRICAL HAZARD To protect yourself against shock hazards use a properly wired three terminal outlet Do not use an adapter to a two terminal outlet since this does not provide positive ground protection Instrument Configuration Main Fuse Rating Part Number All configurations 10 A 4377690 Acceptable AC line voltage tolerances 100 120 220 230 10 240 VAC 6 10 50 60 Hz 1 Required e Two 10 A Type M 250 V 5 x 20 mm fuses Materials e Fine flat tip screwdriver Procedure 1 Turn off the instrument and disconnect the power cord from the back of the instrument N TITI 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 electrical shock disconnect the power supply to the instrument unplug the power cord and wait at least 1 minute before working on the instrument 6 4 Veriti Thermal Cycler User Guide Chapter6 Maintenance The fuses are in the power entry module 0020202020202020 Onnan nla a aLaaa ane CLA D D D I D D e a i a i Ga G Onana na Aan An Dn Nn Nnn 20 0 0 0 0 0 0 0 0 0 eoeaqeoeaeeoe0eeee o E Electrical Rating Fuse Rating 0 0 0 08 ooto o o abata ata nih S S O O pree i evevevete En O otote o O 0000ta amp KS Power entry mod
43. eenie nra ta a ire Cait ater Re ee eS ae ek eee oe ee 1 6 ADOUERUN MCINOGS rimi tnrane fate See e E AENA A GEENE Hee 1 8 ADOULCFOIJOS ateni a a het a a e ED 1 15 Getting Started Installing the Veriti Thermal Cycler 2 0 aaa eee ees 2 2 BEE YOR Slat gine beta dena sun te tet aaueha tai eeueee rae eas 2 2 Environmental Requirements 00 e eee eee eee teens 2 3 PY QV Tih garrenen n seta es Sos a ed aks Se ae aoa ae A 2 3 Unpacking the Venti System 2 lt s ecseaduwesdchetardeaweereeues 2 3 Setting Up the Veriti System 0 eee 2 4 Connecting to a Network Printer auaa aaaea eae 2 5 Connecting Together Multiple Instruments 0 0 eee ee 2 5 Veriti Thermal Cycler User Guide POWCHNOQV OM s ia b capueg titrda a a eens toe aon y dea ea ag ed 2 6 Setting Up the Veriti Thermal Cycler nannaa ees 2 7 Recommended Instrument SettingS 00 ees 2 7 Setting Up Instrument Security and User Accounts 0000 eee 2 9 PONG IS CUS rasa sec ake rset ra Sen tice lh ed Sek We ole amp Vea eae a 2 10 SCHING OUNGr ODUONS deintaoo Gone eid besarte ead OR eens wah atwe aes 2 14 Chapter3 Performing a Run Selecting Disposables 0 cc teen eee ens 3 2 Loading Samples into the Instrument 0 ce ee ee tees 3 4 Creating a New RUN MENO cirar pena woe os els ie BE ed Nd 3 6 EqiUnG Detalls a 20t0245 saseehe eee wad oe eue eee eee nae ee ee pee aes 3 8 Pemon a RUN esrar ieri ot art oak ee aaace eee al
44. emperature in early cycles to maximize the yield of specific products C 6 Veriti Thermal Cycler User Guide ChapterC Predefined Run Methods XL PCR Run Method Use this run method for amplification of 5 to 40 kb PCR products using r7th DNA Polymerase XL and unique reaction conditions 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 allowing more introns to be spanned You can use XL PCR to amplify the control target a 20 8 kb product from Lambda DNA supplied in the kit Veriti Thermal Cycler User Guide C 7 ChapterC Predefined Run Methods C 8 Veriti Thermal Cycler User Guide Certificate of Decontamination D This appendix contains the certificate of instrument decontamination required when returning either the Veriti Thermal Cycler or the 0 1 mL or 0 2 mL Temperature Verification Kit for service Veriti Thermal Cycler User Guide D 1 Chapter D Certificate of Decontamination D 2 Applied Biosystems an Applera Corporation Business Certificate of Instrument Decontamination This document must be completed in full and signed by the Customer a before returning an instrument or part hereinafter referred to as instrument to an Applied Biosystems Repair Center and b prior to any on site service to be performed by Applied Biosystems 1 Refer to page 2 for special instructions conce
45. en OK to save your changes and return to the Admin Menu screen Setting Up Instrument Security and User Accounts By default the Veriti Thermal Cycler has all security settings disabled allowing anyone to use the instrument and or change instrument settings To change the security settings for the instrument l 2 3 4 If login is required log in as a user with Administrator access In the Main Menu screen touch Settings Menu In the Settings Menu screen touch Admin Menu In the Admin Menu screen touch Security C Yes Require Login Enable Guest Account Yes Allow Empty Password Yes Touch the buttons to enable or disable login and or a guest account to allow disallow user accounts with no password then touch Done In the Security screen to require each user to log in when using the instrument touch Yes next to Require Login To allow anyone to log in as a guest touch Yes next to Enable Guest Account A guest user can perform runs view and print run methods and run tests Also for run methods stored on a USB drive a guest can create view edit delete save and print run methods A guest user cannot manage users or set instrument preferences To allow new user accounts with empty passwords touch Yes next to Allow Empty Password Note If existing user accounts have passwords those passwords are required to log in when this option is Yes Touch Done then Veriti
46. er Visa MasterCard credit card information e Your address and contact information Billing address Return shipping address Name and phone number of a contact person most familiar with the thermometer Note If payment is not included with the package Alpha Technics bills you for 150 00 plus a 10 administrative fee The total for the purchase order is then 165 00 5 Send the package freight prepaid to Alpha Technics at the address in step 1 Veriti Thermal Cycler User Guide Ix Preface X Veriti Thermal Cycler User Guide Safety and EMC Compliance Information This section covers Safety Conventions Used in This Document 0 0 0 eee X Symbols on nstruments cosse sarees aa eet a e ee ee xi Safety Labels on Instruments 4 24 cy od odievies raian eek E e a 4448 xii General Instument Salety lt 4 636 9404 bee eda een ea eea XIV Chemical SATCU a ete sa argh keera Ries Ge SEH Go a bce a Pee eee gee Oe BS XV Chemical Waste SAL Cty waked Seis A cided Aries Sade d dria ty e BR Ramen a ee A xvi PICCihiCal SeN re ea woe Sa E a N xviii PhysicakH azard SA eN eeur a a s a Bee e ees xviii Biological Hazard Safe 52 os esa oo eet ce ee a oe Nad a XIX Safety and Electromagnetic Compatibility EMC Standards xxii Veriti Thermal Cycler User Guide xi Safety and EMC Compliance Information Safety Conventions Used in This Document xii Safety Alert Four safety alert words ap
47. er User Guide Index test results files bcalevents txt 4 10 CyclePEvents txt 4 9 heatedCover txt 4 10 tnuEvents txt 4 11 test results saving 4 9 4 10 4 11 tests Cycle Performance 4 8 Heated Cover Verification 4 10 Temperature Nonuniformity 4 11 Temperature Verification 4 10 text conventions vii time editing 3 10 elapsed for run 3 18 remaining for run 3 18 setting current 2 8 Time Release run method C 6 Tools Menu screen 1 8 total cycles for block 4 7 total degrees for block 4 7 Touchdown PCR description 3 12 predefined run method C 6 touchscreen calibrating 4 7 cleaning 6 2 training information on viii TVK See temperature verification kit 4 9 U upgrading firmware 4 4 USB port A 2 user attention words described vii users access levels 2 10 adding 2 10 changing 2 12 default administrator user name and password 2 10 deleting 2 13 V version number for firmware 4 4 W WARNING description xii X XL PCR run method C 7 E 3 Index E 4 Veriti Thermal Cycler User Guide 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 Applera is committed to providing the world s leading technolo
48. for service 1 To unpack the Veriti System a Cut the straps securing the instrument box b Cut the tape securing the top flaps of the instrument crate then open the flaps c Remove the Veriti System Accessories from the instrument and set them aside d Lift and remove the cover from the instrument crate Veriti Thermal Cycler User Guide 2 3 Chapter 2 Getting Started e Remove the packing material from the Veriti System then inspect the instrument for shipping damage IMPORTANT If the Veriti System is damaged note the location and appearance of the damage then contact Applied Biosystems Technical Support or your service representative see How to Obtain Support on page viii 2 Move the Veriti System to the desired installation site Follow these guidelines for lifting and moving e Make sure that you have a secure comfortable grip e Keep your spine in a neutral position e Bend at the knees and lift with your legs e Do not lift and twist your torso at the same time 3 Open the bag containing the Veriti System Accessories then verify that it contains e Applied Biosystems Veriti Thermal Cycler User Guide CD PN 4376993 e Cable Power 13A 125V North America PN 4382067 e Cable Power 1OA 220V Europe PN 4382068 e Veriti System Starter Kit PN 4376634 Setting Up the Veriti System 1 Remove the packing material a Open the Veriti System heated cover b Remove the
49. g time too long Peltier failure Run the Cycle Performance Test When running on multiple instruments cannot see instruments in Select Instruments screen No screen display No response when you power on the instrument Instrument s not connected to network Switch powered off Ethernet cable bad IP address conflict Blown fuse Not connected to power source Are all Ethernet cables connected to the instruments Are all Ethernet cables connected to the router Try a different Ethernet cable Change the IP addresses on the instruments Is power switch on Is power cord connected Check fuses Heated cover not responsive Heated cover failure Returning an Instrument for Service Run the Heated Cover Verification Test Before returning an instrument for service back up the run methods and instrument settings as described in Backing Up Run Methods and Other Settings on page 1 13 This practice ensures that if the service center sends you a replacement instrument you can restore the run methods and other settings To return an instrument for service 1 Contact your local customer care center or technical support group to obtain a service notification a service call number and if required packaging 5 2 Veriti Thermal Cycler User Guide Chapter5 Troubleshooting 2 Decontaminate the instrument IMPORTANT If the sample block becomes contaminated with radio
