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N11467 ver 1.2 Arktik Thermal Cycler User Manual

1. Thermo Scientific Arktik Thermal Cycler User Manual Rev 1 2 Cat no N11467 Copyright 2013 Copyright Thermo Fisher Scientific Inc First edition published in 2010 All rights reserved All trademarks are the sole property of Thermo Fisher Scientific Inc and its subsidiaries Reproduction of the accompanying user documentation in whole or in part is prohibited License and trademark information This product is covered by the following patents and patents pending EP1973664B1 JP5248503B2 and US20080061429A1 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 Canadian Patent 1 339 653 owned by Applied Biosystems No right is conveyed expressly by implication or by estoppel under any other patent claim 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 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 omi
2. No disk connection Press F1 to go back MAIN BACK Thermo Scientific Arktik Thermal Cycler User Manual 39 Tools Menu USB link 40 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Chapter 6 Maintenance Contact local authorized technical service or your local Thermo Fisher Scientific representative for assistance if necessary Cleaning the fins 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 of the heat sink dirty or covered in dust You can use a cotton swab a brush or compressed air to remove dust Clean ng the 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 Arktik Thermal dusty A mild soap solution may be used if needed Cycler Clean the block wells with swabs moistened with water 95 ethanol or a 1 100 dilution of bleach in water Replacing the To replace the fuse s you will need the new fuse s 250 V 8A fast fuse s 5x20 mm IEC 60127 2 II and a small flat screwdriver 1 First turn the instrument off Unplug the instrument and disconnect the power cable from the power input socket The fuses are located at the back of the instrument see Figure 2 3 on page 11 2 Use the small flatl1 screwdriver to pry the fuse block assembly away from the power entry port hous
3. 099 C ee R 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 72 0 72 0 60 0 01 00 02 00 00 15 30 TEMP MODE SAMPLE BLOCK Back SAMPLE BLOCK In the next screen the vessel type is specified by pressing UTW F4 or COMMON F5 28 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Running protocols with the 48 dual block Thermo Fisher Scientific Operation Running a protocol 72 0 72 0 60 0 01 00 02 00 00 15 30 VESSEL TYPE UTW COMMON Back UTW COMMON In the next screen the sample volume is specified by typing in a volume 5 to 50 ul for 48 dual and 96 blocks 5 to 20 ul for a 384 block Confirm the selection by pressing YES F4 or return to the vessel section screen by pressing NO F5 72 0 72 0 60 0 01 00 02 00 00 15 30 Sample Volume kO uL Accept Oo T YES no After confirming the volume the protocol will start immediately see Monitoring a run on page 30 Note When a run begins the running protocol will be displayed in graphical mode on a Status screen see Monitoring a run on page 30 A When using a 48 dual block choose block A left hand block or block B right hand block with the switch key The active block is indicated by a highlighted letter at the top of the instrument s display A RUN
4. 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 SCR cts 099 e 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 F1 CHANGE Enables the user to change the default hot lid temperature F2 OFF 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 F3 No action F4 BACK Returns to the previous screen F5 MAIN Returns to the Main screen Sensors 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 Tools Menu Diagnostics BLOCK 24 6 C LID 67 9 C SINK 24 4 C pC BACK MAN 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
5. Infectious waste 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 Weight Electrical Power supply Line voltage Frequency Power failure recovery Fuses Type 5020 Instrument configuration Interchangeable block formats User interface Heated lid Memory Communications Programming Adjustable ramp rate Touchdown Thermal control Thermal performance Ramp rate Gradient range Thermal uniformity Thermal accuracy Thermal range 29 cm wide 38 cm deep 29 cm high 10 5 kg includes block 600 W 100 240 VAC 50 60 Hz Yes Fuses 2 x 8A 250V IEC 60127 2 lI II fast blow Approved manufacturer Littelfuse type 217 series Markings CE cTUVus Warranty 2 year 96 x 0 2 ml 384 x 0 03 ml dual independent 48 x 0 2 ml semigraphical Manually adjustable advanced lid design ensures proper pressure while preventing over tightening 50 folders with 99 programs in
6. Thermo E Cursor keys Figure 2 4 Arktik Thermal Cycler user interface Note The function keys are marked here as F1 F5 to help read the pE instructions A Interchan gea ble The Arktik Thermal Cycler accommodates three interchangeable blocks the 96 block 48 dual block and the 384 block Figure 2 5 blocks through Figure 2 8 Release button Heated lid Dial Handle Locking hande 99 S f gt N Main unit connector Figure 2 5 Block unit 12 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Arktik Thermal Cycler Main Parts Interchangeable blocks 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 e Two spare fuses 250 V fast 8A 5x20 mm e Quick Reference Guide e User Manual CD Required blocks are sold separately If you have not received the above items in your shipment contact your local distributor or Thermo Fisher Sci
