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5-7

Veriti™ Thermal Cycler User Guide

Chapter 5

Utilities

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:

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 µM.

c. Enter each primer sequence.

4. Touch

Calculate

The melting temperature for each primer is displayed:

Summary of Contents for Veriti

Page 1: ...Applied Biosystems Veriti Thermal Cycler User Guide ...

Page 2: ......

Page 3: ...Applied Biosystems Veriti Thermal Cycler User Guide ...

Page 4: ...REOF NOTICE TO PURCHASER The Veriti Thermal Cycler is covered by US patent claims and corresponding claims in their non US counterparts No right is conveyed expressly by implication or by estoppel under any other patent claim such as claims to apparatus reagents kits or methods such as 5 nuclease methods Further in formation on purchasing licenses may be obtained by contacting the Director of Lice...

Page 5: ...Waste Safety xvii Electrical Safety xvii Physical Hazard Safety xvii Safety and Electromagnetic Compatibility EMC Standards xvii Chapter 1 System Overview Introducing the Veriti Thermal Cycler 1 2 Using the Touchscreen 1 3 Menu Overview 1 6 About Run Methods 1 8 About Folders 1 15 Chapter 2 Getting Started Installing the Veriti Thermal Cycler 2 2 Before You Start 2 2 Environmental Requirements 2 3...

Page 6: ...Cycler 3 6 Loading Samples in the Veriti 60 Well Thermal Cycler 3 7 Creating a New Run Method 3 8 Editing Details 3 10 Performing a Run 3 18 Monitoring a Run 3 21 Viewing and Printing the Run Report 3 25 Removing the Samples from the Instrument 3 25 Chapter 4 Troubleshooting Troubleshooting 4 2 Returning an Instrument for Service 4 3 Chapter 5 Utilities Using GeneAmp PCR System 9700 Run Methods 5 ...

Page 7: ...ndix B Disposables Disposables B 2 Other Supplies for Sample Handling B 4 Appendix C Predefined Run Methods Predefined Run Methods C 2 AmpliCycle Seq Run Method C 2 AmpliTaq Gold DNA Polymerase Run Method C 3 AmpliTaq Gold Fast PCR Run Method C 3 BigDye Kit Fast Run Method C 4 BigDye Kit Standard Run Method C 4 Fast PCR Run Method C 5 General PCR Run Method C 5 LMS2 Run Method C 6 Time Release Run...

Page 8: ...vi Veriti Thermal Cycler User Guide ...

Page 9: ...A right arrow symbol separates successive commands you select from a drop down or shortcut menu For example Select File Open Spot Set Right click the sample row then select View Filter View All Runs User Attention Words Two user attention words appear in Applied Biosystems user documentation Each word implies a particular level of observation or action as described below Note Provides information ...

Page 10: ...omments 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 l...

Page 11: ...ping package with Black case containing the digital thermometer and probe assembly Completed copy of the Certificate of Instrument Decontamination Payment for shipping handling in one of the following forms Purchase order Company letterhead with the words verbal purchase order Visa MasterCard credit card information Your address and contact information Billing address Return shipping address Name ...

Page 12: ...x Veriti Thermal Cycler User Guide Preface ...

Page 13: ...s Safety Conventions Used in This Document xii Symbols on Instruments xiii Safety Labels on Instruments xiv General Instrument Safety xv Chemical Safety xvi Chemical Waste Safety xvii Electrical Safety xvii Physical Hazard Safety xvii Safety and Electromagnetic Compatibility EMC Standards xvii ...

Page 14: ...n 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 o...

Page 15: ...sition 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 prot...

Page 16: ...mbol Description Do not dispose of this product as unsorted municipal waste Follow local municipal waste ordinances for proper disposal provisions to reduce the environmental impact of waste electrical and electronic equipment WEEE 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...

Page 17: ...nd specific safety practices for the instrument Read and understood all applicable Material Safety Data Sheets MSDSs See About MSDSs on page xvi Cleaning or Decontaminating the Instrument 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 WARNING Hot Replace lamp with...