50. ge Required The appropriate Temperature Verification Kit for your Veriti Thermal Cycler model Materials see table above Procedure This test takes 10 to 15 minutes to complete but you can cancel before it is complete ANETTE PHYSICAL INJURY HAZARD Hot Surface Use care when working around the heated cover and sample block to avoid being burned 1 In the Main Menu screen touch Tools Menu 2 In the Tools Menu screen touch Run TNU Test 3 To save the test results to the USB drive insert the drive now Otherwise the test results are not saved but are displayed when the test is complete 4 Follow the instructions on the screen to perform the test The results are saved to the file tnuEvents txt if the USB drive is present 5 Ifthe test fails repeat the procedure Make sure that the e Cables are securely seated in the digital thermometer and in the instrument Heated cover is closed 6 Ifthe test fails again contact Applied Biosystems Technical Support TVK Recalibration Applied Biosystems recommends that your Temperature Verification Kit be recalibrated once a year Calibrating the thermometer and probe of the Temperature Verification Kit requires that you e Decontaminate the probe assembly as described below e Send the equipment to the manufacturer SeeT VK Support on page ix Decontaminating 1 Gently wipe the probe cones with a cotton swab that has been moistened with the Probe with a 1 10 v v s
51. gy and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses 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 03 2007 Applied Biosystems Part Number 4375799 Rev A
52. h the new firmware then touch the field to show the list Select the file then touch Upgrade to copy it to the instrument 7 Touch Source File to display a list of the files on the USB drive Veriti system firmware files end with update Veriti Thermal Cycler User Guide 4 5 Chapter 4 Utilities 8 Touch the name of the file with the new firmware then touch Select 9 Touch Upgrade then Yes When the upgrade process is complete a message box opens 10 Restart the instrument and follow the prompts to calibrate the touchscreen a Remove the USB drive then power off the instrument using the switch on the back b Power on the instrument It takes a few minutes for the firmware upgrade to complete Do not power off the instrument again until the entire upgrade process is complete and the opening screen is displayed c Follow the instructions on the screen to calibrate the touchscreen After you complete the touchscreen calibration the firmware is upgraded and the instrument is ready Calculating Melting Temperatures To calculate the melting temperatures for a DNA primer pair 1 In the Main Menu screen touch Tools Menu 2 In the Tools Menu screen touch Calculate Tm to open the Tm Calculator screen n Tm Calculator f Salt Concentration s0 mM Primer Concentration 0 20 uM Primer 1 Sequence Primer 2 Sequence Touch the fields to enter concentrations and the primer sequences t
53. he cover Touch Browse New Methods Locate the run method you want to use see Viewing a Run Method on page 1 9 then touch the run method to select it Touch Start Run The Run Parameters screen opens f Run Parameters Reaction Volume ho a L Cover Temperature 105 0 C Run ID 200702140925 Notes This is a quick test for Joe s samples with a5 minute vortex step Touch each field then use the keyboard to edit the contents When you are finished touch Start Run Now Touch Reaction Volume to edit the reaction volume By default the reaction volume you entered when you saved the method is displayed Reaction volumes are specific to the type of instrument e Veriti 96 Well Fast Thermal Cycler 5 to 50 uL e Veriti 96 Well Thermal Cycler 10 to 100 uL Touch Cover Temperature Run ID and or Notes then enter the applicable information The default Run ID is YYYYMMDDHHMM where Y YYYMMDPD is the date and HHMM is the current time If you are making runs on e Only this instrument Touch Start Run Now then OK The cover is heated to the required temperature then the run begins When the run is complete the Run Report is displayed Or Veriti Thermal Cycler User Guide 3 15 Chapter 3 Performing a Run e Multiple instruments Touch Start Multiple Runs The Select Instrument screen is displayed n Select Instruments J LocalHub lab2 lab3 Ready Ready Incomp
54. hen touch Calculate Tm to calculate the melting temperatures Maximum input for each primer sequence is 30 3 Enter the required information a Touch Salt Concentration then enter the salt concentration in mM b Touch Primer Concentration then enter the DNA concentration in uM c Enter each primer sequence 4 Touch Calculate The melting temperature for each primer is displayed 4 6 Veriti Thermal Cycler User Guide Chapter 4 Utilities C Salt Concentration s0 mM Primer Concentration lo 20 uM Primer 1 Sequence CGTTTTAGCT Primer 2 Sequence CCCCCCCGTATATIITIGC TM for Primer 1 17 6 TM for Primer 2 59 8 ale Touch the fields to enter concentrations and the primer 2 sequences then touch Calculate Tm to calculate the melting temperatures Maximum input for each primer sequence is 30 Oo Viewing Instrument Statistics The instrument records information about how it has been used You can view this information 1 In the Main Menu screen touch Tools Menu 2 In the Tools Menu screen touch Show Statistics The following statistics are shown e Total Cycles for Block The total number of cycles the sample block has performed over its lifetime e Total Degrees for Block The total degrees the sample block has climbed over its lifetime For example if the sample block was heated from 10 degrees to 30 degrees for 3 cycles the total degrees would be 60 3
55. his is indicated by 9700M in the Time field for each step see Figure 4 1 Figure 4 1 Converted run method showing 9700M for the ramp rate Upgrading System Firmware About the Upgrade Upgrading the Veriti Thermal Cycler Firmware 4 4 If Applied Biosystems provides a new version of the firmware for the Veriti Thermal Cycler you may be required to load the new firmware on the instrument You will need a USB drive and if your instrument requires login Administrator access to upgrade the firmware IMPORTANT You cannot upgrade the firmware while a run is in progress 1 Determine the version number of the existing firmware a b In the Main Menu screen touch Settings Menu In the Settings Menu screen touch About the Instrument record the version number of the firmware then touch Done to return to the Settings Menu Applied BS Bibsystems Veriti 96 Well Thermal Cycler Firmware Version v1 00 0 22 0 2 62 3 1 95 MAC ID 00 17 80 00 00 5A Copyright 2007 by Applera Corporation All rights reserved Applied Biosystems is a registered trademark and Applera is a trademark of Applera Corporation or its subsidiaries in the US and or certain other countries All other trademarks are the sole property of their respective owners es om 2 Determine the version number of the new firmware Veriti Thermal Cycler User Guide Chapter 4 Utilities a On a computer connected to the
56. hod in the Shared folder can be set as the default method To designate a run method as the default l 2 3 Log in as a user with User or Administrator access In the Main Menu screen touch Settings Menu In the Settings Menu screen touch Set Default Method The Set the Default Run Method screen opens with only the run methods in the Shared folder displayed In the Set the Default Run Method touch the run method you wish to designate as the default then touch Make Default In the message box that opens touch OK The Settings Menu screen is displayed and the selected run method is now the default Veriti Thermal Cycler User Guide Chapter1 System Overview Backing Up Run You can back up the instrument s run methods and other settings to a USB drive All Methods and run methods folders user information and other instrument settings are saved Other Settings Note If your instrument requires login you must have Administrator level permissions to back up run methods and instrument settings 1 Insert the USB drive into the USB port on the front of the instrument USB Port 2 Log in as a user with Administrator access 3 In the Main Menu screen touch Settings Menu then Admin Menu 4 In the Admin Menu screen touch Back Up Methods amp Settings The Back Up Method and Settings screen opens f Back Up Methods and Settings Insert a USB drive then touch Back Up to save all run meth
57. i H hazard icons See safety symbols on instruments hazard symbols See safety symbols on instruments hazards See safety heated cover cleaning 6 3 decontaminating 6 4 temperature when idle 2 14 verification 4 10 Help system accessing viii IMPORTANT description xii Information Development department contacting viii installation category xviii instrument operation safety xvi italic text when to use vii L linkage mapping C 5 LMS2 run method C 5 M Main Menu screen 1 6 maintenance schedule 6 2 melting temperatures calculating 4 6 menu commands conventions for describing vii moving parts safety xviii MSDSs description xvi obtaining xvii MSDSs obtaining viii O online Help See Help system overvoltage category rating xviii E 2 P part numbers disposable supplies B 2 Temperature Verification Kits 6 6 thermal cycler parts 6 6 Pause Run button 3 18 pausing before a step in run method 3 14 default duration 2 15 during a run 3 19 physical hazard safety xviii printing run methods 1 12 run report 3 21 R ramp rates 9700M 4 4 editing 3 10 in converted methods 4 4 viewing 1 9 recalibrating temperature verification kit 4 11 remaining time for run viewing 3 18 renaming folders 1 15 restoring run methods and settings 1 14 RS232 serial port A 2 rTth DNA polymerase C 7 run methods backing up 1 13 copying 1 11 creating 3 6 deleting 1 12 predefined C 1 printing 1 12 restoring 1
