Arktik Thermal Cycler User Manual
Contents
1. Highlight LID and press OPEN F1 Thermo Scientific Arktik Thermal Cycler User Manual 33 Managing Diagnostics Log Files and USB Link Using the Tools Menu Diagnostics F1 CHANGE F2 OFF F3 F4 BACK F5 MAIN Sensors E DIAGNOSTICS LID SENSORS CLOCK SOUND GRADIENT OPEN BACK MAIN The Lid screen displays the hot lid default temperature as well as the setting determining whether the hot lid is ON or OFF by default Hotlid Default 009 ec Block Type 96 well Hotlid On Note These are default settings only The user has the opportunity to change these parameters each time they begin a new run A Function key actions Enables the user to change the default hot lid temperature Toggles the default lid setting to OFF at this point the option changes to ON In order to save the change to this setting press CHANGE No action Returns to the previous screen Returns to the Main screen Highlight DIAGNOSTICS and press OPEN F1 Highlight SENSORS and press OPEN F1 The Sensors menu simply displays the current sensor reading for the temperature sensors located in the lid the block and the heat sink 34 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific F1 F2 F3 F4 BACK F5 MAIN Clock F1 SAVE F2 FORMAT F3 F4 BACK F5 MAIN Thermo Fisher Scientific Managing Diagnostics Log Files and USB Link Usin2. Notes Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 51 Notes 52 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Notes Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 53 Thermo Fisher Scientific Oy Ratastie 2 P O Box 100 Fl 01621 Vantaa Finland www thermoscientific com N11467
3. Page 1 of 1 BACK COPY Note A message will be displayed if the same folder file already exists on the Arktik giving the option to overwrite the existing file A When the transfer is complete the FILE SAVED message will be displayed Press the BACK F1 key to transfer additional files from the USB drive or F5 to return to the main screen oe Note If the USB flash drive is not inserted the NO DISK CONNECTION message will be displayed A No disk connection Press F1 to go back MAIN BACK Thermo Scientific Arktik Thermal Cycler User Manual 39 Managing Diagnostics Log Files and USB Link Using the Tools Menu USB link 40 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Cleaning the fins of the heat sink Cleaning the Arktik Thermal Cycler Replacing the fuse s Disposal of the Thermo Fisher Scientific instrument Chapter 6 Maintenance Contact local authorized technical service or your local Thermo Fisher Scientific representative for assistance if necessary Inspect the fins of the heat sink on a regular basis Dirty heat sinks have a significantly lower capacity to eject heat Clean the fins if they become dirty or covered in dust You can use a cotton swab a brush or compressed air to remove dust Clean the outside of the Arktik Thermal Cycler with a damp soft cloth or tissue whenever something has been spilled on it or the cover is dust
4. e Two spare fuses 250 V fast 8A 5x20 mm e Quick Reference Guide e User Manual e Sample pack of UTW PCR vessels Required blocks sold separately If you have not received the above items in your shipment contact your local distributor or Thermo Fisher Scientific Oy directly Save all packing material in case you need to return the Arktik Thermal Cycler for maintenance Setting up the Arktik Thermal Cycler can be performed in 5 simple steps 1 Remove all components from the packaging 2 Place a 96 well block 384 well block or a dual block into the Arktik Thermal Cycler base unit see Installing blocks in the Arktik base unit on page 17 Note Never lift or carry the block only by the handle always support the block from the side or underneath A 3 Plug the power cord into the back of the Arktik Thermal Cycler 4 Insert the power cord into the outlet Thermo Scientific Arktik Thermal Cycler User Manual 15 Installation Vessels compatible with Arktik Thermal Cycler 5 Turn on the power switch on back of the instrument Vessels compati ble The Arktik Thermal Cycler is compatible with both standard vessels and with Arktik Thermal ultra thin wall UTW reaction vessels Cycler 16 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Chapter 4 Operation The operation of the Arktik Thermal Cycler is described below Insta Il ing bloc ks in 1 Make sure that the Arktik base
5. ee 1 of 1 Save file in SHARED ee YES amp RUN BACK Function key actions Saves the protocol file to the selected folder and returns to the Main menu Saves protocol file to selected folder and proceeds to the Running a protocol step see Running a protocol on page 27 No action 24 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific F4 BACK F5 Editing a protocol F1 START F2 EDIT F3 F4 BACK F5 MAIN Thermo Fisher Scientific Operation Creating a new protocol Returns to the previous screen No action Note If a file with the same name already exists in the folder the user will be warned and offered the choice of overwriting the file or going back to choose a different file name or folder A To edit a protocol 1 Select RUN F1 in the Main menu 2 Highlight a folder using the cursor keys 3 Press OPEN F1 to open the selected folder 4 Highlight a protocol file using the cursor keys 5 Press OPEN F1 to open the selected protocol file This will display the semigraphical representation of the protocol 60 0 01 00 02 00 00 15 30 START EDIT BACK MAIN Function key actions Begins to run selected protocol Allows editing of the protocol in semigraphical mode No action Returns to the previous screen Returns to the Main menu Thermo Scientific Arktik Thermal Cycler User Manual 25 Operation Managing folders M
6. 60 Hz Power failure recovery Yes Fuses 2 x 250 V F8A Type 5020 Certifications CE Warranty 1 year Instrument configuration Interchangeable block formats User interface 96 x 0 2 ml 384 x 0 03 ml dual independent 48 x 0 2 ml Semigraphical Heated lid Manually adjustable advanced lid design ensures proper pressure while preventing over tightening Memory 50 folders with 99 programs in each Communications Ethernet USB memory port for protocol transfer Programming Adjustable ramp rate Yes Touchdown Yes Thermal control Thermal performance Optimized for standard and UTW vessels Ramp rate 2 5 C s Gradient range 30 C max Thermal uniformity 0 4 C at 90 C Thermal accuracy 0 3 C at 90 C Thermal range 4 C to 99 9 C Thermo Scientific Arktik Thermal Cycler User Manual 43 Technical Specifications Safe use guidelines Safe use The Arktik Thermal Cycler is designed to be used safely under the y 8 y gu idelines following conditions e Indoor use e Altitudes up to 2000 m e Ambient environmental temperatures between 5 C 30 C e Up toa maximum non condensing humidity of 80 e Transient over voltage per Installation Category 2 IEC664 e Pollution degree 2 in accordance with IEC664 44 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Chapter 8 Troubleshooting Guide Note Do not use the instrument if it appears that it
