User Manual SuperCycler
Contents
1. User Manual SuperCycler SC 200 Revision 2 5 2010 lt Kyratec Korea Kyratec Life Science IT Premier Tower 1304 345 50 Gasan dong Geumcheon gu Seoul Korea 153 803 Website www kyratec com Australia Kyratec Pty Ltd 3 17 Dividend St Mansfield Brisbane Queensland Australia 4122 Website www kyratec com Sec BEE 14 8 Device SOMO FY Y FY HF FY HF Y HEFY HY EEF EWN 14 Kyratec SuperCycler User Manual v2 5 1 Foreword Congratulations on purchasing a Kyratec SuperCycler You are now one of a growing number of highly skilled customers worldwide to adopt the SuperCycler as their preferred Thermal Cycling Engine Our philosophy has been to generate user friendly yet powerful cycling workhorse We trust you will be most pleased with our product however always welcome any suggestions you may have to make our products better for the future Feel free to email us support kyratec com Kyratec SuperCycler User Manual v2 5 2 Features General The SuperCycler is a high performance block cycling system configured and optimised for Industry standard 200ul individual or strip tubes domed or flat capped or 96 well plates low or high skirt with strip caps or adhesive film seals It incorporates state of the art electronics precision quality Ferrotec peltier devices and a flexible user interface Configuration The SuperCycler utilises eight Peltier devices to actively heat and cool the block2. If you select to wait for the top heater to achieve temperature a waiting screen will be displayed You may skip the waiting step at any time if you wish to commence the run immediately Depending on the set temperature of the Top Heater it will take up to several minutes to pre heat to this temperature When the run commences the software will automatically proceed to the Run screen You are not able to modify the profile once a run has commenced From the run review screen you may also check the option run in virtual mode This will make the SC simulate the run rather than performing the actual thermal steps on the block This can be useful if you wish to check complicated runs prior to performing them Kyratec SuperCycler User Manual v2 5 8 5 Advanced Profile Generation and Execution Untitled Experiment User lt Hold Temp 95 Time Oh1 0m0s UL Cycling 40 Repeats op Step 1 D Temp 95 Time OhOm20s Step 2 Ed Temp 60 Time OhOm1 5s Step 3 Temp 72 Time OhOm15s Default The profile generation screen contains 6 icon buttons with the following functionality START RUN This button is used to activate a run Pressing this button will show a profile review ADD EVENT Evokes the Add Step wizard to build the profile step ADD NOTES Allows the operator to write and save any notes along with the run SAVE Allows a given profile to be saved to internal flash memory disk
3. The unit has very large internal memory allowing virtually unlimited profiles to be saved in the order of millions Saving a profile also stores the device options configurable under the setup menus ie top heater temperature and other functionality You may enter any valid file name for saving Profile file will be saved to the current user directory or the Default directory if no user is selected LOAD Loads a presaved profile from the internal flash memory The SuperCycler displays a list of the saved files on the unit in the directory of the currently selected user If no user is selected it will show the files saved in the default user directory To access a different users files you need to log in as that user CLEAR PROFILE will erase the current profile User confirmation is reguested before execution The graph in the centre of the screen will display the thermal profile of the currently selected The event list shows each of the events in the current profile To see or edit any step in the profile select it in the event list box The selected event will be displayed in the graph area Note that only the first few minutes of any step are displayed graphically When an event is selected a sub menu will be displayed giving further options for this event The selected event may be moved up or down in order within the profile events deleted or edited Kyratec SuperCycler User Manual v2 5 9 5 1 Creating a new Event The first
4. increasing time mode feature is often used to provide gradually extended times for enzymatic polymerization of longer products during later cycle repeats of an amplification reaction It is most useful for targets longer than about 1kb Long Range decreasing time mode can be used to shorten the total run time During later cycles the majority of enzymatic polymerization is occurring on previously generated amplicons which are shorter in length than the original template Shorter hold times are often sufficient for polymerization of these shorter length products TouchDown The Touchdown function enables the temperature of a step to be automatically decreased by a preset amount over a range of successive cycle repeats Its primary use is as a mechanism to minimise primerdimer artifacts by gradually decreasing the annealing temperature during initial Kyratec SuperCycler User Manual v2 5 4 cycle repeats of an amplification profile Pause The Pause function allows the user to pause the profile at any number of pre programmed points with an audible beep The current set temperature is held indefinitely until the Continue button is pressed Holds are useful if there is a need to remove tubes or add reagents at a particular point in a run Manual Control The SuperCycler also supports Manual Mode control This mode enables the user to set the block to a specific temperature guickly without creating a thermal profile This function is useful for