58. in Figure p A Run Monitor Button Displays the estimated temperature of the sample and Status Bar the estimated time remaining in the run and the name of the current stage B Hot Icon Indicates that the heated cover has achieved a temperature sufficient to burn skin C Stage Indicator Indicates the stage that the Veriti System is performing and the current cycle in that stage D Step Temperature Indicates the temperature for the step E Hold Time Indicates the time for the step When this is the current step this field counts down F Step Indicator Indicates the step that the Veriti System is performing G Status Report Displays the run status and any errors that occur during the run Touch the triangle to view the entire report H Arrow Button Touch this to see the additional steps in the run method See Actions in the Run Monitor Screen During a Run on page 3 18 for information about what you can do during a run Veriti Thermal Cycler User Guide 3 17 Chapter 3 Performing a Run Actions in the Run Monitor Screen During a Run During a run the touchscreen is active allowing you to perform the actions indicated in the table Table 1 Actions in the Run Monitor Screen Allowed During a Run To Do This View other stages Touch the scroll right and scroll left buttons Pause the run x La j Touch Pause Run see Pausing a Run on page 3 19 View run meth
59. ing a Run 3 22 Veriti Thermal Cycler User Guide Utilities This chapter covers Using GeneAmp PCR System 9700 Run Methods 00 0 000000 4 2 Upgrading 5Sysiem Pao s bcs wow on bes ESRARI EREET RRRA Er 4 4 Calculating Melting Temperatures 4 6i5 4 bs 6444644045455 5 0 arreen 4 6 Viewing Insiument SIADSOCS s be 5 ho eee EV OO eRe eR EE ed 85S EES 4 7 ue he Oe oc on ooh 4 cee e808 e 55eens 6495488 cae wes 4 7 Running the Cycle Performance Test 0 0 0 4 8 Tests Using the Temperature Verification Bil ccc 45644 c04504e404 0 cas ehes 4 9 Veriti Thermal Cycler User Guide 4 1 Chapter 4 Utilities Using GeneAmp PCR System 9700 Run Methods The Veriti Thermal Cycler has a Convert Method tool to guide you through importing existing run methods from a GeneAmp PCR System 9700 thermal cycler The tool is designed to create a method for the Veriti Thermal Cycler with ramp rates that simulate those on the 9700 thermal cycler Although the ramp rates may be similar in the two methods the results on the Veriti Thermal Cycler may differ from those from the GeneAmp PCR System 9700 and therefore additional optimization may be needed To use a run method from a GeneAmp PCR System 9700 thermal cycler 1 Obtain a copy of the original method you want to convert either by printing it from the instrument or copying it manually to a piece of paper 2 In the Main Menu screen touch Tools Menu 3 In the T
60. ing subsequent cycles at lower temperatures they outcompete the nonspecific sequences to which the primers bind at lower temperatures Note AutoDelta steps are allowed only in cycling stages To create an AutoDelta step 1 Touch a step then Options Edit Run Method LMS2 Run Add Delete Options Save Touch a stage or a step to insert a stage or step Touch a time or temperature to edit it Touch Options to create AutoDelta or VeriFlex steps to show ramp rates or to add a pause 3 12 Veriti Thermal Cycler User Guide Chapter 3 Performing a Run 2 In the Options menu touch AutoDelta The Create an AutoDelta Step screen opens Edit Run Method LMS2 3 Touch Starting Cycle then enter the cycle at which the AutoDelta step begins 4 Select the parameter s to increment e Touch Delta Temperature then enter the number of degrees that the temperature changes for each cycle To enter a temperature that decreases with every cycle touch to change it to To enter a temperature that increases the button should show and or e Touch Delta Time then enter the minutes and seconds that the step duration should change with each cycle To enter a time that decreases with each cycle touch to change it to To enter a time that increases the button should show Note Make sure the parameters you enter result in a final temperature greater than 4 0 C and less than 99 9 C Also the Delta Ti
61. ire replace fuses only with fuses of the type and rating specified for the instrument Power JN D Nle ELECTRICAL HAZARD Grounding circuit continuity is vital for the safe operation of equipment Never operate equipment with the grounding conductor disconnected Use properly configured and approved line cords for the voltage supply in your facility Plug the system into a properly grounded receptacle with adequate current capacity Overvoltage The Veriti Thermal Cycler has an installation overvoltage category of II and is Rating classified as portable equipment Physical Hazard Safety aa Moving Parts gt PHYSICAL INJURY HAZARD Moving parts can crush and cut Keep hands clear of moving parts while operating the instrument Disconnect power before servicing the instrument Safety and Electromagnetic Compatibility EMC Standards This section provides information on e U S and Canadian Safety Standards e Canadian EMC Standard e European Safety and EMC Standards e Australian EMC Standards U S and The Veriti Thermal Cycler has been tested to and complies with standard c be UL 61010A 1 CAN CSA C22 2 No 1010 1 92 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements c UL us xviii Veriti Thermal Cycler User Guide Safety and EMC Compliance Information UL 61010A 2 010 Particular Requirements for Laboratory Equipment for the
62. is test takes 10 minutes to complete 1 In the Main Menu screen touch Tools Menu 2 In the Tools Menu screen touch Run Cycle Performance Test 3 To save the test results to the USB drive insert the drive now Otherwise the test results are not saved but are displayed when the test 1s complete 4 Follow the instructions on the screen to perform the test The results are saved to the file CyclePEvents txt if the USB drive is present 5 If the test fails repeat the procedure Make sure that the heated cover is closed 6 If the test fails again contact Applied Biosystems Technical Support Tests Using the Temperature Venfication Kit You need the Temperature Verification Kit to perform the e Heated Cover Verification e Temperature Verification e Temperature Nonuniformity Test About the The Temperature Verification Kit consists of Tem perature e A probe Either a 0 1 mL or 0 2 mL probe assembly ordered separately or as Verification Kit part of the kit e Digital thermometer Model 4690 Digital thermometer with 9 V battery e Light mineral oil e Cotton swabs You need the appropriate model of the Temperature Verification Kit for your Veriti Thermal Cycler as shown below wget meat Part Veriti Thermal Cycler Model Temperature Verification Kit Number Veriti Fast 96 Well Thermal Cycler PN 4375593 with 0 1 mL 0 1 mL Temperature Verification Kit 4373997 Sample wells Veriti 96 Well Thermal Cycler PN 43757
63. it Touch Options to create AutoDelta or VeriFlex steps to show ramp rates or to add a pause IMPORTANT If you are logged on as a Limited User or a Guest you can make changes to the run method but you cannot save them 2 To view e Other steps in the run method Touch the arrow buttons at the end of the run method e View steps with ramp rates Touch Options then Ramp Rate The fields showing times update to show the corresponding ramp rates 3 When you are done touch X to return to the Browse Run Methods screen Edit Run Method LMS2 Run Add Delete Options Touch a stage or a step to insert a stage or step Touch a Kte or temperature to edit it Touch Options to create AutoDelta or VeriFlex steps to show ramp rates or to add a pause Veriti Thermal Cycler User Guide 1 9 Chapter1 System Overview Managing Run To see the run methods in the current folder Methods e Inthe Main Menu screen touch Browse New Methods The Browse Run Methods screen opens The title includes the number of run methods in parentheses x 7 n Browse Last Accessed Run Methods 14 Sn Foe Coo D LMS2 2007 02 15 Touchdown_PCR Shared 2007 02 15 AmpliTaq_Gold Shared 2007 02 14 r Time_Release Shared 2007 02 14 L_PCR Shared 2007 02 14 3 Selected 1 Start Run New View Edit Copy Print Delete Touch arun method to select it then touch any of the buttons to perform an action Touch a column title t
64. itor a Touch the field b Touch the keys in the editor c Repeat for any other field 3 Touch Done to close the editor Editing Ramp You can edit the rate at which the instrument ramps to the temperature for the step Rates The default ramp rate is 100 1 Touch a step to select it 2 Touch Options then Ramp Rate The field displaying time changes to display the ramp rate 3 Touch the ramp field then enter the desired ramp rate Ramp rates from 0 1 to 100 are valid 4 Touch Done to close the editor The ramp rate symbol J appears next to any step with a ramp rate less than 100 3 10 Veriti Thermal Cycler User Guide Chapter 3 Performing a Run Creating a Step The sample block of the Veriti Thermal Cycler has six temperature zones You can for the VeriFlex _ specify temperatures for each zone or treat the entire sample block as one zone the Block default A step that has different temperatures for areas in the VeriFlex Block is called a VeriFlex step This feature is useful for quickly optimizing new run methods To create a step with different temperatures for the VeriFlex block 1 Touch a step then Options The options menu appears Edit Run Method mu Ny Run Add Delete Options Save Touch a stage or a step to insert a stage or step Touch a time or temperature to edit it Touch Options to create AutoDelta or VeriFlex steps to show ramp rates or to add a pause 2 In the