7. F1 Then select EXPORT F5 USB flash Drive Connected Please Choose Import of Export File Press F1 to go Back Press F4 to Import File Press F5 to Export File MAIN BACK IMPORT EXPORT Navigate to the desired file and folder and press VIEW F5 Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 37 Managing Diagnostics Log Files and USB Link Using the Tools Menu USB link Importing a file from a USB flash drive Local User List RECENT SHARED t Page 1 of 1 BACK VIEW To export the selected file press COPY F4 Local File List test Page 1 of 1 Note A message will be displayed if the same folder file already exists on the USB drive giving the option to overwrite the existing file A When the transfer is complete the FILE SAVED message will be displayed Press the BACK F1 key to transfer additional files to the USB drive or F5 to return to the main screen Insert the USB flash drive From the Tools menu highlight USB LINK and press OPEN F1 Then select IMPORT F4 Navigate to the desired file and folder and press VIEW F5 Usb Disk User list SHARED Page 1 of 1 BACK VIEW To import the selected file press COPY F4 38 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific Managing Diagnostics Log Files and USB Link Using the Tools Menu USB link File List
8. SAVE F5 Note Text entry is similar to that of a mobile phone A number or character is automatically entered after a one second delay Pressing key will toggle through the assigned number and three characters for example press the key labeled 2 A B C once to select A and wait 1 second For capital letters press CAPS F2 To delete a letter press DEL F3 A file name can be a maximum of 11 characters long Files may be password protected by entering a password up to 11 characters into both the Password and Password Check fields A Note The passwords in both fields must match exactly A Press BACK F4 to resume editing the protocol without saving Press SAVE F5 to save the protocol to a folder The screen will display the folder options Thermo Scientific Arktik Thermal Cycler User Manual 23 Operation Creating a new protocol F1 SELECT F2 NEW F3 F4 BACK F5 A F1 YES F2 YES amp amp RUN F3 FOLDERS SHARED Page 1 of 1 SELECT NEW BACK Function key actions Selects the folder to which the protocol will be saved Creates a new named folder see Creating a new folder on page 26 No action Returns to the previous screen No action Cursor actions Highlights the folder for selection Note A protocol may not be saved to the RECENT folder Before a protocol is saved to a folder final confirmation will be presented A cel FOLDERS i SHARED
9. does not function properly A Error log If an error message Table 8 2 appears in the display window of the Arktik Thermal Cycler it may indicate that the system cannot complete the requested action for example Heatsink temperature is too high Should you receive an error message regarding block sensors contact Thermo Fisher Scientific Oy for support Table 8 2 Error codes reported Block sensor error Single block 96G 384G Suggested action Heatsink temperature is too high Ensure that airflow is unobstructed see Conditions for proper use on page 6 Heatsink temperature is too low Temperature sensor No 1 is disconnected block left temperature sensor Do not run the instrument immediately if it has been stored in a cold location Allow to warm to room temperature before operation Contact Thermo Fisher Scientific Temperature sensor No 1 is shorted Contact Thermo Fisher Scientific Temperature sensor No 2 is disconnected block mid temperature sensor Contact Thermo Fisher Scientific Temperature sensor No 2 is shorted Contact Thermo Fisher Scientific Temperature sensor No 3 is disconnected block right temperature sensor Contact Thermo Fisher Scientific Temperature sensor No 3 is shorted Contact Thermo Fisher Scientific Hotlid sensor is disconnected Contact Thermo Fisher Scientific Hotlid sensor is shorted Con
10. found 46 Thermo Scientific Arktik Thermal Cycler User Manual The protocol is corrupted or removed Try again or create a new protocol Thermo Fisher Scientific Thermo Fisher Scientific Arktik Chapter 9 Ordering Information Contact your local Thermo Fisher Scientific representative for ordering and service information Table 9 3 Table 9 3 Instrument catalog number Code Item TCA0001 Arktik Thermal Cycler base unit TCA0002 Arktik Thermal Cycler base unit without gradient TCA0096 Arktik 96 well block TCA4848 Arktik 24 well dual block TCA0384 Arktik 384 well block Thermo Scientific Arktik Thermal Cycler User Manual 47 Ordering Information 48 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Glossary gradient PCR A protocol in which the temperature across the sample block is varied column by column for a particular hold step PCR Polymerase chain reaction touchdown PCR A protocol in which time and or temperature is changed in small increments and are added or subtracted to each step in a loop These changes continue to progress from cycle to cycle throughout the entire loop section of the protocol UTW Ultra thin wall reaction vessel provided by Thermo Fisher Scientific Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 49 Glossary 50 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific
11. protocol is running The current running temperature step in the protocol is represented by a flashing line and the protocol and host folders are displayed on the top of the screen The time remaining in the current step and the current block temperature are displayed below this A Returning to the Main menu allows users to write or edit protocols while the instrument is running A STATUS F3 option will appear on the Main menu screen to return to the Status screen when a protocol is running FINNZY MES Version 00 00 Block 96 well SN RUN NEW DACS TOOLs Press TIME F3 The Time Status screen displays additional information about the run As with the Status screen the file name and host folders are displayed on the top of the screen Additionally the following status parameters are displayed e CYCLE Displays the current cycle number within a GOTO loop e TEMP Displays the current temperature of the block e TIME Displays the estimated time remaining in the current step e STEP Displays the step number of the currently running temperature step 0 07 0 TEMP 95 0 C TIME 00 04 51 STEP 1 0 6 CANCEL PAUSE NEXT STATUS MAIN 30 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific F1 CANCEL F2 PAUSE F3 NEXT F4 STATUS F5 MAIN Operation Monitoring a run Note The co s