Page 18: ...at appears in the MSDS of interest then click Search 3 Find the MSDS of interest click the link or right click the MSDS title then select any of the following Open To view the MSDS Print Target To print the MSDS Save Target As To download a PDF version of the MSDS Note For the MSDSs of chemicals not distributed by Applied Biosystems contact the chemical manufacturer Chemical Safety Guidelines To m...

Page 19: ...protection against the risk of fire replace fuses only with fuses of the type and rating specified for the instrument Power 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 properl...

Page 20: ... instrument has been tested to and complies with standards 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 ...

Page 21: ... 1 Veriti Thermal Cycler User Guide 1 System Overview 1 This chapter covers Introducing the Veriti Thermal Cycler 1 2 Using the Touchscreen 1 3 Menu Overview 1 6 About Run Methods 1 8 About Folders 1 15 ...

Page 22: ...an transmit run methods from one Veriti thermal cycler to another and start multiple thermal cyclers at once The Veriti Thermal Cycler has a run recovery feature If a power failure occurs during a run the instrument will attempt to continue the run when the power returns In addition the Veriti 96 Well Thermal Cyclers have VeriFlex Blocks These are six independently regulated thermal blocks to aid ...

Page 23: ... 1 Buttons in the Veriti Thermal Cycler touchscreen Button Function Returns to the Main Menu screen 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 Scrolls up and down through a list of items Displays the run method folders Creates a shortcut...

Page 24: ... 2 The Veriti Thermal Cycler text editor To Touch Enter a lowercase letter A letter button Enter an uppercase letter Caps then the letter s 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 and save any changes ...

Page 25: ...e 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 ...

Page 26: ...ration options If you have administrative privileges you access the Admin Menu screen from this screen see The Settings Menu Screen on page 1 7 Tools Menu to access instrument tests tools such as a Tm calculator and run method conversion as well as viewing the results of the last run and statistics about the instrument see The Tools Menu Screen on page 1 8 My Account to view and edit your account ...

Page 27: ...tings Menu screen with the Admin Menu button shown The Admin Menu Screen Use this screen to manage user accounts set instrument security back up run methods and settings upgrade the firmware and perform other functions If your system does not require login the Manage Users button is not shown For instruments that require login only Administrators have access to this menu Figure 1 6 The Admin Menu ...

Page 28: ...methods are stored in the instrument firmware Predefined Methods The Veriti Thermal Cycler firmware has ten predefined run methods AmpliCycle Seq Run Method AmpliTaq Gold DNA Polymerase Run Method AmpliTaq Gold Fast PCR Run Method BigDye Kit Standard Run Method BigDye Kit Fast Run Method Fast PCR Run Method General PCR Run Method LMS2 Run Method Time Release Run Method Touchdown PCR Run Method XL ...

Page 29: ... User you can make changes to the run method but you cannot save it If you are logged on as a Guest you can make changes to the run method but you can only save it to a USB drive 2 To view Other steps in the run method Touch the arrow buttons at the end of the run method View steps with ramp rates Touch Options then Ramp Rate The fields showing times update to show the corresponding ramp rates 3 W...

Page 30: ... 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 criteria Touch the title of the column with the criteria by which you want to sort the run methods Touch the title a second time to sort in the opposite o...

Page 31: ...lect it then touch View Edit see Editing Details on page 3 10 Copy one 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...

Page 32: ...that opens verify the deletion 5 Touch Yes in the message box The run method is deleted Designating a Run Method as the Default 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 l...

Page 33: ...s appear as buttons in the Main Menu screen The name of the method is followed by the name in parentheses of the folder where the method is stored Note Run method names longer than twelve characters will appear truncated on the shortcut button To delete a shortcut to a run method see Configuring Main Menu Shortcuts to Functions on page 2 15 Backing Up Run Methods and Other Settings You can back up...