65. lean the heated cover 1 Follow the steps in Preparation on page 6 2 2 Open the heated cover 3 Soak a cotton swab or piece of clean cloth with pure isopropanol and gently wipe the heated platen Nore CHEMICAL HAZARD Isopropanol is a flammable liquid and vapor Exposure may cause eye skin and upper respiratory tract irritation Prolonged or repeated contact may dry skin and cause irritation Exposure may cause central nervous system effects such as drowsiness dizziness and headache Read the MSDS and follow the handling instructions 4 Remove any remaining isopropanol from the cover Note If the platen becomes contaminated with amplified DNA then raise the heated cover to the cleaning position wipe the platen with a cloth or cotton swab soaked in bleach then rinse with water Clean the heated platen once a month or as needed Veriti Thermal Cycler User Guide 6 3 Chapter6 Maintenance Decontaminating Ifthe heated cover become contaminated with amplified DNA raise the heated cover the Heated Cover tothe cleaning position and wipe the cover with a cloth or cotton swab soaked in 1 10 v v dilution of 5 25 sodium hypochlorite Chlorox bleach then wipe the cover with a damp cloth Replacing Fuses Fuse Overview The instrument has two 10 A Type M 250 V 5 x 20 mm fuses PN 4377690 Nore FIRE HAZARD For continued protection against the risk of fire replace fuses only with Listed and Certified fuses of th
66. levant information Permission Level Last Update 5 In the Edit User Account screen make the required changes e Touch Phone and or Email to edit the contents e Touch Set Access to change the access level for the user e Touch Set Password to change the password for the user 6 Touch Done then OK to return to the Manage Users screen 7 When you finish touch x Close to return to the Admin Menu To delete a user 1 Log in as a user with Administrator access 2 In the Main Menu screen touch Settings Menu 3 In the Settings Menu screen touch Admin Menu 4 In the Admin Menu screen touch Manage Users The Manage Accounts screen opens n Manage Users f ee Coe admin 2006 12 07 Administrator myuser 2006 12 07 User myadmin 2006 12 07 Administrator rage Delete User Edit User Add User Touch a user name to select it then touch any of the buttons to perform an action Touch a column title to sort the table 2 13 Chapter 2 Getting Started 5 In the list touch the user name for the account you want to delete then touch Delete User A confirmation message appears 6 Touch OK to delete the user and any run methods or folders for that user then OK 7 When you finish touch x Close to return to the Admin Menu Setting Other Options Table 2 lists additional options that can be adjusted or activated These settings apply to all users Table 2 Additional options and their def
67. me must be less than the total time for the stage 5 Touch OK to save the step and return to the screen that displays the run method The AutoDelta symbol EJ appears on the step with the AutoDelta step In this example Step 2 in Stage 2 is an AutoDelta step Veriti Thermal Cycler User Guide 3 13 Chapter 3 Performing a Run Adding a Pause You can add a pause before any step in any cycling stage 1 In the Edit Run Method screen touch a step in a cycling stage to select it then touch Options 2 In the Options Menu touch Pause Edit Run Method Mt bey 4 Enter e The first cycle in which the run will pause e The frequency of the pause e The duration of the pause in mm ss 5 Touch Done to save the pause and return to editing the method The step preceded by the pause is indicated by the iJ see Step 3 in Stage 3 below Deleting a Stage 1 In the Edit Run Method screen touch the stage or step to select it orStep 5 Touch Delete then OK The stage or step is deleted from the run method 3 14 Veriti Thermal Cycler User Guide Chapter 3 Performing a Run Performing a Run Before You Begin Prepare your samples and load the sample block as described in Loading Samples into the Instrument on page 3 4 Y IMPORTANT You can start a run on multiple instruments at the same time if your instruments are on a network To start a run from the Main Menu screen l 2 3 5 7 Close t
68. n You can create a new folder when you save a run method see step 6 on page 3 7 Deleting Custom You can delete any custom folder All run methods a custom folder that is deleted are Folders also deleted 1 In the Main Menu screen touch Settings Menu 2 In the Settings Menu screen touch Manage Folders 3 In the Manage Folders screen touch the check box next to the folder you want to delete then touch Delete 4 Touch Yes in the dialog box that opens then OK The folder is deleted 5 Repeat steps 3 and 4 to delete other folders 6 When you are done making changes to folders touch x Close to return to the Settings Menu screen Renaming You can rename any custom folder Custom Folders 1 In the Main Menu screen touch Settings Menu 2 In the Settings Menu screen touch Manage Folders 3 In the Manage Folders screen touch the check box next to the folder you want to rename then touch Rename 4 Enter up to 12 characters for the folder s new name then touch Done to return to the Manage Folders screen 5 Repeat steps 3 and 4 to rename any other folders i When you are done making changes to folders touch X Close to return to the Settings Menu screen Veriti Thermal Cycler User Guide 1 15 Chapter1 System Overview 1 16 Veriti Thermal Cycler User Guide Getting Started This chapter covers Installing the Veriti Thermal Cycler Setting Up the Veriti Thermal Cycler Veriti The
69. n methods C 3 C 4 bold text when to use vii C calibrating temperature verification kit 4 11 touchscreen 4 7 CAUTION description xii certificate of decontamination D 1 chemical safety xvi xvii chemical waste safety xvii cleaning heated cover 6 3 sample wells 6 2 touchscreen 6 2 conventions bold text vii for describing menu commands vii IMPORTANTS vii in this guide vii italic text vii Notes vii Veriti Thermal Cycler User Guide safety xii user attention words vii creating folders 3 7 run methods 3 6 users 2 10 customer feedback on Applied Biosystems documents viii Cycle Performance Test 4 8 cycles changing during arun 3 18 editing in a run method 3 9 D DANGER description xii date setting current 2 8 decontaminating heated cover 6 4 sample wells 6 3 temperature verification kit 4 11 decontamination certificate D 1 default administrator user name and password 2 10 deleting folders 1 15 run methods 1 12 steps or stages 3 14 users 2 13 documentation related viii electrical safety xviii electromagnetic compatibility standards See EMC standards EMC standards xviii Ethernet port A 2 F FAST PCR run method C 4 firmware upgrading 4 4 version number 4 4 folders creating 3 7 deleting 1 15 E 1 Index renaming 1 15 fuses changing 6 4 specification 6 4 G General PCR run method C 5 guest users 2 9 guidelines chemical safety xvii chemical waste disposal xvi
70. nu screen touch Set IP Address n IP Settings f B Assign IP address dynamically using DHCP y Static IP Address 182 168 000 040 Subnet Mask 255 255 255 000 Default Gateway 182 168 000 001 Choose how the IP address is assigned For static IP addresses enter the required information from your system administrator When you are finished touch Done 4 In the IP Settings screen set the IP address Veriti Thermal Cycler User Guide 2 7 Chapter 2 Getting Started Setting the strument Name Configuring the Instrument for a Printer Setting the Date 2 8 and Time 5 e Dynamically Touch Assign IP address dynamically using DHCP A check mark appears when DHCP 1s selected Or e Manually Touch Static then enter the appropriate IP addresses for the instrument the subnet mask and optionally the default gateway using the numeric editor Addresses are in the form of X X X X where each X is a 3 digit number from 001 to 255 Touch Done then OK to save your changes and return to the Admin Menu screen By default the instrument name is set to the instrument serial number The instrument name appears in the Run Report screen and if you connect together multiple instruments in the Select Instruments screen You can change the name to something more descriptive In the Main Menu screen touch Settings Menu In the Settings Menu screen touch Admin Menu 1 2 3 4 In the Admin Me
71. nu screen touch Set Instrument Name Touch the field to enter the new name Names cannot contain spaces and cannot be more than 24 alphanumeric characters or for numeric only names 10 characters Touch Yes to make the instrument available for remote runs a run on this instrument can be started from another instrument otherwise touch No Touch Done then OK to save your changes and return to the Admin Menu screen If you want to print the run report and or a run method you must configure the instrument with information about the printer In the Main Menu screen touch Settings Menu In the Settings Menu screen touch Configure Printer 2 RI 4 Touch the fields to set the printer s name and IP address Touch Done to save your changes and return to the Settings Menu screen The date and time appear in the run report and at the bottom of many of the screens on the instrument 1 In the Main Menu screen touch Settings Menu 2 In the Settings Menu screen touch Admin Menu 3 4 To set the date touch Date then enter today s date using the format Y Y Y Y In the Admin Menu screen touch Set Date amp Time 66 99 MM DD The instrument automatically enters the To set the time touch Time enter the current time using the format HH MM SS then touch AM or PM The instrument automatically enters the Veriti Thermal Cycler User Guide 6 Chapter 2 Getting Started Touch Done th