12. 4 block Confirm the selection by pressing YES F4 or return to the vessel section screen by pressing NO F5 28 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Monitoring a run F1 CANCEL F2 PAUSE F3 NEXT F4 TIME F5 MAIN Thermo Fisher Scientific Operation Monitoring a run 72 0 72 0 01 00 02 00 30 Sample Volume 3 uL Accept YES NO After confirming the volume the protocol will start immediately see Monitoring a run on page 29 Note When a run begins the running protocol will be displayed in semigraphical mode on a Status screen see Monitoring a run on page 29 A Upon initiation of a run the Arktik Thermal Cycler will display the Status screen Time Remaining 00 05 00 Block Temp 61 3 95 0 92 0 05 00 99 15 72 0 72 0 01 00 02 00 CANCEL PAUSE NEXT TIME MAIN Function key actions Terminates the run after confirming with the user Pauses the run on the present temperature step or the next step if ramping When paused this option becomes RESUME Skips to the next step Toggles to the Time Status screen Returns to the Main menu Thermo Scientific Arktik Thermal Cycler User Manual 29 Operation Monitoring a run Note Returning to the Main menu allows users to write or edit protocols while the instrument is running A STATUS F3 option will appear on the Main menu screen to return to the Status screen when a
13. Thermo Scientific Arktik Thermal Cycler User Manual Rev 1 0 Part of Thermo Fisher Scientific SCIENTIFIC Thermo Scientific Arktik Thermal Cycler User Manual Rev 1 0 Cat no N11467 Copyright Copyright 2010 Thermo Fisher Scientific Corporation All rights reserved Reproduction of the accompanying user documentation in whole or in part is prohibited License and trademark information Notice Purchase of this instrument conveys a limited non transferable immunity from suit for the purchaser s own internal research and development and applied fields other than human in vitro diagnostics under one or more of Canadian Patent 1 339 653 U S Patent 5 475 610 claims 160 163 only or corresponding claims in their non U S counterparts owned by Applied Biosystems No right is conveyed expressly by implication or by estoppel under any other patent claim including under U S Patent No 6 814 934 or any global equivalent thereof which claims thermal cycler apparatus and systems capable of real time detection Further information on purchasing licenses may be obtained by contacting the Director of Licensing Applied Biosystems 850 Lincoln Centre Drive Foster City California 94404 USA Trademarks Arktik and UTW are trademarks or registered trademarks of Finnzymes Oy or its affiliates Finnzymes Oy and its affiliates are part of Thermo Fisher Scientific All other trademarks and registered trademarks are the prope
14. age 20 Exits edit mode without saving Saves the protocol Thermo Scientific Arktik Thermal Cycler User Manual 19 Operation Creating a new protocol Cursor actions A V lt 4 gt Navigate between temperature time and cycling loop fields Use the keypad 0 9 to edit the values The temperature or time value may be edited by moving the cursor to the field and then editing it directly To enter values use the numbers on the keypad as you would write them The decimal point will be added automatically For a temperature of 60 5 C enter the following 6 0 5 Similarly for a time value enter the numbers as you would write them for a 1 minute and forty five second hold enter the following O 1 4 5 e Note To enter an infinite hold press the lower right key on the keypad af with the symbol a Entering advanced From the protocol editing screen press the OPTION selection using the programming F3 key options 60 0 01 00 02 00 00 15 30 The function key actions FI INC Adds or subtracts a defined temperature increment to a temperature step such that the amount of the increment will be added to or subtracted from each successive cycle This is used for Touchdown protocols Input range 0 1 C to 9 9 C per cycle F2 EXT Adds or subtracts a defined time extension to a temperature step such that the amount of the extension is added to or subtracted from each succ
15. anaging folders F1 OPEN F2 NEW F3 DEL F4 RENAME F5 MAIN Creating a new folder F1 Select RUN F1 in the Main menu jiems FOLDERS Page 1 of 1 OPEN NEW DEL RENAME MAIN Function key actions Opens a folder and displays its contents Creates a new folder Deletes a folder Allows renaming a folder Returns to the Main menu Press F1 RUN to access the Managing folders selection Press NEW F2 and a prompt will appear in the folder name box Enter the desired folder name using the keypad 11 character maximum Note Text entry is similar to that of a mobile phone A number or character is automatically entered after a one second delay Pressing the key will toggle through the assigned number and three characters for example press the key labeled 2 A B C once to select A and wait 1 second A folder name can be a maximum of 11 characters long A Function key actions No function 26 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific F2 CAPS F3 DEL F4 BACK F5 SAVE Running a protocol Thermo Fisher Scientific Operation Running a protocol Toggles between capital and lowercase letters Deletes a character Returns to the folder selection screen Saves the new folder and returns to folder selection screen Press RUN F1 in the Main menu E FOLDERS l RECENT Pree eee 1of1 Pree eee NEW MAIN There are two
16. asic protocol Thermo Fisher Scientific F1 ADD F2 DELETE F3 OPTION F4 BACK F5 SAVE Operation Creating a new protocol The red button with labeled SHIFT BLOCK shifts between the two blocks when a dual block is inserted into the machine A refers to the block on the left and B to the block on the right To create a new protocol is described below From the main screen press the NEW button using the second blue function key F2 This will bring up a DEFAULT protocol The DEFAULT protocol is a semigraphical representation of a typical PCR temperature cycling routine A temperature step is represented by a horizontal line with a temperature value with a resolution of 0 1 in C above the line and a time value in mm ss below the line If a step is highlighted this line will flash Use the cursor keys lt 4 and P to toggle between temperature steps DELETE OPTION BACK Function key actions Adds a temperature step to the right of the highlighted step or allows the addition of a GOTO routine see Editing a cycling loop on page 22 Deletes the highlighted temperature step Also deletes a GOTO routine if it is highlighted Allows the programming of advanced options into the highlighted step temperature increment extend time or slow ramp rate and temperature gradient in the instruments with this feature enabled see Entering advanced programming options on p