5. between 4 C and 99 C These are arranged into four zones with independent sensing and control capabilities This Configuration of peltiers and sensors enables a highly linear gradient to be established via a sophisticated computer control system Linear Gradient Available in selected regions Thermal gradient technology enables a varying temperature to be set across the reaction wells of the block Applications of this feature include the ability to optimize the annealing temperature of an assay in a single experiment by determining the temperature of the wells that yield the best result The SuperCycler is capable of generating a linear gradient of between 0 C and 20 C across the block The software interpolates and displays the temperature of each column of wells in real time during a run Thermal profile engine The SuperCycler has a powerful thermal profile engine implemented within A profile may contain up to 100 events Each event can be either a hold at temperature pause or 2 to 5 step cycling with up to 100 repeats Any event or step can contain gradient touchdown or long range features An almost unlimited number of profiles may be stored on the device for re running Despite its capabilities profile setup is straightforward LongRange The Long Range feature enables the time of a particular cycling step to be automatically increased or decreased by a preset amount over a specified range of cycle repeats The Long Range
6. button to the right allows you to change the number of steps between 2 and 5 for the cycling event Within the cycling configuration screens there are numerous options Once again If the Gradient option is selected both the left and right temperatures may be set separately and the predicted well temperatures can be shown by clicking the Predicted Temps link There are also options for Touchdown and Long range features Selecting these checkboxes will display extra buttons to configure these features Kyratec SuperCycler User Manual v2 5 10 Touchdown allows for the temperature of a given step within a cycling event to be progressively increased or decreased from an initial value to a final value over a defined number of steps LongRange allows the hold time of a given step within a cycling event to be progressively increased or decreased from an initial value to a final value over a defined number of steps Any or all of the steps within a cycling event may use these features The following picture displays the same screen with all options Gradient Touchdown amp LongRange enabled Set time and temperature Temp Initial Right c 60 Temp Final Right c 60 E Gradient W Touchdown avigtem W long Range IU The Next button will proceed through each of the parameter screens for each step contained within the cycling After the parameters for each step are configured the operator is prompted to enter the number of times
7. cycle numbers for when a profile is being executed At the bottom of this display box is the top heater TH and internal heatsink HS temperatures Note gradient feature not available all regions Kyratec SuperCycler User Manual v2 5 13 7 User Accounts an V AD En d Jenny James T Andrew S Add New User Kim Masters Ki Select User x Cancel Delete User In the users area you are able to select an existing user or create or delete a user profile When a user is selected Thermal profiles will be loaded or saved to a directory specific to that user Logging out will change back to default user To create a new user select the Add New User icon and then enter the user name and select a user profile image 8 Device Setup The setup area allows various device parameters to be changed Once in the setup area use the tab buttons to navigate the different setup features 8 1 File Manager USB Memory Stick File Transfer Utility SuperCycler USB Drive SCFileList 3 USBFileList to Ce y elete me Home File Manager System Setup TopHeater setup Callibration Software Update Extras Idle Elapsed 0 00 Total est 0 00 User Jenny AS The file manager area enables you to transfer run files between the default or individual user Kyratec SuperCycler User Manual v2 5 14 directories and a USB memory drive Plug your USB drive into the connector on the front of the unit and you may browse the directories
8. Configuration Information EN Idle Elapsed 0 00 Total est 0 00 User Jenny The 6 icons on the screen access the following features USERS allows you to select and setup a user profile for the machine PROFILE is the advanced mode to configure a thermal profile and initiate its execution MANUAL MODE allows immediate manual setting of block temperature WIZARD is a utility which allows quick easy profile setup CONFIGURATION allows configuration of machine options INFORMATION Displays a general information screen which includes such information as serial number software and hardware version numbers The bar at the bottom of the screen displays some useful information about the device and run status The first box displays the current activity it displays such information as idle ramping to temperature and hold xx with a countdown of the remaining hold time at the particular step The second box displays the Elapsed run time and the last box the total Estimated run time The actual run time may slightly differ from the estimated time depending on factors such as the ambient air temperature humidity and the type of plasticware and liguid volumes on the block The current user name and profile picture is also displayed as well as the current time and date Kyratec SuperCycler User Manual v2 5 DH 4 Wizard Mode Basic profile setup The SuperCycler software includes a Wizard utility which enables the user to c