72. o sort the table Figure 1 8 The Browse Run Methods screen showing the most recently accessed run methods To select a run method 1 Ifarun method is already selected in the Browse Run Methods screen a Touch the row for the selected method to deselect it b Touch the row for the method of interest 2 To select more than one method touch each method Table 2 lists the administrative tasks you can perform for run methods Table 2 Managing run methods If you want to Do this Sort run methods by different Touch the title of the column with the criteria by which criteria you want to sort the run methods Touch the title a second time to sort in the opposite order View more run methods in the Touch E Page Down current folder View run methods in a different Touch o folders In the Browse All Folder screen folder that opens touch the folder you want to view Start a run In the list of run methods touch a run method to select it then touch Start Run see Performing a Run on page 3 15 1 10 Veriti Thermal Cycler User Guide Chapter1 System Overview Table 2 Managing run methods continued If you want to Do this Create a new run method Touch New see Creating a New Run Method on page 3 6 View or edit a run method In the list of run methods touch the run method to select it then touch View Edit See Editing Details on page 3 8 Copy one
73. od information S Touch View Method Information The information you entered in the Run Parameters dialog box is shown Display the time for the run S L i z Touch Display Method Time The elapsed time and time remaining for the run are shown Skip to the next step S jy Touch SKIP l Skip works only when the instrument is holding Stop the run Touch STOP see Stopping a Run on page 3 19 Change the number of cycles for a cycling stage Touch the Cycle field then change the number of cycles see Changing the Number of Cycles on page 3 18 Go to the Main Menu screen Touch Home From the Main Menu Screen you can access most of the Veriti Thermal Cycler functions while the run continues View the Status Report Touch A Status Changing the You can change the number of cycles for a cycling stage while a run is in progress Number of Cycles 1 If needed click the orange run monitor button to return to the run monitor screen 2 Touch the cycles field below the Stage Name for a cycling stage then enter the new value You cannot e Edit a stage that is already complete e Enter a number that is smaller than the number of cycles that have already been completed 3 Touch Send to return to the Run Monitor screen The run continues using the new number of cycles Veriti Thermal Cycler User Guide Chap
74. ods and instrument settings to the memory stick 5 Touch Back Up If a back up file already exists you are prompted to overwrite it The instrument copies all run methods folders user information and other instrument settings to the USB drive then displays a message box when the backup is complete 6 Touch OK then touch x Close to return to the Admin Menu screen Veriti Thermal Cycler User Guide 1 13 Chapter1 System Overview Restoring Run Methods and Other Settings 7 Remove the USB drive and store it in a safe place You can restore run methods and other settings from a USB drive to an instrument The restore feature can also be used to load run methods onto another instrument in your lab Note If your system requires login you must have User or Administrator level permissions to restore saved run methods and settings to your instrument To restore run methods and instrument settings i 5 6 7 Insert the USB drive containing the saved run methods and settings into the USB port on the front of the instrument Log in as a user with User or Administrator access In the Main Menu screen touch Settings Menu then About the Instrument Applied BS Bibsystems Veriti 96 Well Thermal Cycler Firmware Version MAC ID In the About the Veriti Thermal Cycler screen touch Restore Methods amp Settings then Yes in the message box The instrument copies all run methods folders
75. olution of 5 25 sodium hypochlorite Chlorox bleach Assembly IMPORTANT Do not submerge the probe in bleach solution Do not disassemble the probe assembly 2 Complete a copy of the Certificate of Decontamination Appendix D Veriti Thermal Cycler User Guide 4 11 Chapter 4 Utilities 4 12 Veriti Thermal Cycler User Guide Troubleshooting This chapter covers Troubleshooting Returning an Instrument for Servic s 44524204 eeeeeiee edn diedeuweses Veriti Thermal Cycler User Guide 5 1 Chapter5 Troubleshooting Troubleshooting Use the following table to help troubleshoot problems with your Veriti Thermal Cycler Problem Possible Causes Check and or Remedy Cooling rate too slow Peltier assembly failure Run the Cycle Performance Test Temperature does not match Specified temperature Instrument may require calibration Run the Temperature Verification Test Heating rate too slow Printing fails Peltier failure Printer incorrectly configured on instrument Printer not connected to network Instrument not connected to network Ethernet cable bad Run the Cycle Performance Test Make sure the printer IP address on the instrument matches the IP address from the system administrator Is Ethernet cable connected to the printer Is Ethernet cable connected to the instrument Is network functioning Try a different Ethernet cable Cyclin
76. on page 1 7 e Tools Menu to access instrument tests and tools such as a Tm calculator run method conversion and touchscreen calibration see The Tools Menu Screen on page 1 8 e My Account to view and edit your account information This button is not displayed if your system is does not require login e The Shortcut buttons allow you to configure options you frequently use to appear in the Main Menu screen see Configuring Main Menu Shortcuts on page 2 15 e Log Off to log off the instrument You can still log off when a run is in process D Help to access the Help system 1 6 Veriti Thermal Cycler User Guide Chapter1 System Overview The Settings Use this screen to set various instrument configuration options For instruments that Menu Screen require login only Users and Administrators have access to this menu 3 Ss 2007 03 10 11 24 AM Figure 1 5 The Settings Menu screen with the Admin Menu button shown The Admin Menu Use this screen to manage user accounts set instrument security back up run Screen methods and settings upgrade the firmware and perform other functions For instruments that require login only Administrators have access to this menu Ss a 2007 01 16 3 42 PM User gregor 2 Figure 1 6 The Admin Menu screen available only to users with administrative privileges Veriti Thermal Cycler User Guide 1 7 Chapter1 System Overview The Tools Menu
77. ools Menu screen touch Convert a Method to open the Convert Method wizard Convert Method Step 1 of 2 f Convert from y 9700 Max Mode Press the right arrow to proceed to input the method 2 4 Touch Next 4 2 Veriti Thermal Cycler User Guide Chapter 4 Utilities 5 In the second page enter the original run method You can include AutoDelta steps pauses and VeriFlex steps and you can edit the ramp rates Touch Next when you are done Convert Method Step 2 of 2 lt Delete Options Enter the original run method then touch the right arrow button to proceed to save the method 6 In the Save Run Method page below enter a name and select a folder for the run method Names are limited to 16 characters with no spaces By default the name begins with 9700 Max Mode Also enter the reaction volume the temperature for the heated cover and any notes for this method Save Run Method D Hun Method ls700 Max Mode Folder Defaut v Reaction Volume hio Cover Temperature 105 0 Notes Enter a name reaction volume and choose a folder for this run method Notes can also be added When you are finished touch Save amp Exit When you finish touch Save amp Exit The Tools Menu is displayed Veriti Thermal Cycler User Guide 4 3 Chapter 4 Utilities Note You cannot edit the ramp rates in the method created by the Convert Method tool T
78. ou have selected Allow Empty Password in the Security screen in which case you can leave the password empty c Touch Set Access then touch one of the following e Limited User e User e Administrator d Touch Done to close the Permission screen 7 Touch Done then OK to add the user account to the instrument The new user appears in the Manage Accounts screen 8 When you finish touch x Close to return to the Admin Menu screen Changing a User To edit a user 1 Log in as a user with Administrator access 2 In the Main Menu screen touch Settings Menu 3 In the Settings Menu screen touch Admin Menu 4 In the Admin Menu screen touch Manage Users The Manage Users screen opens n Manage Users C Seed Seo admin 2006 12 07 Administrator myuser 2006 12 07 User myadmin 2006 12 07 Administrator ar Add User Edit User Delete User Touch a user name to select it then touch any of the buttons to perform an action Touch a column title to sort the table In the list touch the user in the list then touch Edit User 2 12 Veriti Thermal Cycler User Guide Deleting a User Veriti Thermal Cycler User Guide Chapter 2 Getting Started The Edit User screen opens Edit User ccount f User Name admin Password Re enter Password Phone 123456 Email tcadmin appliedbiosystems com Administrator Update Account information accordingly by touching on the re