Page 34: ...dmin Menu screen 7 Remove the USB drive and store it in a safe place Restoring Run Methods and Other Settings 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 To restore run methods and instrument settings 1 Insert the USB drive containing the saved run methods and settings ...

Page 35: ... network you should change the instrument s name See Setting the Instrument Name on page 2 8 About Folders Each run method is saved in a folder There are three folders available by default 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 h...

Page 36: ...uch 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 Close to return to the Settings Menu screen Renaming Custom Folders You can rename any custom folder 1 In the Main Menu screen touch Settings Menu 2 In the Settings Menu screen touch Manage Folders 3 In the Manage Folde...

Page 37: ...2 1 Veriti Thermal Cycler User Guide 2 Getting Started 2 This chapter covers Installing the Veriti Thermal Cycler 2 2 Setting Up the Veriti Thermal Cycler 2 7 ...

Page 38: ...m Specifications Table 1 Physical dimensions weight and power consumption Parameter Instrument Footprint Recommended Clearance Total Length 48 5 cm 19 1 in 15 5 cm 6 1 in At the rear of the instrument to ensure adequate airflow and cooling 64 cm 15 2 in Width 23 7 cm 9 3 in 0 cm 0 in 23 7 cm 9 3 in Height With the heated cover open 40 0 cm 15 7 in 15 5 cm 6 1 in Above the instrument to provide ade...

Page 39: ...terials Scissors pocket knife or box cutter Compressed air Protective hardware as appropriate see below Optional Protective Hardware Applied Biosystems supports the use of the following devices to protect the Veriti Thermal Cycler 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 Powe...

Page 40: ... grip Keep your spine in a neutral position Bend at the knees and lift with your legs 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 Applied Biosystems Veriti Thermal Cycler User Guide CD Cable Power 13A 125V North America PN 4382067 Cable Power 10A 220V Europe PN 4382068 Veriti System Starter Kit Setting Up th...

Page 41: ...ycler 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 Thermal Cyclers you need An Ethernet cable for each Veriti Thermal Cycler A network switch A TCP IP printer if you want to print For best results do not connect the network switch to your laboratory s network Communication betwee...

Page 42: ...he Instrument for a Printer on page 2 8 7 Continue with Powering On below 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 The instrument powers on and the Main Menu screen is displayed ...

Page 43: ...uses and stand by page 2 15 Shortcuts to instrument functions to be displayed on the Main Menu page 2 15 Setting the IP Address Note If your instrument is not on a network you do not need to set the IP 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 ...

Page 44: ... be more than 24 alphanumeric characters or for numeric only names 10 characters 5 Touch Yes next to Allow Remote Runs to make the instrument available for remote runs a run on this instrument can be started from another instrument otherwise touch No 6 Touch Done then OK to save your changes and return to the Admin Menu screen Note If you edit the Instrument Name field you can still view the seria...

Page 45: ...or the instrument 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 Security 5 To allow VeritiLink Remote Management Software to control this instrument touch Yes next to Allow VeritiLink Software Control 6 To require each user to log in when using the instrument touch Yes next ...

Page 46: ...three access levels 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 User Can perform runs create view edit delete save and print run methods and run tests Cannot manage users or set instrument preferences Administrator Can access all instrument functions including setting security managing users and...

Page 47: ...ing 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 In the Admin Menu screen touch Manage Users The Manage Users screen is displayed 5 Touch Add User The Create New User Account screen is displayed 6 Enter information for the new user The required fields are User Name Password Re enter P...

Page 48: ...n 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 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 ...

Page 49: ...evel for the user Touch Set Password to change the password for the user 7 Touch Done then OK to return to the Manage Users screen 8 When you finish touch Close to return to the Admin Menu Deleting a User 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 ...

Page 50: ...ttings apply to all users Setting Idle Temperatures for the Block s and Cover 1 In the Main Menu screen touch Settings Menu 2 In the Settings Menu screen touch Set Idle Temperatures 3 In the Idle State Temperatures screen to set the temperatures for the sample block s and the cover touch Table 2 Additional options and their default values for the Veriti Thermal Cycler Option Default Value See Page...

