manualshive.com logo in svg

ThermoFisher Scientific Applied Biosystems Veriti 4375305, User Manual, Page: 94 / 106

Share
Download
ThermoFisher Scientific Applied Biosystems Veriti 4375305 User Manual Download Page 94

BigDye

™

 Kit 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.

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

™

 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.thermofisher.com

.

Appendix E 

Predefined run methods

Predefined run methods

E

94

Veriti

™

 Thermal Cycler User Guide

Summary of Contents for Applied Biosystems Veriti 4375305

Page 1: ...arch Use Only Not for use in diagnostic procedures Veriti Thermal Cycler USER GUIDE Catalog Numbers 4375305 4375786 4384638 4388444 4413751 4413964 and ZGEXSCVERTI3Y Publication Number MAN0018441 Revi...

Page 2: ...ECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING YOUR USE OF IT Revision history Pub No MAN0018441 Revision Date Description B 0 17 June 2021 Addition of information on Fleet Control with Instrumen...

Page 3: ...sks for run methods 16 Copying a run method 17 Printing a run method 17 Deleting a run method 18 Designating a run method as the default 18 Creating a shortcut to a run method 19 Backing up run method...

Page 4: ...l Cycler 44 Loading samples into the instrument 44 Loading Samples in 96 well instruments 45 Loading samples in the 384 well instrument 46 Loading samples in the Veriti 60 well Thermal Cycler 47 Creat...

Page 5: ...d cover verification 73 Running the temperature verification 74 Running the temperature nonuniformity test 75 TVK recalibration 76 CHAPTER 5 Maintenance 77 Scheduled maintenance 77 As Needed maintenan...

Page 6: ...ranty 96 APPENDIX F Safety and EMC compliance information 97 Safety conventions used in this document 97 Safety alert words 97 Symbols on instruments 98 Electrical symbols on instruments 98 Environmen...

Page 7: ...APPENDIX G Documentation and support 105 Customer and technical support 105 Limited product warranty 105 Contents Veriti Thermal Cycler User Guide 7...

Page 8: ...n you can 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 durin...

Page 9: ...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 li...

Page 10: ...button Enter an uppercase letter Caps then the letter s When you are done select Caps again Enter punctuation or other symbols Symbols then the symbol s When you are done select Symbols again Remove...

Page 11: ...editor opens Figure 3 Figure 3 The instrument numeric editor To Select Enter a number A number button Delete the last number Remove the entire contents of the field Close the editor and save any chang...

Page 12: ...from this screen see Settings Menu screen on page 13 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 s...

Page 13: ...e 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 b...

Page 14: ...ware Predefined methods The instrument firmware has 10 pre defined run methods IMPORTANT The customer is responsible for validation of run methods on the instrument before use and for compliance with...

Page 15: ...annot 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 Use the arrow buttons at the end of...

Page 16: ...to view in the Manage Folders All screen Start a run Select a run method in the list of run methods then select Start Run see page 57 Create a new run method Select New see page 47 View or edit a run...

Page 17: ...hod then select Copy 4 In the Save Run Method screen a If you are copying one method select Name then rename the method and or select Folder to save the run method to a different folder or If you are...

Page 18: ...ge 95 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 meth...

Page 19: ...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...

Page 20: ...o 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 Select OK then se...

Page 21: ...t the Instrument screen is displayed 3 In the About the Instrument screen select Restore Methods Settings then Yes in the message box The instrument copies all run methods folders user information and...

Page 22: ...you can create one by selecting New in the Manage Folders screen Deleting custom folders You can delete any custom folder When you delete a custom folder all run methods in that folder are also delet...

Page 23: ...22 and 4 on page 22 to rename any other folders 6 When you are done making changes to folders select Close to return to the Settings Menu screen Chapter 1 System overview About folders 1 Veriti Therm...

Page 24: ...consumption Parameter Instrument Footprint Recommended Clearance Total Length 48 5 cm 19 1 in 15 5 cm 6 1 in 1 64 cm 15 2 in Width 23 7 cm 9 3 in 0 cm 0 in 23 7 cm 9 3 in Height 2 40 0 cm 15 7 in 15...

Page 25: ...t vibrates such as a refrigerator or centrifuge Pollution The Veriti Thermal Cycler has a Pollution Degree rating of 2 It may be installed in an environment that has nonconductive pollutants only such...