7. BRUN 2011 04 21 08 48 31 Thermo SCIENTIFIC Version V01 07 Gradient Enabled Block 48 dual SN AKC011104302 RUN NEW __ TOOLS Note that you can edit the protocol of one block while the other block is running Thermo Scientific Arktik Thermal Cycler User Manual 29 Operation Monitoring a run RUN Tc RUN eee Cae 00 30 00 05 72 0 72 0 00 20 01 00 35 ADD DELETE OPTION BACK SAVE The flashing RUN text indicates which block is running and the highlighted letter A or B indicates the block that is being edited Monitori ng arun 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 72 0 72 0 60 0 01 00 02 00 00 15 30 CANCEL PAUSE NEXT TIME MAIN Function key actions F1 CANCEL Terminates the run after confirming with the user F2 PAUSE Pauses the run on the present temperature step or the next step if ramping When paused this option becomes RESUME F3 NEXT Skips to the next step F4 TIME Toggles to the Time Status screen F5 MAIN Returns to the Main menu 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 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
8. Continued Block sensor error Temperature sensor is shorted Hotlid sensor is disconnected Hotlid sensor is shorted USB input output error File Input error File Qutput error Memory error Memory is full File find error File not found 46 Thermo Scientific Arktik Thermal Cycler User Manual Suggested action Contact Thermo Fisher Scientific Contact Thermo Fisher Scientific Contact Thermo Fisher Scientific 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 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 Delete older protocols or back them up into a USB drive and then delete the protocols The protocol is corrupted or removed Try again or create a new protocol Thermo Fisher Scientific Arktik products List of spare parts and accessories Thermo Fisher Scientific 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 TCAQ001 Arktik Thermal Cycler base unit with gradient option TCAQ002 Arktik Thermal Cycler base unit without gradient option TCAQ096 Arktik 96 well block TCA4848 Arktik 24 well
9. F PREVIEW BACK DONE 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 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 1 23 4 5 6 7 8 9 10 11 12 60 0 60 6 62 1 64 6 67 9 72 1 77 1 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 90 0 72 0 72 0 01 00 02 00 04 0 100 207304 ke eee Oe OD 12 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 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 Note The gradient feature cannot be used with 48 dual blocks A Editing a cycling loop To edit a cycle loop is described below Modifying a cycling loop In the default protocol edit the cycling loop by highlighting the loop Use the lt 4 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 th
10. OPEN F1 The clock menu allows the editing of the Arktik Thermal Cycler s internal date and time settings INLA AA AULE HE 09 07 07 TIME 18 31 43 DISPLAY FORMAT YY MM DD 24H SAVE FORMAT BACK MAIN 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 Tools Menu Log files AI V lt gt Sound F1 SAVE F2 ON F3 OFF F4 BACK F5 MAIN lt 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 UNE OFF Nahi ON Function key actions Accepts 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 th
11. START EDIT BACK MAIN Function key actions Begins to run selected protocol Allows editing of the protocol in graphical mode No action Thermo Scientific Arktik Thermal Cycler User Manual 25 Operation Managing folders F4 BACK F5 MAIN Managing folders Fl OPEN F2 NEW F3 DEL F4 RENAME F5 MAIN Creating a new folder Returns to the previous screen Returns to the Main menu Select RUN F1 in the Main menu NO 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 Note Function key commands F3 and F4 are visible only when a modifiable folder is selected Folders Recent and Shared cannot be modified A 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 26 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific F1 F2 CAPS F3 DEL F4 BACK F5 SAVE Running a protocol Operation Running a protocol CAPS DEL BACK SAVE 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
12. STATUS F4 F5 TOOLS jd To access the sample blocks open the lid by grasping the handle and pulling it forward 2 To close the sample block apply downward pressure 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 Version V01 07 Gradient Enabled Block 96 well SN AKC011104302 RUN NEW _ TOOLS 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 Sho
13. indicated Caution This symbol indicates risk of harm or 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 a 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
14. 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 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 ne FOLDERS l RECENT 2 1of1 There are two permanent folders the 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 graphical mode Thermo Scientific Arktik Thermal Cycler User Manual 27 Operation Running a protocol 72 0 72 0 60 0 01 00 02 00 00 15 30 START EDIT BACK MAIN Press START F1 A lid temperature screen will be displayed showing the default lid temperature see Lid on page 33 for details Lid temperatures between 30 C and Note The default lid temperature may be set in the Tools Lid menu 110 C are allowed A es Note The heated lid may be turned off completely by pressing the co pi button A Press OK F5 to proceed 72 0 72 0 60 0 01 00 02 00 00 15 30 LID TEMP
15. the screen The time remaining in the current step and the current block temperature are displayed below this A Note Returning to the Main menu allows users to write or edit 30 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific F1 CANCEL F2 PAUSE Operation Monitoring a run 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 hermo SCIENTIFIC Version V00 00 Block 96 well SN RUN NEW BAN 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 CYCLE 0 TEMP 95 0 C TIME 00 04 51 STEP 1 OO CANCEL PAUSE NEXT STATUS MAIN Note The co symbol is displayed on the screen if programmed into the protocol If not programmed into the protocol the time left is displayed A Functi