17. d waste The proposals for the procedures vary by country Pollution degree 2 see Safe use guidelines on page 44 Method of disposal Electronic waste Contaminated waste Infectious waste WEEE symbol Thermo Fisher Scientific has contracted with one or more recycling disposal companies in each EU Member State European Country and this product should be disposed of or recycled through them Further information on Thermo Fisher Scientific s compliance with these Directives the recyclers in your country and information on Thermo Scientific products which may assist the detection of substances subject to the RoHS Directive are available at www thermo com WEEEROHS A Regarding the original packaging and packing materials use the recycling operators known to you For more information contact your local Thermo Fisher Scientific representative 42 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific Instrument specifications Chapter 7 Technical Specifications Thermo Fisher Scientific reserves the right to change any specifications without prior notice as part of our continuous product development program Table 7 1 Table 7 1 Instrument specifications Instrument specifications Dimensions Size 29 cm wide 38 cm deep 29 cm high Weight 10 5 kg includes block Electrical Power supply 600 W Line voltage 100 240 VAC Frequency 50
18. e Clean fins of heat sink Refer to Chapter 6 Maintenance 6 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific Chapter 1 Chapter 2 Chapter 3 Chapter 4 Contents ntended SES irin iaieiiea Sedia 3 How to use this user manual vs cciastacctvaccustevazenstivagdeanttesdiechenctssteunereets 3 For more miormatoh naeron nnn A EE ns 3 Safety WaT OS Aaen ia ais RAR aR eee RA Electromagnetic interference s s sesseseseseseseserersrsrsrsrtererererereesesrere 5 Good laboratory practices esesesseesesesesesesessssesrsetesrteterterereresessse 5 General chemical warnings ssesesesssessssssssssrsssrsesrsesrsesesesesesreereeersee 5 General biohazard warnings ssssssssssssssessssssssssrsrsrstsrsrseseseseseseseseses 5 Conditions for proper use s ssesssssesssessssessesrsrsrstsrstststststseseseseseseseseses 6 Absolute environmental requirements lt 2c 22 0 aieds eens ees 6 Recommended working conditions 2440seie dee Gate 6 PUTO W ieeiaswhasvsvachonnstunnviusedelade iai iie aiai 6 Arktik Thermal Cycler Overview sscsssssssssessessesseeseessessesseseaees 9 Arktik Thermal Cycler Main Patts cccsssssssssessseesessessesseneeeenees 11 Pront WIC WE gence tales sh eects ah st rE E An SeS AORERE EEE ERr 11 Rear VIEW oenig disidir iiinn ienne ad iei KEE EE EE EA 11 Instrument user interface seeseseseseseererersrersrersreisisistseseseseseses
19. e on the lid while pulling the handle forwards To tighten the lid turn the dial clockwise To prevent over tightening the lid mechanism will begin ratcheting when the proper pressure has been achieved 3 To open the block after a run first turn the dial counterclockwise to raise the heated lid then open as in Step one Note that failure to raise the internal heated lid may result in crushing of tubes if the cycler is used with low profile tubes and subsequently used for standard profile tubes Note In some cases a slight expansion of the plate during thermal cycling may occur and this may cause difficulties in opening the lid In this case press the release button on top of the dial down while turning the dial counterclockwise A The Arktik Thermal Cycler user interface features five function keys which are used to select different menu options Note that the markings from F1 to F5 are not present in the actual user interface but instead are shown is this manual in order to help read the instructions FINNZYMES Version V00 00 Block 48 well SN The function keys on the Main menu have the following actions Runs saved protocols Allows editing of saved protocols Begins programming of a new protocol Shows Status screen when running Not used Accesses global settings or diagnostic routines 18 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific SHIFT BLOCK Creating a new protocol B
20. es carefully This symbol indicates a chemical hazard risk Warning Some of the chemicals used with the instrument might be potentially hazardous Before handling chemicals read through the material safety data sheets provided by the chemical manufacturer Use protective equipment when handling hazardous chemicals Do not inhale any fumes from chemicals Refer to chemicals material safety data sheets for more information about storage handling and disposal A This symbol indicates a biological hazard biohazard risk Warning When handling biological material appropriate protective clothing is required Many biological materials for example microorganisms cell cultures tissues body fluids and parasites have the potential to transmit infectious diseases Personnel handling biologically hazardous material should be trained beforehand A Thermo Scientific Arktik Thermal Cycler User Manual 5 About This User Manual Conditions for proper use Co n d iti ons fo r This section describes the environmental requirements of the Arktik Thermal Cycler p ro p er use Note Important It is highly recommended that all users of the Arktik Thermal Cycler read the following section carefully The performance and reliability of the Arktik Thermal Cycler are closely linked to the working conditions in which the system is run To ensure that your Arktik Thermal Cycler will provide years of top level performance and have the fewest problems adhere t
21. eseses 12 Interchangeable blocks sssssesssesessesssssssssssssssrsssesrsrsrsrsrsesesesesesrseses 12 Installation isi i aaaea aeai aiat 15 Items included n a a e ea a 15 Setting up the Arktik Thermal Cycler sessen 15 Vessels compatible with Arktik Thermal Cycler sss 16 Operation ana aa aaa aa a Aaa enn 17 Installing blocks in the Arktik base unit sssr 17 Opening and closing the Arktik blocks ssesssseseseseseeeesseseeessesssessss 18 Main CHD ase cc ene a R A at acd ites 18 Creating a new Protocol A gnu it okece se a Ret let eects 19 Basie protocols tested tinder are Dy aca tate hehe diesen Scale ees 19 Entering advanced programming Options 20 Gradient setup MERU sccascit csc zecceh hubenteiuedd nth cateeetered tals bcbeowed 21 Editing a cycling loopainieta ascnde adie datiek 22 Modifying a cycling loop scssauincsece oceiceleeantes lean ate 22 Adding new cycling loopiisc issue eal ena ak 22 Saving a protocol oiee nO ye oe eee 23 Eding a protocol oerien Or oe err enr etn ey eton a Meee ire rnrecetY err 25 Managing folders cci icicitiaziontmcsientiaantncen nian aided 26 Creating a new fold n codesti secr aeae aane Epei arei ees 26 Running a protocol s ssssssessseeseeesisesesesrsrsrsrsrsrsrstststststststseseseseseseses 27 Monitoring a rU siare arne oieri ie a eais ease 29 Thermo Scientific Arktik Thermal Cycler User Manual 7 Contents Chapter 5 Managing Diagnostics Log Files and USB Link Using the Tools PVN ices tcstravncac