Page 51: ...hat 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 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 Menu Shortcuts to Functions You can add buttons to t...

Page 52: ...ouch Page Up and Page Down to scroll through the list 3 Touch Done to return to the Settings Menu screen The selected shortcut s appear in the Main Menu screen Deleting Shortcuts To delete a shortcut follow the steps above but uncheck the function to remove it from the Main Menu Any run methods for which there is a shortcut are shown at the bottom of the list and can also be deleted ...

Page 53: ... chapter covers Selecting Disposables 3 2 Loading Samples into the Instrument 3 5 Creating a New Run Method 3 8 Editing Details 3 10 Performing a Run 3 18 Monitoring a Run 3 22 Viewing and Printing the Run Report 3 25 Removing the Samples from the Instrument 3 25 ...

Page 54: ...r these items Disposables for 96 Well Veriti Thermal Cyclers 96 Well Tube Configurations IMPORTANT The tray or the tray retainer is required for the operation of the Veriti Thermal Cycler You can use three different types of tube configurations to hold your samples as shown in Figure 3 1 Figure 3 1 Different tube configurations for use in 96 Well Veriti Thermal Cyclers GR1086c Sedona Tubes Caps St...

Page 55: ...e with Cap 0 1 mL 96 Well Tray for VeriFlex Blocks MicroAmp Reaction Tube with Cap 0 2 mL MicroAmp 8 Tube Strip 0 2 mL or MicroAmp Reaction Tube without Cap 0 2 mL MicroAmp 8 Cap Strip and MicroAmp 96 Well Tray Retainer Set for Veriti Systems GR2006 MicroAmp 8 Cap Strip MicroAmp Fast Optical 96 Well Reaction Plate 0 1 mL or MicroAmp Optical 96 Well Reaction Plate 0 2 mL MicroAmp Splash Free 96 Wel...

Page 56: ... Figure 3 2 MicroAmp Optical 384 Well Reaction Plate with MicroAmp Clear Adhesive Cover Disposables for the 60 Well Veriti Thermal Cycler You can use three types of tubes to hold your samples as shown in Figure 3 3 Figure 3 3 Different tubes for use in the Veriti 384 Well Thermal Cycler GeneAmp Thin Walled Reaction Tube with Flat Cap 0 5 mL GeneAmp Thin Walled Reaction Tube with Domed Cap 0 5 mL o...

Page 57: ...en pressure on all tubes eliminating condensation on the tubes 1 Set the 96 well tray on a splash free 96 well base 2 Place the reaction tubes in the tray 3 Pipette the samples into the reaction tubes 4 Cap the tubes 5 See Placing the Sample Tray or Plate onto the Sample Block s on page 3 6 Loading the Reaction Plate 1 Place the reaction plate on a splash free 96 well base 2 Pipette the samples in...

Page 58: ...ase in the sample block s 3 Close the heated cover Loading Samples in the Veriti 384 Well Thermal Cycler This section describes how to load samples in 384 well reaction plates 1 Pipette the samples into the sample wells 2 Cover the plates with MicroAmp Clear Adhesive Film 3 Place the MicroAmp Optical 384 Well Reaction Plate onto the sample block s so that well A1 is at the upper left corner of the...

Page 59: ...ure in the tubes The GeneAmp Thin Walled Reaction Tubes fit tightly in the wells and the heated cover exerts an even pressure on all tubes eliminating condensation on the tubes 1 Pipette the samples into the reaction tubes 2 Cap the tubes 3 Place the GeneAmp Thin Walled Reaction Tubes with Flat or Domed Caps 0 5 mL onto the sample block s 4 Place the GeneAmp Thermal Isolation Frame around the samp...