79. packing material from the sample block c Using a can of compressed air deliver a blast of air into each well of the sample block to remove any particles that may have collected during transportation d Close the heated cover 2 4 Veriti Thermal Cycler User Guide Chapter 2 Getting Started Connect the power cable to the Veriti System Optional Install any of the recommended protective devices see Optional Protective Hardware on page 2 3 Connect the power cable to the 800 VA power source receptacle Connecting to a Network Printer Requirements The Veriti Thermal Cycler requires a printer that l Has an Ethernet port Supports the LPD LPR protocol often called a TCP IP printer Plug the Ethernet cable into the Ethernet port on the back of the instrument Plug the other end of the cable into a network port You must also configure the instrument firmware with printer information before you can print see Configuring the Instrument for a Printer on page 2 8 Connecting Together Multiple Instruments You Will Need Making the Connections Connecting your Veriti Thermal Cycler to other Veriti Thermal Cyclers allows you to use one instrument to control others You can connect together up to 12 instruments To connect together multiple Veriti instruments you need e An Ethernet cable for each Veriti Thermal Cycler e A network switch e A TCP IP printer if you want to prin
80. pear in Applied Biosystems user documentation at points Words in the document where you need to be aware of relevant hazards Each alert word IMPORTANT CAUTION WARNING DANGER implies a particular level of observation or action as defined below Definitions IMPORTANT Indicates information that is necessary for proper instrument Operation accurate chemistry kit use or safe use of a chemical N 07ta el Indicates a potentially hazardous situation that if not avoided may result in minor or moderate injury It may also be used to alert against unsafe practices NOE Indicates a potentially hazardous situation that if not avoided could result in death or serious injury N aAa Indicates an imminently hazardous situation that if not avoided will result in death or serious injury This signal word is to be limited to the most extreme situations Except for IMPORTANTS each safety alert word in an Applied Biosystems document appears with an open triangle figure that contains a hazard symbol These hazard symbols are identical to the hazard symbols that are affixed to Applied Biosystems instruments see Safety Symbols on page xiii Examples The following examples show the use of safety alert words IMPORTANT You must create a separate sample entry spreadsheet for each 96 well plate AN oF Veale The lamp is extremely hot Do not touch the lamp until it has cooled to room temperature
81. r Comments The following document is shipped with the system Applied Biosystems Veriti Thermal Cycler Quick Reference Card Provides a summary of information about the thermal cycler its installation and accessories It is designed to help you quickly learn to use the Veriti Thermal Cycler A portable document format PDF version of this guide is available on the Veriti Thermal Cycler Documentation CD Note To open the user documentation on the Veriti Thermal Cycler Documentation CD use the Adobe Reader software available from www adobe com Note For additional documentation see How to Obtain Support on page viti The Veriti Thermal Cycler has a Help system that describes how to use each feature of the user interface Access the Help system by touching 2 Help at the bottom right corner of the instrument touchscreen Applied Biosystems welcomes your comments and suggestions for improving its user documents You can e mail your comments to techpubs appliedbiosystems com IMPORTANT The e mail address above is for submitting comments and suggestions relating only to documentation To order documents download PDF files or for help with a technical question go to http www appliedbiosystems com then click the link for Support See How to Obtain Support below How to Obtain Support Support Information viii For the latest services and support information for all locations go to
82. ray or the tray retainer is required for the operation of the Veriti Thermal Cycler Selecting Tube You can use three different types of tube configurations to hold your samples as Configurations shown in Figure 3 1 MicroAmp Fast Reaction Tube with Cap 0 1 mL Y or SS MicroAmp Reaction Tube with Cap 0 2 mL MicroAmp Reaction Tube 0 2 mL with MicroAmp 8 Cap Strip MicroAmp Fast 8 Tube Strip 0 1 mL or MicroAmp 8 Tube Strip 0 2 mL with MicroAmp 8 Cap Strip Figure 3 1 Different tube configurations for use in the Veriti Thermal Cycler 3 2 Veriti Thermal Cycler User Guide Chapter 3 Performing a Run Selecting Sample The following table lists the possible sample tray and plate configurations Tray and Plate Configurations IMPORTANT The MicroAmp Splash Free 96 Well Base shown below is used only when pipetting samples into tubes or trays Do not place it in the sample block Run Vessel Compatible Component Illustration MicroAmp Fast Optical 96 Well Reaction Plate 0 1 mL MicroAmp Optical 96 Well Reaction Plate 0 2 mL MicroAmp Caps 8 Cap Strip or MicroAmp Clear Adhesive Film not shown MicroAmp 8 Cap Strip MicroAmp Fast Optical 96 Well Reaction Plate 0 1 mL gr MicroAmp Optical 96 Well Reaction Plate 0 2 mL MicroAmp Splash Free 96 Well Base MicroAmp Fast Reaction Tube with Cap 0 1 mL MicroAmp
83. rmal Cycler User Guide Chapter1 System Overview Entering When you touch a field that requires only numerical input the numeric editor opens Numerals Figure 1 3 Reaction Volume 10 Figure 1 3 The Veriti Thermal Cycler numeric editor To Touch Enter a number A number button The instrument automatically adds the decimal point for those fields that include a decimal point such as a temperature value Colons for entering times and dashes for entering dates are also automatically added Delete the last number Remove the entire contents of the field Close the editor and save any changes Veriti Thermal Cycler User Guide 1 5 Chapter1 System Overview Menu Overview The Main Menu After you log in to the system the Main Menu screen opens This screen is the Screen starting point for operating the Veriti Thermal Cycler The date current time and current user are shown at the bottom of the screen gt aaa E 2007 01 16 3 42 PM User gregor 2 Figure 1 4 The Veriti Thermal Cycler Main Menu screen In the Main Menu screen touch e Browse New Methods to view and work with all the run methods to which you have access see Viewing a Run Method on page 1 9 e Settings Menu to access various instrument configuration options If you have administrative privileges you access the Admin Menu screen from this screen see The Settings Menu Screen
84. rmal Cycler User Guide 2 1 Chapter 2 Getting Started Installing the Veriti Thermal Cycler Before You Start Site The Veriti Thermal Cycler is for indoor use Ensure that the installation site Requirements e Meets the spatial and weight requirements for the Veriti System see System Specifications below e Meets environmental requirements see Environmental Requirements below e Is within 1 m 3 ft of a 800 VA power receptacle e Is away from water System Specifications Table1 Physical dimensions weight and power consumption Instrument Recommended paramere Footprint Clearance not 48 5 cm 15 5 cm 64 cm Length 19 1 in 6 1 in 15 2 in 23 7 cm 0 cm 23 7 cm Width 9 3 in 0 in 9 3 in Height 40 0 cm 15 5 cm 55 5 cm eight 15 7 in 6 1 in 21 8 in 10 6 kg Weight 22 6 Ibs Power 800 VA Maximum consumption Consumption 260 VA Average during thermal cycling 10 VA During sleep standby At the rear of the instrument to ensure adequate airflow and cooling With the heated cover open Above the instrument to provide adequate space for opening the heated cover as shown below 1 square 10 cm 3 94 in 2 2 Veriti Thermal Cycler User Guide Chapter 2 Getting Started Environmental Requirements Temperature and Humidity Requirements Pollution Altitude Materials Required Materials Optional Protective Hardware
85. rning Mass Spectrometers 2 The form must be attached to the outside of transport packaging prior to returning the instrument to an Applied Biosystems Repair Center for repair maintenance trade in or loan European customers of Thermal Cyclers should fax the form to Applied Biosystems Customer Services and enclose a copy in the shipping container 3 The form must be given to the Applied Biosystems Engineer prior to any service of an instrument that has been located within a laboratory in which biological agents hazardous chemicals or radioactive materials have been used Please note that Applied Biosystems cannot accept any instruments that may be contaminated with viable biological agents harmful quantities of hazardous chemicals or radioactive materials AB Instrument Number Serial Number AB Instrument Description Reason for return service RMA or RA Number if required Decontamination Information and Procedures 1 Biological Agents Has this instrument been exposed to viable biological agents YES E NO O If YES please state the viable biological agent s their Hazard Group s and Biosafety Level Category of Containment If YES please describe the procedures used to decontaminate the instrument 2 Radioactive Materials Has this instrument been exposed to radioactive materials YES O NO A If YES please identify the radioactive isotopes If YES please describe the procedures used to decontaminate the instrument If