22. essive cycle Input range 1 to 99 seconds per cycle F3 RAMP Slows the ramp rate going to a highlighted step to a value below the maximum Input range 0 1 to 4 0 C second F4 GRAD Set gradient for gradient blocks only For any hold step it is possible to set up a horizontal temperature gradient across the block each column of wells will have a different temperature To program a gradient step select this feature from the OPTION menu and input the desired upper and lower temperatures the maximum range is 30 C using keypad 0 9 See Gradient setup menu on page 21 20 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Operation Creating a new protocol F5 DONE Accepts advanced option values and returns to protocol editing screen will be reverse displayed have a white text when the modified step is highlighted This will remind the user that an option has been programmed into that step A Note If advanced options have been entered the OPTION menu label Gradient setup menu The function keys on the Gradient setup Menu have the following actions 72 0 72 0 01 00 02 00 30 Set from 60 0 C to 90 0 C F1 No function F2 No function F3 PREVIEW Displays the temperature setting for each column with the given upper and lower temperatures F3 back returns to gradient setup screen F4 BACK Exits mode without saving F5 DONE Sets displayed gradient and
23. g the Tools Menu Diagnostics BLOCK 24 6 LID 67 9 SINK 24 4 BACK MAIN Function key actions No function Returns to the Diagnostics main screen Returns to the Main screen Highlight DIAGNOSTICS and press OPEN F1 Highlight CLOCK and press OPEN F1 The clock menu allows the editing of the Arktik Thermal Cycler s internal date and time settings Py NE ER AG Ee HE 09 07 07 TIME 18 31 43 DISPLAY FORMAT YY MM DD 24H Function key actions Accepts date and time changes Changes the time and date format displayed No action Returns to the previous screen without changing the date and time settings Returns to the Main screen without changing the date and time settings Thermo Scientific Arktik Thermal Cycler User Manual 35 Managing Diagnostics Log Files and USB Link Using the Tools Menu Log files A V lt gt Sound F1 SAVE F2 ON F3 OFF F4 BACK F5 MAIN lt 4 gt Log files Cursor actions Toggles between editable fields Use the keypad 0 9 to insert numbers Highlight DIAGNOSTICS and press OPEN F1 Highlight SOUND and press OPEN F1 The sound menu allows the editing of the Arktik Thermal Cycler s Settings for tones produced during Keystrokes KEY at the end of a run RUN END and at the beginning of an infinite hold INFINITE KEY OFF 0 Soe OFF NFNITE ON Function key actions Acce
24. ging of returned goods If necessary please contact the company that sold the Arktik Thermal Cycler to receive new shipping materials prior to shipment and instructions for proper shipment 3 Defects caused by use of improper materials including tubes plates or sealers not designed and approved for the Arktik Thermal Cycler or solvents and agents such as radioactivity or biohazardous agents not approved for use or allowable for public shipment 4 Defects caused by negligence accidents unreasonable or improper use natural disasters or by other causes unrelated to defective materials or workmanship No liability for consequential damages Thermo Fisher Scientific shall not be liable for any damages whatsoever arising out of the use or inability to use this product Intended users How to use this user manual For more information Thermo Fisher Scientific About This User Manual The Arktik Thermal Cycler can be used in research and routine test laboratories by professional personnel This user manual is for the following instruments Arktik Thermal Cycler base unit Cat no TCA0001 and Arktik Thermal Cycler base unit without gradient Cat no TCA0002 It has been designed to give you the information you need to e Review safety precautions e Install the Arktik Thermal Cycler e Operate the instrument e Adjust the settings and service the instrument e Troubleshoot the instrument performance This user manual also de
25. is turned off the Arktik base unit Caution Do not insert or remove a block with the cycler turned on Doing so can cause electrical arcing that can melt the contacts in the connector joining the Arktik block to the cycler A 2 Raise the handle at the back of the Arktik block and hold the block by the front and back edges Lower the block into the Arktik base unit leaving at least 2 cm between the front edge of the block and the front of the Arktik base unit Note Never lift or carry the block by the handle only always support I1 the block from the side or underneath A 3 Slide the block forward as far as it will go and push the handle down Do not use force The block should click into place and the handle should be completely horizontal 4 To remove the block lift the handle slide the block backwards and lift out of the base unit A m W jl S SS f SSS SSS SII SS ll SSS il SSS i il AN aiti pl S muh ii il il I jill i cm il il wl a ml 0 j 38 il Figure 4 9 Installing a block in the Arktik base unit Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 17 Operation Opening and closing the Arktik blocks Opening and closing the Arktik blocks F1 RUN F2 NEW F3 STATUS F4 F5 TOOLS To access the sample blocks open the lid by grasping the handle and pulling it forward 2 To close the sample block apply downward pressur