9. Stylus check with your local distributor 11 Terms of Use END USER LICENCE AGREEMENT Kyratec SuperCycler SC200 IMPORTANT THIS END USER LICENCE AGREEMENT or EULA IS ALEGAL AGREEMENT BETWEEN THE PERSON COMPANY OR ORGANIZATION THAT HAS PURCHASED THIS EQUIPMENT YOU OR CUSTOMER AND KYRATEC BY USING THIS DEVICE CUSTOMER AGREES TO THE TERMS OF THIS AGREEMENT IF YOU DO NOT AGREE TO BE BOUND BY THESE TERMS OR DO NOT HAVE AUTHORITY TO BIND CUSTOMER TO THESE TERMS THEN DO NOT CONTINUE AND RETURN THE DEVICE TO YOUR PLACE OF PURCHASE FOR A REFUND IN ACCORDANCE WITH ITS REFUND POLICIES 1 Definitions a Supplier means Kyratec or one of its distributors b Device means Kyratec SuperCycler SC200 Thermal Cycler c Region means the country group of countries or area in which device is located d Features means software or hardware operational functionality 2 License Grants Customer is only granted rights to use the device features which are offered to them in the region in which device was purchased and resides Customer warrants that the selected region is the true region of its purchase and physical operational location Incorrect selection of region is in breach of supplier terms of license and may or may not breach any 3rd party license terms Customer accepts sole responsibility for incorrect region selection and consequences of any breach of 3rd party intellectual property associated with said featu
10. ay the logo and take a few moments to initiate the software 3 1 Region Selection When the unit is powered on for first time ever the region selection and End User Licence Agreement EULA will be displayed The operator is required to select their correct region of purchase and operation read the terms of use and check the agree box then press the green tick to continue Note that available features vary between different regions The features that are available for your use are always as specified to you before your purchase of the equipment IMPORTANT THIS END USER LICENCE AGREEMENT or EULA IS A LEGAL AGREEMENT BETWEEN THE PERSON COMPANY OR ORGANIZATION THAT HAS PURCHASED THIS EQUIPMENT YOU OR CUSTOMER AND KYRATEC BY USING THIS DEVICE CUSTOMER AGREES TO THE TERMS OF THIS AGREEMENT IF YOU DO NOT AGREE TO BE BOUND BY THESE TERMS OR DO NOT HAVE AUTHORITY O BIND CUSTOMER TO THESE TERMS THEN DO NOT CONTINUE AND RETURN THE DEVICE TO YOUR PLACE OF PURCHASE FOR A REFUND IN ACCORDANCE WITH ITS REFUND POLICIES 1 Definitions a Supplier means Kyratec or one of its distributors b Device means Kyratec SuperCycler SC200 Thermal Cycler c Region means the country group of countries or area in which device is located d Features means software or hardware operational functionality D License Grants ustomer is only granted rights to use the device features which are offered to them in the region i
11. incubating reactions such as DNA digestion or ligation Manual Mode also supports thermal gradient Condensation Free Heated Lid The SuperCycler employs a heated lid design to keep the air contained within the tube hotter than the reaction volume This causes any evaporation to condense back into the cooler reaction liguid thereby eliminating the need for oil or wax condensation overlay User Interface The SuperCycler has a 7 colour touch screen giving a vibrant and flexible means of run setup and monitoring This internal graphical user interface controller provides a powerful yet intuitive and easy to use interface All SuperCyclers have a USB port and soon to be released Windows based PC software This software opens the user up to easier profile setup sharing of files and post run examination of any temperature data New software features and updates are regularly incorporated and available for either system as free upgrades via web download Kyratec SuperCycler User Manual v2 5 5 3 Initial Power On Plug the unit into a power outlet and power the unit on with the switch located on the rear of the unit Do not worry about selecting the correct power voltage for your country The SuperCycler is designed to operate in any country in the world with no changes The unit is also designed to be be resistant to power surges and drop outs that occur in countries with less reliable power grids On power up the SuperCycler will displ