Page 60: ...signating a Run Method as the Default on page 1 12 3 Edit the default run method as needed Insert a stage see Adding a Stage on page 3 10 Insert a step see Adding a Step on page 3 11 Add an AutoDelta step see Creating an AutoDelta Step on page 3 13 Add a pause see Adding a Pause on page 3 15 Delete a step or stage see Deleting a Stage or Step on page 3 15 For Veriti 96 Well Thermal Cyclers you can...

Page 61: ...d 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 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 Set the cover temperature if any Cov...

Page 62: ...locks page 3 16 Available only on Veriti 96 Well Thermal Cyclers Adding a Stage The two types of run method stages are 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 Holding The steps in a holding stage are not repeated To add a stage 1 In the Edit Run Method scree...

Page 63: ...he Stage Name to select it 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 12 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 2 Touch Add A copy of the selected step is added to the run method ...

Page 64: ...e keys in the editor c Repeat for any other field 3 Touch Done to close the editor Editing Ramp Rates You can edit the rate at which the instrument ramps to the temperature for the step The default ramp rate is 100 Note You cannot edit ramp rates for methods created using the Convert Method wizard see Using GeneAmp PCR System 9700 Run Methods on page 5 2 1 Touch a step to select it 2 Touch Options...

Page 65: ...ed 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 during subsequent cycles at lower temperatures they outcompete the nonspecific sequences to which the primers bind at l...

Page 66: ...mperature that increases the button should show and or 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 th...

Page 67: ...isplay the Add a Pause Before a Step dialog box 3 4 Enter The first cycle in which the run will pause The frequency of the pause 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 see Step 3 in Stage 3 below Deleting a Stage or Step 1 In the Edit Run Method screen touch the stage or step to select it...

Page 68: ...ch VeriFlex block the same the default The VeriFlex blocks can be used to provide up to six different temperature zones for the 96 wells A step that has different temperatures for different VeriFlex blocks 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 blocks 1 Touch a step then Options The optio...

Page 69: ... 4 Repeat step 3 for each of the six VeriFlex blocks then touch Done Note To set each block 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 Touch Time enter the duration in minutes and seconds then touch Done or Touch Ramp Rate enter the ramp rate as a percentage value t...

Page 70: ...hod to select it 4 Touch Start Run The Run Parameters screen is displayed 5 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 Veriti 96 Well Fast Thermal Cycler 5 to 40 µL Veriti 96 Well Thermal Cycler 10 to 100 µL Veriti 384 Well Thermal Cycler 5 to 30 µL Verit...

Page 71: ...h 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 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 t...

Page 72: ...hapter 3 Performing a Run 10 While the cover heats the Cover Heating dialog box appears in the Run Monitor screen If you want to Start the run immediately before the cover reaches the specified temperature Touch Skip Stop the run Touch Stop ...

Page 73: ...imated time remaining in the run and 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 fie...

Page 74: ...ber of cycles 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 Touch Pause Run see Pausing a Run on page 3 23 View run method information Touch View Method Information The information you entered in the Run Parameters dialog box is shown Display the time for the run Touch Display Method Time The...

Page 75: ...emaining time for the pause Elapsed Time is continually updated to show the time the run has been in process 2 If you want to Pause until the default pause has elapsed Do nothing 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 Resume the run immediately Touch Resume Run to the left of the dialog box Stop...

Page 76: ... stage in the middle of the button is replaced by an alert icon Figure 3 2 Alert icon shown in the Run Monitor button when an error occurs If the Power Fails If a power failure occurs during a run the instrument attempts to continue the run when the power returns The run begins at the first step of the stage where the power failed For example the power fails during step 2 of the tenth cycle for a ...

Page 77: ... in the Tools Menu Note The run report is saved only until the next run is finished 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 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 ge...

Page 78: ...3 26 Veriti Thermal Cycler User Guide Chapter 3 Performing a Run ...

Page 79: ...4 1 Veriti Thermal Cycler User Guide 4 Troubleshooting 4 This chapter covers Troubleshooting 4 2 Returning an Instrument for Service 4 3 ...