26. o the environmental requirements described here A Absolute The Arktik Thermal Cycler is rated to operate reliably in the following environmental vironmental conditions Avoid extremes of these environmental ranges to best preserve the long term performance and life span of the requirements instrument e Ambient temperature 5 C 30 C e Ambient relative humidity up to 80 e Altitude under 2000 m Recommended The Arktik Thermal Cycler will perform optimally and exhibit highest working conditions ibility when the working conditions are as close to standard g laboratory conditions 20 C ambient relative humidity 40 Airflow Airflow is paramount to high speed performance and high reliability It is important to maintain good heat sink cooling capability It is best to have a cool source of incoming air and an unobstructed exhaust for outgoing air Follow these four guidelines to best ensure optimum heat sink function e Obstruction free intake of air Do not place on a hot surface or on laboratory bench paper Do not slide any paper or other material under the system as this may hamper the airflow or be sucked into the system e Obstruction free exhaust for outgoing air Always keep a distance of at least 10 cm between the exhaust vents and any large solid object such as walls larger instruments or other thermal cyclers Do not have other instruments exhaust blowing directly at the Arktik Thermal Cycler system
27. omponents may cause burns A Do Not Tamper with Electronics Coming in contact with the electronics even when the system is off or unplugged may cause an electrical shock or harm A Do Not Use Flammable or Hazardous Liquids with the Arktik Thermal Cycler a 4 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Electromagnetic interference Good laboratory practices General chemical warnings A General biohazard Thermo Fisher Scientific warnings About This User Manual Good laboratory practices This product conforms to the Class A standards for electromagnetic emissions intended for laboratory equipment applications It is possible that emissions from this product may interfere with some sensitive appliances when placed nearby or in the same circuit as these appliances The user should be aware of this potential risk and take appropriate measures to avoid interference The polymerase chain reaction PCR is an extremely sensitive assay and therefore the risk of false positive amplification is high if precautions during sample preparation and reaction setup are not observed e Clean lab coats e Clean gloves e Clean lab benches and equipment e Pre amplification areas should be separate from the amplification areas e Pre amplification and amplification areas should both have their dedicated lab equipment e Open reagent component tubes only when needed e Uncap and close tub
28. permanent folders the RECENT folder stores the last nine protocols that were run on the Arktik Thermal Cycler and the SHARED folder can be saved to and accessed by all users Highlight a folder and press OPEN F1 The protocols residing in that folder will be displayed Highlight the protocol and press OPEN F1 The protocol will be displayed in semigraphical mode 72 0 01 00 02 00 Press START F1 A lid temperature screen will be displayed showing the default lid temperature Note The default lid temperature may be set in the Tools Lid menu see Lid on page 33 for details Lid temperatures between 30 C and 110 C are allowed a Note The heated lid may be turned off completely by pressing the co button A Thermo Scientific Arktik Thermal Cycler User Manual 27 Operation Running a protocol Press OK F5 to proceed 72 0 72 0 01 00 02 00 30 LID TEMP 099 C BACK OK In the next screen the sample or block mode is specified by pressing SAMPLE F4 or BLOCK F5 Note Sample mode is strongly recommended for most protocols A 01 00 02 00 30 TEMP MODE SAMPLE BLOCK SAMPLE BLOCK In the next screen the vessel type is specified by pressing UTW F4 or COMMON F5 72 0 72 0 60 0 01 00 02 00 00 15 30 VESSEL TYPE UTW COMMON In the next screen the sample volume is specified by typing in a volume 5 to 50 pl for 48 dual and 96 blocks 5 to 20 pl for a 38
29. personal injury Always consult the User Manual before touching the area of the Arktik Thermal Cycler that displays this symbol a Caution This symbol indicates a risk of personal injury or harm by electrical shock Always consult the User Manual before touching the area of the Arktik Thermal Cycler that displays this symbol a Caution This symbol indicates risk of personal injury or burn by contact with a very hot surface Avoid touching such surfaces A WEEE symbol This product is required to comply with the European Union s Waste Electrical amp Electronic Equipment WEEE Directive 2002 96 EC a Note Marks a hint important information that is useful in the optimum operation of the system or an item of interest A Read the User Manual Operating the Arktik Thermal Cycler without first reading the entire User Manual may constitute a risk to your health Only a person capable of handling electrical equipment should use the Arktik Thermal Cycler NOT FOR CHILDREN Do Not Attempt to Repair Do not remove the cover of the system Do not try to repair or replace broken components you put yourself at risk for electrical shock Removing the cover or replacing removing components will void the warranty Contact customer service or your local distributor if your system is not functioning properly A Do Not Touch the Sample Block Certain components including the sample block and heated lid will become excessively hot Touching these c
30. pts sound changes Turns on the sound for the highlighted field Turns off the sound for the highlighted field Returns to the previous screen without changing the date and time settings Returns to the Main screen without changing the date and time settings Cursor actions Toggles between editable fields From the Tools menu highlight LOG FILES and press OPEN F1 The Log Files menu displays the recent protocols that were run on the Arktik Thermal Cycler Each protocol log contains information about the protocol and possible error messages 36 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Managing Diagnostics Log Files and USB Link Using the Tools Menu USB link LOGFILES Page 1 of 1 2009 07 07 17 52 test SHARED Stop BACK MAIN Function key actions F1 F2 F3 No function F4 BACK Returns to the Tools menu F5 MAIN Returns to the Main screen Cursor actions lt 4 gt Toggles between pages USB link This section describes how to transfer a file to or from a USB flash drive Exporting a filetoa To export a file to a USB flash drive USB flash drive Note Files are always transferred with the folder in which they exist If a file is transferred to or from a USB drive and its folder does not already exist in that location the folder will automatically be created A Insert the USB flash drive From the Tools menu highlight USB LINK and press OPEN