Page 26: ...al hazards and the resultant loss of data Before installing the system decide what additional hardware if any you want to install Power line regulator 1 5 kVA Surge protector line conditioner 10 kVA U...

Page 27: ...ent accessories from the instrument and set them aside d Lift and remove the cover from the instrument crate e Remove the packing material from the instrument then inspect the instrument for shipping...

Page 28: ...r a blast of air into each well of the sample block s to remove any particles that may have collected during transportation d Close the heated cover 2 Connect the power cable to the instrument 3 Optio...

Page 29: ...ect the Ethernet cable to the back of the thermal cycler and connect the other end of the cable to the network switch 2 Repeat step 1 on page 29 for each thermal cycler 3 Connect the printer to the ne...

Page 30: ...erforming a run be sure to set the following instrument settings Instrument IP address Setting the IP address on page 31 Instrument name Setting the instrument name on page 32 Current date and time Se...

Page 31: ...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 Ma...

Page 32: ...ent Name field you can still view the serial number in the About the Instrument screen You can access the About the Instrument screen from either the Login screen or the Settings Menu screen Configuri...

Page 33: ...n Menu 4 In the Admin Menu screen select Security 5 To allow VeritiLink Remote Management Software to control this instrument select Yes next to Allow VeritiLink Software Control 6 To require each use...

Page 34: ...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 t...

Page 35: ...ator Adding users To add a user 1 Log in as a user with Administrator access 2 In the Main Menu screen select Settings Menu 3 In the Settings Menu screen select Admin Menu 4 In the Admin Menu screen s...

Page 36: ...on screen 7 Select Done4OK to add the user account to the instrument The new user appears in the Manage Accounts screen 8 When you finish select Close to return to the Admin Menu screen Changing a use...

Page 37: ...for the user Select Set Password to change the password for the user 7 Select Done4OK to return to the Manage Users screen 8 When you finish select Close to return to the Admin Menu Deleting a user T...

Page 38: ...can be adjusted or activated These settings apply to all users Table 4 Additional options and their default values for the instrument Option Default Value See Page Idle temperatures for the cover and...

Page 39: ...led the temperature for the cover and or block s is not maintained by the instrument and will eventually come to room temperature b The Temperature field then enter the temperature The temperature for...

Page 40: ...rwise the shortcut buttons are displayed for all instrument users You can also create shortcuts to run methods see Creating a shortcut to a run method on page 19 1 In the Main Menu screen select Any b...

Page 41: ...clers The Thermal Cycler Fleet Control Software can be purchased separately and is not included with the Veriti Thermal Cycler For more information visit thermofisher com Connect the thermal cycler to...

Page 42: ...bles for the 60 well Veriti Thermal Cycler on page 44 See Appendix C Disposables for part numbers for these items Disposables for 96 well instruments 96 well tube configurations IMPORTANT The tray or...

Page 43: ...Amp Fast Optical 96 Well Reaction Plate 0 1 mL MicroAmp Caps 8 Cap Strip or MicroAmp Clear Adhesive Film not shown MicroAmp Optical 96 Well Reaction Plate 0 2 mL MicroAmp Fast Reaction Tube with Cap 0...

Page 44: ...Cycler You can use three types of tubes to hold your samples as shown in Figure 10 Figure 10 Different tubes for use in the Veriti 384 well Thermal Cycler Loading samples into the instrument See the a...

Page 45: ...cing the sample tray or plate onto the sample block s on page 46 Loading the reaction plate 1 Place the reaction plate on a MicroAmp Splash Free 96 Well Base 2 Pipette the samples into the sample well...

Page 46: ...the MicroAmp Tray or Plate onto the sample block s so that well A1 is at the upper left corner of the tray as shown below IMPORTANT Do not place the base in the sample block s 3 Close the heated cove...

Page 47: ...liminating 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...

Page 48: ...n page 55 For 96 well instruments you can add a step to program different temperatures on the VeriFlex Blocks see Creating a VeriFlex step on page 55 4 Select Save Exit to display the Save Run Method...

Page 49: ...d 10 Select Save Exit when you are done The Browse Run Methods screen is displayed Editing details This section describes how to edit a run method by Adding a stage Adding a stage on page 49 Adding a...