Page 80: ...the Cycle Performance Test When running on multiple instruments cannot see instruments in Select Instruments screen Instrument s not connected to network Switch powered off Ethernet cable bad IP address conflict Allow Remote Runs setting in Instrument Name screen set to No Are all Ethernet cables connected to the instruments Are all Ethernet cables connected to the network switch Try a different E...

Page 81: ...ination If the block s 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 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...

Page 82: ...4 4 Veriti Thermal Cycler User Guide Chapter 4 Troubleshooting ...

Page 83: ... Using GeneAmp PCR System 9700 Run Methods 5 2 Upgrading System Firmware 5 5 Calculating Melting Temperatures 5 7 Viewing Instrument Statistics 5 8 Restoring the Factory Settings 5 8 Running the Cycle Performance Test 5 10 Tests Using the Temperature Verification Kit 5 11 ...

Page 84: ...al optimization may be needed The available conversions are specific to the type of instrument Veriti 96 Well Fast Thermal Cycler Only 9700 Max Mode run methods can be converted Veriti 96 Well Thermal Cycler Run methods in 9600 Emulation Mode or 9700 Max Mode can be converted Note Only users who can save run methods all users except Limited Users have access to this function To use a run method fr...

Page 85: ...t when you are done 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 By default the name begins with 9700 Max Mode or 9600 Mode depending on the format selected in step 4 Also enter the reaction volume the temperature for the heated cover if any and any notes for this method When you finish touch Save Exit The Tools Menu is ...

Page 86: ...You cannot edit the ramp rates in the method created by the Convert Method wizard This is indicated by 9600 or 9700M in the Time field when you choose to view ramp rates rather than time see Figure 5 1 Figure 5 1 Converted run method showing 9700M as the ramp rate ...

Page 87: ...a Open the About the Instrument screen Touch Log Off to return to the Login Options screen then touch About the Instrument or In the Main Menu screen touch Settings Menu then About the Instrument The About the Instrument screen opens b Record the version number of the firmware then touch Done 2 Determine the version number of the new firmware a On a computer connected to the Internet go to www app...

Page 88: ... 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 3 Log in as a user with Administrator access 4 In the Main Menu screen touch Settings Menu 5 In the Settings Menu screen touch Admin Menu 6 In the Admin Menu screen touch Upgrade Firmware The Firmware Upgrade screen opens 7 Touch ...

Page 89: ...screen touch Tools Menu 2 In the Tools Menu screen touch Calculate Tm to open the Tm Calculator screen 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 µM c Enter each primer sequence 4 Touch Calculate The melting temperature for each primer is displayed ...

Page 90: ... block s were heated from 10 degrees to 30 degrees for 3 cycles the total degrees would be 60 3 30 10 60 3 When you finish touch Done to return to the Tools Menu screen Restoring the Factory Settings You can reset the instrument to the default values for all instrument settings When you do this the following are lost All run methods except the predefined methods listed in Appendix C Any users and ...

Page 91: ...up No to restore the default settings without first performing a back up Before the restore operation begins you are prompted to confirm the restore with a second dialog box IMPORTANT Touching No erases all run methods user accounts and other settings from the instrument Cancel to cancel the restore operation When the restore process is complete a message box stating Factory settings have been res...

Page 92: ... Reaction Plate PN 4309849 Veriti 60 Well Thermal Cycler GeneAmp Thermal Isolation Frame PN 4308927 Procedure This test takes 10 minutes to complete 1 Place the reaction plate or thermal isolation frame in the instrument 2 In the Main Menu screen touch Tools Menu 3 In the Tools Menu screen touch Run Cycle Performance Test 4 Follow the instructions on the screen to perform the test The results are ...

Page 93: ...ication Kit User Guide PN 4376864 Running the Heated Cover Verification Use this test to verify that the heated cover is within 3 C of the 105 C set point Required Materials The appropriate Temperature Verification Kit for your Veriti Thermal Cycler model see table above Procedure This test takes 10 to 15 minutes to complete PHYSICAL INJURY HAZARD Hot Surface Use care when working around the heate...