86. s Sample Block Dimensions sae at Instrument Model W all Volume Well Veriti Fast 96 Well Thermal Cycler PN 4375593 96 0 1 mL Veriti 96 Well Thermal Cycler PN 4375785 96 0 2 mL Printer Specifications The Veriti Thermal Cycler requires a printer that e Has an Ethernet port e Supports the LPD LPR protocol often called a TCP IP printer Veriti Thermal Cycler User Guide A 3 Chapter A A 4 Instrument Specifications Veriti Thermal Cycler User Guide Disposables This appendix covers i Pees s oes eet ess esteras Other Supplies for Sample Handling Veriti Thermal Cycler User Guide B 1 ChapterB Disposables Disposables B 2 Table B 1 Disposables for the Veriti Thermal Cycler Part DESEnphon Oi m 02m Number 96 Well Plates MicroAmp Fast 96 Well Reaction Plate 0 1 mL X 4346907 MicroAmp Fast Optical 96 Well Reaction Plate X 4346906 with Barcode 0 1 mL X 4366932 MicroAmp Optical 96 Well Reaction Plate X N8010560 X 4316813 MicroAmp Optical 96 Well Reaction Plate with X 4306737 Barcode X 4326659 MicroAmp Optical 96 Well Reaction Plate with X 403012 Barcode and Optical Caps MicroAmp Optical 96 Well Reaction Plate with X 4314320 Barcode and Optical Adhesive Films 12 Well Strips MicroAmp 12 Cap Strip X X N8010534 X X N8011534 MicroAmp
87. strument Specifications System Specifications erse sdr ee ee eee ees Printer Specifications ccc ee eens Appendix B Disposables DISDOSAD CS i pang ond Ste ain We a de SA eh A a aS he A Other Supplies for Sample Handling 000 eee eee Appendix C Predefined Run Methods Predefined Run Methods cc cee eee eens AmpliCycle Seq Run Method 0 0 cece eee eee AmpliTag Gold DNA Polymerase Run Method BigDye Fast Run Method 0 0 ccc eee BigDye Standard Run Method 0 0c e eee ee Fast PCR Run Method ccc ees General PCR Run Method ccc eee es EMSZRUMMEHOA stato a ee niet at Bia le ected el Sean Time Release Run Method 0 cece ee ees Touchdown PCR Run Method 0 cee eee ees XL PCR RUN M CthOd 0 4 s224040ed osu teeng Eade eee eas Appendix D Certificate of Decontamination Index Veriti Thermal Cycler User Guide vi Veriti Thermal Cycler User Guide Preface How to Use This Guide Purpose of This The Applied Biosystems Veriti User Guide provides information about installing Guide using and maintaining the Applied Biosystems Veriti Thermal Cycler Audience This guide is intended for novice and experienced Veriti Thermal Cycler users who use the instrument to perform PCR Assumptions This guide assumes you have knowledge of basic laboratory procedures and PCR chemistry Text Conventions This guide uses the follo
88. t For best results do not connect the network switch to your laboratory s network Communication between Veriti Thermal Cyclers works best on an isolated system free from interference by other network traffic p ae E Connect the Ethernet cable to the back of the thermal cycler and connect the other end of the cable to the network switch Repeat step 1 for each thermal cycler Connect the printer to the network switch Power on the network switch For each thermal cycler follow the instructions in Setting the IP Address on page 2 7 and Setting the Instrument Name on page 2 8 e When you set the instrument s IP address select Assign IP address dynamically using DHCP e Make sure each instrument name is unique Follow the instructions in Configuring the Instrument for a Printer on page 2 8 Veriti Thermal Cycler User Guide 2 5 Chapter 2 Getting Started 7 Continue with Powering On on page 2 6 and Setting Up the Veriti Thermal Cycler on page 2 7 Powering On 1 Verify that the heated cover is closed 2 Press the power button on the back left side of the instrument 02020020 D LI TA nto OOHO A ee a a a a a a a v B D 0 0 0 0 SS SSS Verti 96 Well H reread Cycler anaa evetete e En e e e mn 00202020 o e e e i rE EE on TIADA 029 28 T Q 0 0 0 GS Rus i rasa The instrument powers on and the opening screen is displayed Applied B
89. ted by the decontaminant manufacturer Survey the instrument with an appropriate radioactivity measuring instrument e g Geiger Counter or scintillation counter Satisfactory decontamination is defined as survey results at or below background level or in the US only for service work excluding transportation levels designated to be clean or safe as stated in the Customer s regulatory approved Site Radioactive Materials License Repeat steps a and b until satisfactory survey results are achieved and attach the results to this form 3 Hazardous Chemicals a Areas exposed to hazardous chemicals should be washed with an acceptable solvent such as ethyl alcohol or isopropyl alcohol b Rinse with detergent and water Mass Spectrometer Mass Spectrometers cannot be decontaminated at the customer s site Complete disassembly is required Veriti Thermal Cycler User Guide D 3 ChapterD Certificate of Decontamination D 4 Veriti Thermal Cycler User Guide Index A about box 4 4 adding AutoDelta steps 3 12 folders 3 7 pauses in a run method 3 14 stages 3 8 steps 3 9 steps for the VeriFlex Block 3 11 users 2 10 Admin Menu screen 1 7 AmpliCycle run method C 2 AmpliTaq run method C 3 Applied Biosystems contacting viii customer feedback on documentation viii Information Development department viii Technical Support viii assumptions for using this guide vii backing up run methods and settings 1 13 Big Dye ru
90. ter 2 Getting Started 2 In the list of functions available as shortcuts in the Configure Shortcuts screen touch the functions to select them Touch A Page Up and 8 Page Down to scroll through the list Configure Shortcuts f About the Instrument Set Idle Temperatures Configure Printer Set Instrument Name Number of selected shortcuts 2 ome Select the functions that will be shown on the main menu Jsa Default Method Page 1 3 3 Touch Done to return to the Settings Menu screen The selected shortcut s appear in the Main Menu screen 2 16 Veriti Thermal Cycler User Guide Performing a Run This chapter covers Pee Ts 6s eG oe es Ge he ee ey ee EG ees er des 3 2 Loading Samples into the Instrument 0 0 eee ees 3 4 Creating a New Run MAG 66465 65a 46 4 bod eed ew OOHRS E EEE OOS 3 6 Pore i ko oe ee oe ee ee oO Gs 3 8 ec eke diel ae 4 a ae ee ae re eee eee ae ere ee eer 3 15 PU a RU beeches ne eee 6 ede ode ao oe ee ee 3 18 Viewing and Pine the Run RepOrl 5 6 3444 s se dddede edd hecanhes sueuns 3 20 Removing the Samples from the Instrument 0 0 00 ee eee eee 3 21 Veriti Thermal Cycler User Guide 3 1 Chapter 3 Performing a Run Selecting Disposables Use this section to determine the tube sample tray and plate configurations appropriate for your application See Appendix B Disposables for part numbers for these items IMPORTANT The t
91. ter 3 Performing a Run Pausing a Run 1 In the Run Monitor screen touch Pause Run C i 95 0 C ED 01 02 47 Method LMS2 Owner gregor Stage 2 Stage 3 x 10 00 00 06 00 04 46 Resume Run The run pauses for the duration set in the Time Settings screen see page 2 15 In the Pause Run dialog box e Remaining Time shows the remaining time for the pause e Elapsed Time is continually updated to show the time the run has been paused 2 If you want to e Pause until the default pause has elapsed Do nothing e Pause for a specific amount of time Touch Edit Time enter the duration of the pause then touch Done The run resumes when the pause is complete e Resume the run immediately Touch Resume Run to the left of the dialog box Stopping a Run In the Run Monitor screen touch Stop then OK The run stops and the Run Report opens Veriti Thermal Cycler User Guide 3 19 Chapter 3 Performing a Run Using the Run The Run Monitor button is displayed at the top of the Run Monitor screen If you Monitor Button leave the Run Monitor screen during a run this button also appears at the top of all menu screens You can touch the Run Monitor button to return to the Run Monitor screen at any Stage 1 61 0 C 00 01 17 time Figure 3 1 The Run Monitor button If an error occurs during the run the area showing the current stage in the middle of the button is replaced by an alert icon
92. terminal that can receive or supply alternating or direct current or voltage Safety Symbols The following table describes the safety symbols that may be displayed on Applied Biosystems instruments Each symbol may appear by itself or with text that explains the relevant hazard see Safety Labels on Instruments on page xiv 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 N AN Veriti Thermal Cycler User Guide Indicates the presence of an electrical shock hazard and to proceed with appropriate caution xiii Safety and EMC Compliance Information Environmental Symbol Description Indicates the presence of a hot surface or other high temperature hazard and to proceed with appropriate caution Indicates the presence of a laser inside the instrument and to proceed with appropriate caution gt D e Indicates the presence of moving parts and to proceed with appropriate caution The following symbol applies to all Applied Biosystems electrical and electronic Symbols on products placed on the European market after August 13 2005 Instruments Symbol Description Do not dispose of this product as unsorted municipal waste Follow lo
93. ting techniques Improper lifting can cause painful and permanent back injury Depending on the weight moving or lifting an instrument may require two or more persons Ensure that anyone who operates the instrument has e Received instructions in both general safety practices for laboratories and specific safety practices for the instrument e Read and understood all applicable Material Safety Data Sheets MSDSs See About MSDSs on page xvi Near Before using a cleaning or decontamination method other than those recommended by the manufacturer verify with the manufacturer that the proposed method will not damage the equipment Chemical Safety Chemical Hazard Warning About MSDSs xvi Nore CHEMICAL HAZARD Before handling any chemicals refer to the Material Safety Data Sheet MSDS provided by the manufacturer and observe all relevant precautions Chemical manufacturers supply current Material Safety Data Sheets MSDSs with shipments of hazardous chemicals to new customers They also provide MSDSs with the first shipment of a hazardous chemical to a customer after an MSDS has been updated MSDSs provide the safety information you need to store handle transport and dispose of the chemicals safely Each time you receive a new MSDS packaged with a hazardous chemical be sure to replace the appropriate MSDS in your files Veriti Thermal Cycler User Guide Safety and EMC Compliance Information Obtaining