12. n The native calibration option bypasses all pre programmed calibration and runs un calibrated This mode should only be used if there is a problem with the unit calibration You can also perform a calibration of the touch screen interface using the calibration wizard If the calibration has varied click on this button and follow the instructions to re calibrate the screen If you are having difficulties navigating to this option because the touchscreen is out of calibration then you may use a USB mouse plugged into the front USB port to reach the touchscreen calibration wizard Kyratec SuperCycler User Manual v2 5 16 8 5 Software Update A facility has been provided to update the software which resides on the SuperCycler The upgrade file you receive from our support team or the website should be placed on the main root directory of your USB memory stick You may then select it to upgrade the unit s software IMPORTANT NOTE Do not interrupt the unit while a file upgrade is in progress Switching off the power during upgrade may render the unit inoperable 8 6 Extras Under the extras tab you will find some other programs The Oligo Calculator is useful for calculating the theoretical melt temperature and other information pertaining to the oligo design Simply enter the seguence and it does the rest Several popular Games are also provided for your enjoyment 9 User Tips It is recommended before you use the device for the first
13. n This is the preferred option as it will provide for a longer peltier service life Audible alarm on run completion toggles whether there is an audible alarm or just a screen message to alert the operator that the run has completed Use Predicted Temperature for Hold times The SC software implements a thermal model which predicts the actual liquid temperature inside the reaction vessels Hold times can be based on this model default or based purely on the block temperature Using the predicted temperature effectively increases the hold times and total run time slightly but gives a more accurate representation of the hold time of the actual sample liquid Most manufacturers thermal cyclers purely use the block temperatures for timing Auto Resume Run After Power Outage If this feature is available on your cycler not available on all models then when this box is checked a run will automatically resume at the same place if power should be momentarily lost during a run Set Time amp Date using these drop boxes The Region Configuration button enables the Operational region to be changed should the instrument be moved to a different country Note that available features vary between different regions See Section 2 1 for more information Kyratec SuperCycler User Manual v2 5 15 8 3 TopHeater Setup Use Top Heater Wait for heater to achieve temperature before commencing run E Leave heater enabled on run completion Top hea
14. n completion the post run report screen will show and if enabled an audible alarm will sound The alarm may be muted by pressing the mute alarm button The post run report can be saved to USB memory stick for inclusion into lab books etc Post Run Report Kyratec SuperCycler User Manual v2 5 6 Manual Block Control b Temp Left Temp Right Gradient Top heat E Timed Hold ture ee Heating Elapsed 11 2 Total est 63 00 a 12 32pm 6 10 09 The manual mode screen allows immediate manual setting of the block temperature To activate this mode simply press the blue start button Terminating the mode is achieved by pressing the red stop button To Program the set temperature press the temperature button to the left of the graph and enter the desired value You may program the temperature setpoint to 0 1 degree C resolution If the Gradient checkbox is checked the Temp Right button appears and you are able to set different temperatures for both the left and right sides of the block with a roughly linear thermal gradient presented between the two outer well sides To enable the Top Heater evaporation control click the Top Heat checkbox The target temperature of the top heater is configured under the setup menu Note the top heater will take a few minutes to reach its operating temperature The lower left side of the screen displays the temperatures of each of the 4 zones Other information also displayed is the event step and
15. n which device was purchased and esides Customer warrants that the selected region is the true region of its purchase and physical operational location Incorrect selection of egion is in breach of supplier terms of license and may or may not breach any 3rd party license terms Customer accepts sole responsibility for incorrect region selection and consequences of any breach of 3rd party intellectual property associated with said features B Limitation of Liability Ise of device and any results or information generated by device are at the sole risk of customer Supplier makes no guarantees that expected functions are performed correctly Supplier strongly recommends that customer perform full manner of internal controls within their E agree to Terms of Use for this device If the instrument is moved to a different region of operation at a later date then the region configuration screen may be reached through the system setup tab under the configuration menu A copy of the Terms of use may also be found at the end of this manual Kyratec SuperCycler User Manual v2 5 6 3 2 Navigating the Software After power up the unit defaults to the main screen from where all the features may be accessed You may return to this screen at any time without interrupting a run by pressing the Home logo in the bottom left hand corner for the screen Wie User login out Profile Manual Control Zil tueger L Quickstart Wizard