Page 94: ...s within 0 25 C of the set point temperature Required Materials The appropriate Temperature Verification Kit for your Veriti Thermal Cycler model see table above Procedure This test takes 25 to 30 minutes to complete but you can cancel before it is complete PHYSICAL INJURY HAZARD Hot Surface Use care when working around the heated cover and sample block s to avoid being burned 1 In the Main Menu s...

Page 95: ...les are not damaged no nicks cuts or crimps and are securely seated in the digital thermometer and in the instrument Heated cover is closed Results are saved or printed 6 If the 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 ...

Page 96: ...5 14 Veriti Thermal Cycler User Guide Chapter 5 Utilities ...

Page 97: ...6 1 Veriti Thermal Cycler User Guide 6 Maintenance 6 This chapter covers Scheduled Maintenance 6 2 As Needed Maintenance 6 2 Parts List 6 6 ...

Page 98: ...r decontamination method except those recommended in the manual you risk damaging the equipment Clean the sample wells once a month or as needed 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 During instrument operation the temperature of the heated cover can be as high a...

Page 99: ... contamination If the block s cannot be decontaminated the instrument cannot be returned to Applied Biosystems for service Cleaning the Heated Cover Clean the heated cover once a month or as needed During instrument operation the temperature of the heated cover can be as high as 108 C and the temperature of the sample block s can be as high as 100 C Before performing the procedure keep hands away ...

Page 100: ...t 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 Acceptable AC line voltage tolerances 100 120 220 230 10 240 VAC 6 10 50 60 Hz 1 Required Materials Two 10 A Type M 250 V 5 20 mm fuses Fine flat tip screwdriver Procedure 1 Turn off the instrument and disconnect the power...

Page 101: ...3 Pull out the fuse compartment to inspect the two fuses in the fuse compartment 4 Pull out the blown fuse s from the fuse compartment and replace with new 10 A Type M 250 V 5 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 Power entry module Fuse ...

Page 102: ...e 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 Pr...

Page 103: ...A 1 Veriti Thermal Cycler User Guide A Instrument Specifications A This appendix covers System Specifications A 2 Printer Specifications A 3 ...

Page 104: ...h 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 lbs 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 USB v1 0 port for a connection to an external USB drive RS232 ...

Page 105: ...LCD color display with full VGA resolution Sample Well Specifications Printer Specifications The Veriti Thermal Cycler requires a printer that Has an Ethernet port Supports the LPD LPR protocol often called a TCP IP printer Instrument Model No of Wells Volume Well Veriti 96 Well Fast Thermal Cycler PN 4375305 96 0 1 mL Veriti 96 Well Thermal Cycler PN 4375786 96 0 2 mL Veriti 384 Well Thermal Cycl...

Page 106: ...A 4 Veriti Thermal Cycler User Guide Chapter A Instrument Specifications ...

Page 107: ...B 1 Veriti Thermal Cycler User Guide B Disposables B This appendix covers Disposables B 2 Other Supplies for Sample Handling B 4 ...

Page 108: ...ion Plate with Barcode x 4306737 x 4326659 MicroAmp Optical 96 Well Reaction Plate with Barcode and Optical Caps x 403012 MicroAmp Optical 96 Well Reaction Plate with Barcode and Optical Adhesive Films x 4314320 MicroAmp Optical 384 Well Reaction Plate x 4309849 MicroAmp Optical 384 Well Reaction Plate with Barcode x 4309849 x 4326270 x 4343814 12 Well Strips MicroAmp 12 Cap Strip x x N8010534 x x...

Page 109: ... Cap Assorted Colors 0 2 mL x N8010833 MicroAmp Optical Tube without Cap 0 2 mL x N8010933 GeneAmp Thin Walled Reaction Tube with Flat Cap 0 5 mL x N8010737 GeneAmp Thin Walled Reaction Tube with Domed Cap 0 5 mL x N801537 GeneAmp Thin Walled Reaction Tube with Domed Cap Autoclaved 0 5 mL x N8010611 Seals Covers MicroAmp Clear Adhesive Film x x x 4306311 MicroAmp Optical Adhesive Film x x x 436095...