31. returns to advanced programming options screen Previews for the 96 block and the 384 block respectively 90 0 72 0 72 0 01 00 02 00 04 0 2 3 4 5 6 7 8 9 10 11 12 81 6 84 9 87 7 89 2 90 0 Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 21 Operation Creating a new protocol 01 00 02 00 04 0 1 2 3 4 5 6 7 8 9 10 11 12 60 0 60 3 60 6 61 4 62 1 63 3 64 6 66 3 67 9 69 1 72 1 73 0 13 14 15 16 17 18 19 20 21 22 23 24 73 8 77 1 79 3 81 6 83 2 84 9 86 3 87 7 88 5 89 2 89 6 90 0 BACK The minimum gradient temperature is assigned to the far left column column 1 of the sample block and the maximum temperature is assigned to the far right column column 12 Editing a cycling To edit a cycle loop is described below loop Modifying a cycling loop In the default protocol edit the cycling loop by highlighting the loop Use the lt 4 P gt cursor keys to move the arrow to a different temperature step The number of cycles is displayed in the middle of the loop arrow at the bottom of the screen This value may be edited using the keypad Adding new cycling loop From the protocol editing screen with the cursor on the last step of the desired loop press the ADD selection using the F1 key Select GOTO using the F2 key 01 00 02 00 00 15 i is Accept An arrow will appear that will point by default to the temperature step directly before
32. rhbatedawetapeacteeayaiedy uptecscen T E R RS 47 8 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific Chapter 1 Arktik Thermal Cycler Overview The Arktik Thermal Cycler Figure 1 1 suits the needs of a dynamic laboratory where reliability and user friendliness are appreciated It accommodates three interchangeable blocks 96 block 48 dual block and 384 block allowing versatile use of the cycler You control the Arktik Thermal Cycler through a simple user interface Graphical representation of a cycling routine makes navigation convenient The USB port enables protocol transfer Figure 1 1 Arktik Thermal Cycler Thermo Scientific Arktik Thermal Cycler User Manual 9 ArktikTM Thermal Cycler Overview 10 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Chapter 2 Arktik Thermal Cycler Main Parts This chapter describes the main parts of the Arktik Thermal Cycler Fro nt view The front view of the Arktik Thermal Cycler is shown in Figure 2 2 Lid Air exhaust USB port on the side Air intake Figure 2 2 Arktik Thermal Cycler front view Rear view The rear view of the Arktik Thermal Cycler is shown in Figure 2 3 Locking handle Ethernet port Power switch Power socket Fuse Figure 2 3 Arktik Thermal Cycler rear view Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 11 Arktik The
33. rmal Cycler Main Parts Instrument user interface Instrume nt user The user interface of the Arktik Thermal Cycler is shown in Figure 2 4 interface Display Block shift key for dual blocks F1 F5 Enter key Cursor keys Figure 2 4 Arktik Thermal Cycler user interface instructions A Note The function keys are marked here as F1 F5 to help read the Inte rchangeable The Arktik Thermal Cycler accommodates three interchangeable blocks block the 96 block 48 dual block and the 384 block Figure 2 5 through OCKS Figure 2 8 Release button Heated lid Dial Handle Locking handle gt 4 Heat sink Figure 2 5 Block unit Main unit connector Ve 12 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Arktik Thermal Cycler Main Parts Interchangeable blocks ane A Figure 2 7 48 dual block Figure 2 8 384 block Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 13 Arktik Thermal Cycler Main Parts Interchangeable blocks 14 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Items included Setting up the Arktik Thermal Thermo Fisher Scientific Cycler Chapter 3 Installation This chapter describes the installation and setup of the Arktik Thermal Cycler Inside the Arktik Thermal Cycler package you should find the following e Arktik Thermal Cycler base unit e Power cord
34. rty of their respective holders Disclaimer Thermo Fisher Scientific reserves the right to change its products and services at any time to incorporate technological developments This manual is subject to change without prior notice as part of a continuous product development Although this manual has been prepared with every precaution to ensure accuracy Thermo Fisher Scientific assumes no liability for any errors or omissions nor for any damages resulting from the application or use of this information This manual supersedes all previous editions Warranty Finnzymes Instruments Oy warrants that the Arktik Thermal Cycler is free from defects in materials and workmanship for 1 year from the date of purchase Defects that are covered by this warranty and that occur during this warranty period will be repaired or the system will be replaced free of charge and at the sole discretion of Finnzymes Instruments Oy or its licensed distributors Repairs that occur outside this warranty period will be charged for parts labor and shipping Fulfillment of warranty obligations is the responsibility of the company that sold the Arktik Thermal Cycler For specific information regarding warranty coverage please contact said company directly This warranty shall not apply to any of the following 1 Defects caused by repairs or modifications made by anyone other than Finnzymes Instruments Oy or its licensed distributors 2 Defects caused by improper packa
35. scribes all the features and specifications of the Arktik instrument Read the manual in its entirety before operating the instrument All buttons on the keypad are referred to in brackets The following is an example referring to the shift block button on the keypad press SHIFT BLOCK to shift between the two blocks when a dual block is inserted in the machine Bolded words refer to items or functions that may be selected from the programming menu The following is an example for initiating a protocol To run a protocol first select RUN using the function key Keep the user manual for future reference The user manual is an important part of the instrument and should be readily available during use of the instrument Keep the user manual together with the instrument in case you distribute it onwards For the latest information on products and services visit our websites at http www thermoscientific com arktik In our efforts to produce useful and appropriate documentation we would appreciate any comments you may have on this user manual for your local Thermo Fisher Scientific representative Thermo Scientific Arktik Thermal Cycler User Manual 3 About This User Manual Safety warnings Safety warnings Heap e These symbols are intended to draw your attention to particularly important information and alert you to the presence of hazards as indicated Caution This symbol indicates risk of harm or