Page 50: ...eded a Select the stage b Select the cycles field the box below the Stage Name c Enter the number of cycles then select Done 4 To change the temperature and or time for any step in the stage see Editi...

Page 51: ...rature and time 1 Select any temperature field then edit the temperature as desired or Select any time field then edit the time as desired 2 You can edit any other times temperatures or the number of...

Page 52: ...elta step allows you to increase or decrease the temperature and or change the duration of the cycle during a cycling stage One use for an AutoDelta step is for touchdown PCR a method in which the ear...

Page 53: ...nter the minutes and seconds that the step duration should change with each cycle To enter a time that decreases with each cycle select to change it to To enter a time that increases the button should...

Page 54: ...se to display the Add a Pause Before a Step dialog box 3 Enter The first cycle in which the run will pause The frequency of the pause The duration of the pause in mm ss 4 Select Done to save the pause...

Page 55: ...eriFlex 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 Block...

Page 56: ...ote To set each block to the same temperature select the desired temperature field then select Apply Selected to All 5 Depending on your instrument configuration enter either a duration or a ramp rate...

Page 57: ...the run method 4 Select Start Run The Run Parameters screen is displayed 5 Select Reaction Volume to edit the reaction volume By default the reaction volume you entered when you saved the method is di...

Page 58: ...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 If you want to perform the run...

Page 59: ...Start the run immediately before the cover reaches the specified temperature Select Skip Stop the run Select Stop Monitoring a run Run Monitor screen You can follow the status of a run using the Run...

Page 60: ...atus and any errors that occur during the run Select the triangle to view the entire report H Arrow button Select this to see the additional steps in the run method See Actions in the Run Monitor scre...

Page 61: ...g the number of cycles You can change the number of cycles for a cycling stage while a run is in progress 1 If needed click the orange Run Monitor button to return to the Run Monitor screen 2 Select t...

Page 62: ...tely Select Resume Run to the left of the dialog box Stopping a run In the Run Monitor screen select Stop then OK The run stops and the Run Report opens Using the Run Monitor button The Run Monitor bu...

Page 63: ...e the power returns is more than 18 hours the run is not continued Viewing and printing the run report At the end of a run the Run Report screen is displayed below If the last stage of the run method...

Page 64: ...irmly with both hands and gently rock it back and forth until the tubes or plate are free CAUTION Sample caps may pop off if the cover is opened when the sample block s temperature is above 27 C Chapt...

Page 65: ...efore additional 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 9...

Page 66: ...16 characters By default the name begins with 9700 Max Mode or 9600 Mode depending on the format selected in step 4 on page 66 Also enter the reaction volume the temperature for the heated cover if an...

Page 67: ...the firmware IMPORTANT You cannot upgrade the firmware while a run is in progress Upgrading the instrument firmware 1 Determine the version number of the existing firmware from the About the Instrumen...

Page 68: ...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 w...

Page 69: ...ate the melting temperatures for a DNA primer pair 1 In the Main Menu screen select Tools Menu 2 In the Tools Menu screen select Calculate Tm to open the Tm Calculator screen 3 Enter the required info...

Page 70: ...d be 60 3 x 30 10 60 3 When you finish select 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...

Page 71: ...ith a second dialog box IMPORTANT Selecting 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...

Page 72: ...lect Tools Menu 3 In the Tools Menu screen select Run Cycle Performance Test 4 Follow the instructions on the screen to perform the test The results are displayed at the end of the test 5 At the end o...

Page 73: ...Temperature Verification Kit 4373997 Veriti 96 Well Thermal Cycler PN 4375786 with 0 2 mL sample wells 0 2 mL Temperature Verification Kit 4377669 Veriti 384 Well Thermal Cycler PN 4388444 with 0 02 m...

Page 74: ...ils repeat the procedure Ensure the Probe plate is in the correct location Probe 1 should be in well A5 during this test Cables are not damaged no nicks cuts or crimps and are securely seated in the d...

Page 75: ...aged no nicks cuts or crimps and are securely seated in the digital thermometer and in the instrument Results are saved or printed 6 If the test fails again contact Technical Support Running the tempe...

Page 76: ...ication Kit requires that you Decontaminate the probe assembly as described below Send the equipment and the completed Certificate of Instrument Decontamination to the manufacturer See Appendix G Docu...