94. ts clean the wells the Sample Wells thoroughly with a cotton swab soaked in 1 10 v v dilution of 5 25 sodium hypochlorite Chlorox bleach Use bleach solution in moderation Applied Biosystems recommends the use of 10 bleach solution for removing contamination from the Veriti instrument sample block excessive use of the solution however can corrode the sample block material To prevent damage to the sample block e Avoid applying excessive amounts of bleach solution If possible instead of using a squeeze bottle or soaked cloth use an atomizer to deliver the solution to the wells of the block e After treating with bleach solution rinse the sample block thoroughly using deionized water Note Removing residual bleach from the surfaces of the Veriti instrument using water minimizes the long term effects of bleach treatments If the sample block becomes contaminated with radioactivity use a commercially available decontaminant to remove the contamination If the block cannot be decontaminated the instrument cannot be returned to Applied Biosystems for service Cleaning the Clean the heated cover once a month or as needed Heated Cover ft or Vogue During instrument operation the temperature of the heated cover can be as high as 108 C and the temperature of the sample block can be as high as 100 C Before performing the procedure keep hands away until the heated cover and sample block reach room temperature To c
95. uch the cycles field the box below the Stage Name to select it Edit Run Method LMS2 c Enter the number of cycles then touch Done 4 To change the temperature and or time for any step in the stage see Editing Temperature and Time on page 3 10 Adding a Step 1 In the Edit Run Method screen touch anywhere in the column for a step to select it When the step is selected the column turns red Edit Run Method LM S2 Add Delete Options Touch a stage or a step to insert a stage or step Touch a time or temperature to edit it Touch Options to create AutoDelta or VeriFlex steps to show ramp rates or to add a pause 2 Touch Add A copy of the selected step is added to the run method Veriti Thermal Cycler User Guide 3 9 Chapter 3 Performing a Run Edit Run Method LMS2 X d Run Add Delete Options Save Touch a stage or a step to insert a stage or step Touch a time or temperature to edit it Touch Options to create AutoDelta or VeriFlex steps to show ramp rates or to add a pause 3 To change the temperature and or time for the step see Editing Temperature and Time on page 3 10 Editing 1 Touch any temperature field to select it then edit the temperature as desired Temperature and Or Time Touch any time field to select it then edit the time as desired 2 You can edit any other times temperatures or the number of cycles for a stage without closing the ed
96. ule Fuse compartment 2 Insert a small flat tip screwdriver into the slot in the upper portion of the power entry module and open the door 3 Pull out the fuse compartment to inspect the two fuses in the fuse compartment GRO 6 4 Pull out the blown fuse s from the fuse compartment and replace with new 10 A Type M 250 V 5 x 20 mm fuses 5 Place the fuse compartment back into the power entry module there is only one orientation and close the door 6 Press the door until it locks in place 7 Connect the instrument power cord Veriti Thermal Cycler User Guide 6 5 Chapter6 Maintenance Parts List 6 6 Table 6 1 Kits and Spares Part PN Kits Temperature Verification Kit 0 1 mL 4373997 Temperature Verification 0 2 mL 437 669 Veriti System Starter Kit 4376634 Spares Cable AC Power Supply 4374647 Cam Left Side 4374274 Cam Right Side 4374275 Foot Rubber Package of 4 4375246 Fuse 10A Slo Blo 4377690 Grill Plastic Mold 4374178 Handle Plastic 4374277 Handle Rubber Grip 4374181 Heated Cover 4374276 Panel Left 4374176 Panel Rear Heated Cover 4374280 Panel Right 4374175 Probe Temperature Verification Kit 0 1 mL 4375938 Probe Temperature Verification Kit 0 2 mL 4377670 Veriti Thermal Cycler User Guide Instrument Specifications A This appendix covers Bie ee Sper CAOS ss es dey ea he ee Oe ee 6 Raed
97. user information and other instrument settings from the USB drive to the instrument then displays a message box when the restore is complete Remove the USB drive and store it in a safe place Power off the instrument using the switch on the back Power on the instrument IMPORTANT If you restore information to an instrument that is different from the instrument that provided the backup data and your instruments are on a network you should change the instrument s name See Setting the Instrument Name on page 2 8 Veriti Thermal Cycler User Guide Chapter1 System Overview About Folders Each run method is saved in a folder There are three folders available by default e Default Run methods are stored here if you do not select another folder Run methods stored in this folder run methods can be accessed edited run and deleted only by the user who created them The Default folder has a blue button e Shared Run methods can be accessed edited run and deleted by any user In the Browse Folders screen the Shared folder has a blue button e USB This folder shows all run methods on the USB drive If a USB drive is present in the instrument this button is blue otherwise it is grey In addition you may create up to nine custom folders In a custom folder run methods can be accessed edited run and deleted only by the user who created them In the Browse folders screen custom folders have a yellow butto
98. wing conventions Bold text indicates user action For example Type 0 then press Enter for each of the remaining fields e Italic text indicates new or important words and is also used for emphasis For example Before analyzing always prepare fresh matrix e A right arrow symbol gt separates successive commands you select from a drop down or shortcut menu For example Select File gt Open gt Spot Set Right click the sample row then select View Filter gt View All Runs User Attention Two user attention words appear in Applied Biosystems user documentation Each Words word implies a particular level of observation or action as described below Note Provides information that may be of interest or help but is not critical to the use of the product IMPORTANT Provides information that is necessary for proper instrument Operation accurate chemistry kit use or safe use of a chemical Examples of the user attention words appear below Note The Calibrate function is also available in the Control Console IMPORTANT If your instrument is so configured you need a valid user ID and password to log in Safety Alert Safety alert words also appear in user documentation For more information see Words Safety Alert Words on page xii Veriti Thermal Cycler User Guide vil Preface How to Obtain More Information Related Documentation Obtaining Information from the Help System Send Us You
99. you are done The Browse Methods screen is displayed Veriti Thermal Cycler User Guide 3 7 Chapter 3 Performing a Run Editing Details This section describes how to edit a run method by e Adding a stage page 3 8 e Adding a step page 3 9 e Editing a temperature or a time page 3 10 e Editing a ramp rate page 3 10 e Creating a step to program different temperatures on the VeriFlex Block page 3 11 e Creating an AutoDelta step page 3 12 e Adding a pause page 3 14 Adding a Stage The two types of run method stages are e Cycling The steps in a cycling stage are repeated a specified number of times In general the steps in a cycling stage are template denaturation primer annealing and primer extension e Holding The steps in a holding stage are not repeated To add a stage 1 In the Edit Run Method screen touch the stage name at the top of the stage to select it When a stage is selected the area around the name is red N Edit Run Method LMS2 Delete Options Touch a stage or a step to insert a stage or step Touch a time or temperature to edit it Touch Options to create AutoDelta or VeriFlex steps to show ramp rates or to add a pause 2 Touch Add A copy of the selected stage is added to the run method 3 8 Veriti Thermal Cycler User Guide Chapter 3 Performing a Run 3 For a cycling stage edit the number of cycles as needed a Touch the stage to select it b To
100. ystems 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 piece 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 Veriti Thermal Cycler User Guide XV Safety and EMC Compliance Information General Instrument Safety Moving and Lifting the Instrument Operating the Instrument Cleaning or Decontaminating the Instrument Nee PHYSICAL INJURY HAZARD Using the instrument in a manner not specified by Applied Biosystems may result in personal injury or damage to the instrument N e7 vail PHYSICAL INJURY HAZARD The instrument is to be moved and positioned only by the personnel or vendor specified in the applicable site preparation guide If you decide to lift or move the instrument after it has been installed do not attempt to lift or move the instrument without the assistance of others the use of appropriate moving equipment and proper lif

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