Page 110: ...ith your samples and the Veriti Thermal Cycler Product Part Number MicroAmp 96 Well Base N8010531 MicroAmp Splash Free 96 Well Base 4312063 GeneAmp Thermal Isolation Frame 4308927 MicroAmp Cap Installing Tool Handle 4330015 MicroAmp Multi Removal Tool 4313950 MicroAmp Adhesive Film Applicator 4333183 MicroAmp Centrifuge Adapter N8013822 ...

Page 111: ...C 1 Veriti Thermal Cycler User Guide C Predefined Run Methods C This appendix covers Predefined Run Methods C 2 ...

Page 112: ... AmpliCycle Seq Run Method AmpliTaq Gold DNA Polymerase Run Method AmpliTaq Gold Fast PCR Run Method BigDye Kit Fast Run Method BigDye Kit 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 cannot be edited or deleted but if you save them with a different name or to a different folder y...

Page 113: ...ensitivity of PCR This run method specifies a pre PCR heat step for activation of AmpliTaq Gold DNA Polymerase AmpliTaq Gold Fast PCR Run Method Use this run method for PCR with AmpliTaq Gold Fast PCR Master Mix UP to produce optimal yield and specificity for a 500 bp amplicon This run method is optimized to generate template for DNA sequencing reactions and is only available on Veriti 96 Well The...

Page 114: ...tor Cycle Sequence Ready Reaction Kits BigDye Kit 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 this run method are optimized for AmpliTaq DNA Polymerase FS and the cycle sequencing reagents supplied with the BigDye Termi...

Page 115: ...mp 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 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 ...

Page 116: ...mer pairs for analysis of select microsatellite loci from the Généthon human linkage map 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 slo...

Page 117: ...specific products XL PCR Run Method Use this run method for amplification of 5 to 40 kb PCR products using rTth 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 th...

Page 118: ...C 8 Veriti Thermal Cycler User Guide Chapter C Predefined Run Methods ...

Page 119: ...aintenance 6 1 Performing a Run 3 1 System Overview 1 1 Troubleshooting 4 1 Utilities 5 1 chemical safety xvi 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 safety xii user attention words vii creating folders 3 9 run methods 3 8 shortcuts to ...

Page 120: ... Development department contacting viii installation category xvii instrument operation safety xv instrument properties IP address 2 7 name 2 8 serial number 2 8 Instrument Specifications appendix A 1 IP address setting 2 7 italic text when to use vii L linkage mapping C 6 LMS2 run method C 6 M Main Menu screen 1 6 Maintenance chapter 6 1 maintenance schedule 6 2 Manage Users button missing 4 3 me...

Page 121: ...ety before operating the instrument xv chemical xvi chemical waste xvii conventions xii electrical xvii guidelines xvi xvii instrument operation xv moving and lifting instrument xv moving parts xvii moving lifting xv physical hazard xvii standards xvii safety labels on instruments xiv safety standards xviii safety symbols on instruments xiii sample block s statistics 5 8 temperature when idle 2 14...

Page 122: ...ing 3 12 elapsed for run 3 22 remaining for run 3 22 setting current 2 8 Time Release run method C 6 Tools Menu screen 1 8 total cycles 5 8 total degrees for block s 5 8 Touchdown PCR description 3 13 predefined run method C 7 touchscreen cleaning 6 2 training information on viii Troubleshooting chapter 4 1 TVK See temperature verification kit 5 11 U upgrading firmware 5 5 USB port A 2 user attent...

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Page 124: ...sales office locations and technical support please call our local office or refer to our Web site at www appliedbiosystems com Applied Biosystems is committed to providing the world s leading technology and information for life scientists Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free In North America 1 800 345 5224 Fax 1 650 638 5884 06 2010 ...

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