Page 77: ...ure nonuniformity test on page 75 As Needed maintenance Tests Run the Temperature Nonuniformity Test see Running the temperature nonuniformity test on page 75 Cleaning the instrument Preparation Befor...

Page 78: ...ample tray Decontaminating the sample wells If the sample wells become contaminated with any biological agents clean the wells thoroughly with a cotton swab soaked in 1 10 v v dilution of 5 25 sodium...

Page 79: ...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 instr...

Page 80: ...ll configurations 10 A 4377690 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 Procedu...

Page 81: ...ack 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 Parts list Table 7 Kits and spares Part PN...

Page 82: ...374181 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 P...

Page 83: ...Instruments screen Instrument s not connected to network Make sure Ethernet cables are connected to the instruments Switch powered off Make sure Ethernet cables are connected to the network switch Et...

Page 84: ...sers button is not shown when instrument is monitored byVeritiLink Remote Management Software Use VeritiLink Software to manage user accounts Change Allow VeritiLink Software Control to NO in the Secu...

Page 85: ...ANT If the sample block s become contaminated with radioactivity use a commercially available decontaminant to remove the contamination If the block s cannot be decontaminated the instrument cannot be...

Page 86: ...roAmp Optical 96 Well Reaction 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 Barcod...

Page 87: ...h Cap 0 2 mL x N8010540 x N8011540 MicroAmp Reaction Tube with Cap Assorted Colors 0 2 mL x N8010840 MicroAmp Reaction Tube with Cap Autoclaved 0 2 mL x N8010612 MicroAmp Reaction Tube without Cap 0 2...

Page 88: ...lies 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 4...

Page 89: ...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 Power and communication connections Table 9 Power and communication Port Description 800 VA power cab...

Page 90: ...n specifications 640 480 pixel LCD color display with full VGA resolution Sample well specifications Instrument Model No of Wells Volume Well Veriti 96 Well Fast Thermal Cycler PN 4375305 96 0 1 mL Ve...

Page 91: ...ns The instrument requires a printer that Has an Ethernet port Supports the LPD LPR protocol often called a TCP IP printer Appendix D Instrument specifications Printer specifications D Veriti Thermal...

Page 92: ...t before use and for compliance with regulatory requirements that pertain to their procedures and uses of the instrument AmpliCycle Seq Run Method on page 93 AmpliTaq Gold DNA Polymerase Run Method on...

Page 93: ...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 AmpliTaq Gold Fast PCR Run Me...

Page 94: ...ycle 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 Terminator kits...

Page 95: ...analysis of select microsatellite loci from the G n thon human linkage map Time Release Run Method Use this run method for use with AmpliTaq Gold DNA Polymerase This method minimizes the pre PCR activ...

Page 96: ...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 s...

Page 97: ...s document Safety conventions used in this document Safety alert words Four safety alert words appear in Applied Biosystems user documentation at points in the document where you need to be aware of r...

Page 98: ...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 gr...

Page 99: ...e of a laser inside the instrument and to proceed with appropriate caution Indicates the presence of moving parts and to proceed with appropriate caution Safety labels on instruments The following CAU...

Page 100: ...URY HAZARD Using the instrument in a manner not specified by Applied Biosystems may result in personal injury or damage to the instrument Moving and lifting the instrument CAUTION PHYSICAL INJURY HAZA...

Page 101: ...nstrument verify that the fuses are properly installed and that the instrument voltage matches the power supply in your laboratory CAUTION FIRE HAZARD For continued protection against the risk of fire...

Page 102: ...quipment 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 R...

Page 103: ...ry waste container holds the immediate waste A secondary container contains spills or leaks from the primary container Both containers must be compatible with the waste material and meet federal state...

Page 104: ...duals should be trained according to applicable regulatory and company institution requirements before working with potentially biohazardous materials Follow all applicable local state provincial and...

Page 105: ...s and protocols Certificates of Analysis Safety Data Sheets SDSs also known as MSDSs Note For SDSs for reagents and chemicals from other manufacturers contact the manufacturer Limited product warranty...

Page 106: ...ti Thermal Cycler_UG_MAN0018441 v2 GUID C91D3CB1 6A23 45D6 AFB6 561C237FA546 2019 07 15 14 17 20 en 02 20 59 581 01 00 thermofisher com support thermofisher com askaquestion thermofisher com 17 June 2...

Reviews:

No comments