16. on the SC and transfer files to or from You may also delete any thermal profiles from the SC Press on the Home icons to refresh the directory list back to the root directories Select files in either the SC or the USB stick and press the transfer logos to copy the files across 8 2 System Setup E Hold at last temperature on run completion Dissable Peltiers on run completion Audible alarm on run completion Use predicted liguid temperature for hold times Note Predicted liguid temperature estimation is based on a liguid volume of between 10 and 50ul Leaving this option unchecked bases the hold times on the block temperature alone and may reguire slightly longer hold times for effective run BUER Wednesday 27 January 2010 E 1 24 47 PM a File Manager System Setup TopHeater setup Callibration Software Update Extras Idle Elaps 0 00 Total est 0 00 Default 12 10 09 The following features are available under this tab Hold at last temperature on run completion will maintain the last profile temperature after the run has completed Disable Peltiers on run completion will deactivate the peltiers at the end of the run When this is selected the temperature of the samples will come to rest at approximately the internal heatsink temperature Typically this will be about 35deg C at the completion of a run Selecting this check option will toggle between the Hold at last temperature and this optio
17. ondensation control Heated Lid Temperature Range Dimensions Weight Colour Electrical External Interface Internal Interface Software Functionality Included Accessories Warranty Kyratec SuperCycler User Manual v2 5 High performance active heating and cooling using quality elements x 8 amp precision sensors x 4 49C 999C 0 5 C of set temperature 1 minute after target 0 5 C 30 seconds after target 0 19C increments 3 259C sec maximum block 96 Well block supporting 0 2 mL tubes or strip tubes with flat or domed caps 96 well high or lowskirt plates with strip caps adhesive cover or oil overlay Programmable 0 20 C across block width 12 wells Automatic utilising applied pressure heated lid Controllable 604C 1159C W 180 mm D 270 mm 10 6 340 mm 13 4 including cables H 190 mm lid closed 320 mm 12 6 lid open 5 5kg 12 1 Ibs pearl white on frosted black 100 240 VAC 4 Amp 50 60 Hz Automatic voltage sense Standard IEC Inlet plug USB interface to Windows XP Vista based PC USB host port for memory stick mouse keyboard etc Embedded graphical controller with 7 widescreen touch sensitive colour backlit display Supplied with unlimited user license Free upgrades available via web download Touchdown long range linear thermal gradient program pauses temperature graphing temperature logging PC only Profile load amp saving Manual mode Power Cable User manual
18. onfigure easy to moderate complexity profiles in just moments To activate select Wizard from the main menu Temperature c Time Post Cycling Extension The Wizard screen displays each of the steps which occur in a typical range of profiles At a minimum there are 3 steps Preheat and then denaturation and aneal which are cycled You may enable up to a further 3 steps CDNA Extension amp post run hold by clicking on the corresponding check boxes Each of the steps will be executed in the order they are shown arranged down the screen with the Denaturation Aneal and Extension if enabled steps being cycled After the amplification run has been completed the temperature may be held at a defined temperature until the user disables the unit To adjust any of the parameters click on the corresponding time or temperature boxes and a keypad will be presented allowing entering of new numbers The number of cycles can also be adjusted between 1 single execution no loops and 99 cycles When the user is happy with the profile parameters just click on the tick A run review screen will now be shown with a text description of the profile steps Click on OK to commence run execution or cancel if changes need to be made Once the profile is confirmed if the Use Top Heater checkbox option is selected default then you will be prompted with a screen asking if you wish to wait for the top heater to reach target temperature before commencing the run
19. res 3 Limitation of Liability Use of device and any results or information generated by device are at the sole risk of customer Supplier makes no guarantees that expected functions are performed correctly Supplier strongly recommends that customer perform full manner of internal controls within their reaction volumes to satisfy themselves that expected functions were performed correctly Suppliers sole responsibility is for repair or replacement of defective device within the warranty period Maximum liability of supplier in any circumstance is limited to the amount paid by customer to the supplier for the device Kyratec SuperCycler User Manual v2 5 19