36. tact Thermo Fisher Scientific Dual block 48D Heatsink temperature is too high Ensure that airflow is unobstructed see Conditions for proper use on page 6 Heatsink temperature is too low Temperature sensor is disconnected Do not run the instrument immediately if it has been stored in a cold location Allow to warm to room temperature before operation If not working contact Thermo Fisher Scientific for support Contact Thermo Fisher Scientific Thermo Fisher Scientific Continued Thermo Scientific Arktik Thermal Cycler User Manual 45 Troubleshooting Guide Block sensor error Temperature sensor is shorted Suggested action Contact Thermo Fisher Scientific Hotlid sensor is disconnected Contact Thermo Fisher Scientific Hotlid sensor is shorted Contact Thermo Fisher Scientific USB input output error File Input error Disconnect the USB stick go back to the Main screen attach the USB drive and try again If not working contact Thermo Fisher Scientific for support File Output error Confirm that there is enough free space on the USB drive Disconnect the USB stick go back to the Main screen attach the USB drive and try again If not working contact Thermo Fisher Scientific for support Memory error Memory is full Delete older protocols or back them up into a USB drive and then delete the protocols File find error File not
37. the final step in the loop Use the lt 4 P gt cursor keys to move the arrow to a different temperature step The number of cycles is displayed in the middle of the loop arrow at the bottom of the screen This value may be edited using the keypad Press the DEL selection F2 to delete a cycling routine Press the YES key to accept changes or press the NO key to cancel and go back to the previous screen Function key actions F1 F2 F3 No action 22 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific F4 YES F5 NO lt lt gt Saving a protocol Thermo Fisher Scientific Operation Creating a new protocol Accepts a new cycle loop or edits to the cycle loop Cancels and returns to the previous screen Cursor actions Toggles the arrow between steps to select GOTO destination for cycling Note The GOTO value is the number of repetitions of the loop which is 1 less than the total number of cycles For example to program 35 cycles 34 repetitions should be entered into the GOTO step A Note A second GOTO routine can be added outside of the existing GOTO routine only A From the protocol editing screen press the SAVE selection using the F5 key abc File Name l Password a Password Check as The current file name will be displayed To save changes to current file name press SAVE F5 To change the file name use the keypad to rename the file and then press
38. uqanetscu ie saena naaa anida eiriaa aaia iiaia 33 DIETOS eTe T A T T E 33 lid een n e ER E T TE 33 SENS TS cage Dine Wats ied soe 2 ce E ENESE Ea cane de Mam ca rene 34 NGM ao E ied alata EE R AEE A A Manas N Wha adeidns 35 Sound Yen a e a eee Oe Ne Me Oe te 36 Los TCS sated tes le Sa oes he eh le E TRE Ni oat hed ht and case 36 USB link sions eviarcad acerssts suwaucaibancadest casei avunctateruarsuamicassuseaninetesiesenes 37 Exporting a file to a USB flash drive s c scisteccaseuseseneserciedeecetonstetes 37 Importing a file from a USB flash drive sseeseeeeeeeeeeeeeeeerrsesess 38 Chapter 6 Man ENAN a a Sharan a tai nition e oaa rh nie aaa ogai eioert rea 41 Cleaning the fins of the heat sink c cdinenic de deraedaes 4 Cleaning the Arktik Thermal Cycles csecoercy tpeceeieredteeacteececeees oat 41 Replacing thief ise s arcera an E ie sea eee ask 41 Disposal of the instrument 6st gi tet A ae claret ty cian 4 Chapter 7 Technical Specifications s scscssessecssessssesneecsesseseesnecnssnssneesneeneesees 43 Instrument SPECI CATIONS 2625500 heel od Oa elie uaa eae teat Stacie 43 Date seguldelines srne eissa fice neat tees ead a Aias 44 Chapter 8 Troubleshooting Guide ccsssssessecsessssssseesssesessesseseeseeneesestesseaeeatenees 45 Errorlo gnon os teed ap a e E E ae ea can Sisk calcd 45 Chapter 9 Ordering Information cccsssssessecsessessssssessessesesseeaeenestesseateaeeeaeeneens 47 PEC sag Pa
39. y A mild soap solution may be used if needed Clean the block wells with swabs moistened with water 95 ethanol or a 1 100 dilution of bleach in water To replace the fuse s you will need the new fuse s 250 V 8A fast 5x20 mm and a slotted screwdriver 1 First turn the instrument off and unplug it The fuses are located at the back of the instrument see Figure 2 3 on page 11 2 Use the slotted screwdriver to open the fuse holder 3 Remove the fuse s and replace it with the new one 4 Slide the fuse holder back into the instrument 5 Plug in the instrument and turn it on If the Arktik Thermal Cycler is exposed to potentially infectious biological samples toxic or corrosive chemicals or radioactive chemicals waste management of the complete instrument must be carried out to ensure that there is no risk of contamination Thermo Scientific Arktik Thermal Cycler User Manual 41 Maintenance Disposal of the instrument Follow laboratory and country specific procedures for biohazardous or radioactive waste disposal Warning The used lithium Li battery is regulated waste and must be disposed of according to local regulations The Li battery has to be changed by an authorized service technician only Instructions for changing the Li battery are described in the service manual A Dispose of the instrument according to the legislation stipulated by the local authorities concerning take back of electronic equipment an
40. ymbol is displayed on the screen if programmed into the protocol If not programmed into the protocol the time left is displayed A Function key actions Terminates the run after confirming with the user Pauses the run on the present temperature step or the next step if ramping When paused this option becomes RESUME Skips to the next step Toggles to the Status screen Returns to the Main menu Thermo Scientific Arktik Thermal Cycler User Manual 31 Operation Monitoring a run 32 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Diagnostics Thermo Fisher Scientific Lid Chapter 5 Managing Diagnostics Log Files and USB Link Using the Tools Menu Select TOOLS F5 in the Main menu al TOOLS DIAGNOSTICS LOG FILES USB LINK OPEN MAIN The Tools menu provides three options which are accessed by scrolling to the desired item using the cursor keys and pressing the OPEN F1 key e DIAGNOSTICS Allows users to check or adjust lid parameters sensor parameters sound settings and clock settings see below e LOG FILES Allows users to review log files from previously run protocols e USB LINK Allows users to transfer files to or from a USB Flash device The adjustment of the lid parameters sensor parameters sound settings and clock settings are described below From the Tools menu highlight DIAGNOSTICS and press OPEN F1
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