20. screen of the Add Event Wizard lets the user select the type of event What kind of event would you like to add You may choose from 4 event types HOLD Is a simple hold at given temperature for a set time It may be performed either with or without a gradient across the block The hold screen allows the operator to set the hold time and temperature If the Gradient option is selected both the left and right temperatures may be set separately and the predicted well temperatures can be shown by clicking the Predicted Temps link RAMP Allows the block temperature to be ramped either up or down between two set temperatures over a preset length of time The block target temperature is updated every second and with a 0 025 degree minimum step resolution It may be performed either with or without a gradient across the block The ramp screen shows the initial and final ramp temperatures If the Gradient option is selected both the left and right temperatures may be set separately and the predicted well temperatures can be shown by clicking the Predicted Temps link PAUSE will hold the temperature at the last set point and pause the run with an audible warning This is useful if the operator needs to perform a certain action of the samples at a given point in the run The operator clicks ok when complete and the run will continue with the next event CYCLING x STEP will proceed to generate a multi step cycling event The scroll
21. ter temperature deg C HERR Dissable TopHeater when set temperature lt 30 deg C 0 09 File Manager System Setup TopHeater setup setup Callibration Software Update tal Default 1 The following features are available under this tab for the top heater evaporation control Use Top Heater will cause the top heater to be used during a run if it is checked Leave heater enabled on run completion will cause the top heater to be left on indefinitely at the end of a run This is useful if you are holding the samples at a high temperature on run completion Entry box for top heater temperature Temperature is programmable between 30 110deg C default 100 deg e Disable top heater when set temperature lt 30deg feature is implemented to reduce the high thermal load placed on the peltiers when holding the samples at low temperatures ie 4degrees This prevents excess heat from the top heater heating the chilled samples It is best to leave this option enabled Note that the top heater is only activated when a run is started or the operator enables it in manual mode 8 4 Calibration The calibration screen is used to adjust the machine calibration SuperCyclers are factory calibrated and should not require user recalibration The recalibration procedure is not covered in this user manual If it is required contact the distributor the equipment was purchased through for SC Service note Thermal recalibratio
22. time with biological samples that you experiment with setting up runs and trialling these to familiarise yourself with the machine to ensure correct operation on your valuable samples To achieve the maximum lifespan and best clarity from you SuperCycler touch screen please only use the stylus provided or eguivalent or your fingers for selecting on the touch screen Using a ball point pen pencil or anything sharp will cause the screen to scratch To maximise the lifespan from the peltier devices which effect the heating and cooling there are a number of actions the user may take Do not run the unit with no tubes in the plate and the lid closed When the lid is closed and no tubes are present the top heater rests close to the 96 well block and will place high thermal load on the peltier devices Extended operation in this situation will shorten the lifespan of the peltier devices Attempt to minimise the time holding the samples at below ambient temperatures longer than reguired It is recommended against using the device as a refrigerator to hold samples at 4 degrees C temperature for long periods of time if you wish to maximise the lifespan of your instrument Kyratec SuperCycler User Manual v2 5 17 10 Specifications Thermal Cycling Technology Temperature Range Temperature Accuracy Temperature Uniformity Temperature Resolution Heating Cooling Rate Well Configuration Linear thermal gradient Available selected regions only C
23. to repeat the cycle Note Gradient function not available in all regions 5 2 Starting a run Activating the Start Run button will show a profile review page which allows the operator to check over the profile displayed in text format before confirming commencement The profile review will also contain general run options regarding the Top Heater evaporation control and actions on run completion These are configurable under the configuration menu You have the option to perform the run in virtual mode this will simulate the run without actually thermally varying the block Once the profile is confirmed If the Use Top Heater checkbox option is selected default under the setup menu then you will be prompted with a screen asking if you wish to wait for the top heater to reach target temperature before commencing the run If you select to wait for the top heater to achieve temperature a waiting screen will be displayed You may skip the waiting step at any time if you wish to commence the run immediately Depending on the set temperature of the Top Heater it will take up to several minutes to pre heat to this temperature Kyratec SuperCycler User Manual v2 5 11 Confirm Run Profile Edit profile manually SuperCycler Cancel E Run in virtual simulated mode Once the run commences the software will automatically proceed to the Run screen You are not able to modify the profile once a run has commenced On ru
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