16. total Ethernet USB memory port for protocol transfer Yes Yes Optimized for standard and UTW vessels 3 0 C s 30 C max 0 4 C at 90 C 0 3 C at 90 C 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 g u l d e nes 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 Mains supply voltage fluctuations 10 from nominal e Transient over voltage per Installation Category 2 IEC 60664 1 e Pollution degree 2 in accordance with IEC 60664 1 44 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific Chapter 8 Troubleshooting Guide Note Do not use the instrument if it appears that it does not function f 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 for support Table 8 2 Error codes reported Block sensor error Single block 96G 384G Heatsink temperature is too high Heatsink temperature is too low Temper
17. LOS PINES Gesenre ss 8c ose E A E 36 UO SB Lik ceaest ws se aeeessete use xa seGeeecasteteeastaue ese tonst uaa sous A 37 Exporting a file to a USB flash drive eee eeeeeeeeseeeeeneeeeeaeeees 27 Importing a file from a USB flash drive 38 Chapter 6 Maintenant Goss ccc cescates ca ayctacaccatensusoaaie hcasmenascuncnetucantiaisenarteicaameunauienens 41 Cleaning the tns of the heatsink sinc ciara ected i 4 Cleaning the Arktik Thermal Cycler 0 eeeeeeeseeeeeseeeeeneeeeeaees 4 Replace thie tsel o iania to haised ey shen iaate hed iota toetastenedeecauabie 4 Disposalor thie instr Un nton a oe a 42 Chapter 7 Technical Specifications cccsssssssssessssseseeeeseseseseessessseeenaeaees 43 Instiument SPECIICALION Sieis rinna widen eee 43 Sae Res e bb 6 ct Loomer en ene E ee eee 44 Chapter 8 Troubleshooting Guide cisissiccisticiniiitieiihintindinieaetiened tele ets 45 Eroro siete at eee gt a ea aa adc id eA aig tee cB as A 45 Chapter 9 Ordering nformati Maissana 47 Arktik Prod ees E rr ne tren nee 47 Kistof spare part and acCESSOTIES sisrreupo aun enni a aN Ai 47 8 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Chapter 1 Arktik Thermal Cycler Overview The Thermo Scientific 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 b
18. amming 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 page 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 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 Note To enter an infinite hold press the lower right key on the keypad Bt with the symbol A Entering advanced From the protocol editing screen press the OPTION selection using the programming 3 key options 60 0 01 00 02 00 00 15 30 INC EXT RAMP GRAD DONE The function key actions F1 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
19. and heated lid will become excessively hot Touching these components 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 rea
20. ature sensor No 1 is disconnected block left temperature sensor Temperature sensor No 1 is shorted Temperature sensor No 2 is disconnected block mid temperature sensor Temperature sensor No 2 is shorted Temperature sensor No 3 is disconnected block right temperature sensor Temperature sensor No 3 is shorted Hotlid sensor is disconnected Hotlid sensor is shorted Dual block 48D Heatsink temperature is too high Heatsink temperature is too low Temperature sensor is disconnected Continued Suggested action Ensure that airflow is unobstructed see Conditions for proper use on page 6 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 Contact Thermo Fisher Scientific Contact Thermo Fisher Scientific Contact Thermo Fisher Scientific Contact Thermo Fisher Scientific Contact Thermo Fisher Scientific Contact Thermo Fisher Scientific Contact Thermo Fisher Scientific Ensure that airflow is unobstructed see Conditions for proper use on page 6 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 Scientific Arktik Thermal Cycler User Manual 45 Troubleshooting Guide
21. d outside of the existing GOTO routine only A From the protocol editing screen press the SAVE selection using the F5 key Password Check ys P CAPS DEL BACK SAVE 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 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 Thermo Scientific Arktik Thermal Cycler User Manual 23 Operation Saving a protocol 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 iol FOLDERS i SHARED E E 1of1 DE Function key actions F1 SELECT Selects the folder to which the protocol will be saved F2 NEW Creates a new named folder see Creating a new folder on page 26 F3 No actio
22. dual block TCA0384 Arktik 384 well block Not available in USA or Germany Table 9 4 Codes for spare parts and accessories Code Item Quantity N11467 Arktik Thermal Cycler User Manual 1 5180220 Power cable UK 1 1210550 Power cable Euro 1 1210520 Power cable USA Japan 1 N08421 Power cable China 1 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 Notes Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 51 Notes 52 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific Oy Ratastie 2 P 0 Box 100 Fl 01621 Vantaa Finland www thermoscientific com N11467
23. e 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 F1 F2 F3 F4 BACK F5 MAIN lt USB link Exporting a file to a USB flash drive Thermo Fisher Scientific Tools Menu USB link LOGFILES Page 1 of 1 2009 07 07 17 52 test SHARED Stop Function key actions No function Returns to the Tools menu Returns to the Main screen Cursor actions Toggles between pages This section describes how to transfer a file to or from a USB flash drive To export a file to a 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 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 Scientific Arktik Thermal Cycler User Manual 37 Tools Menu USB link Import
24. e 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 05 00 00 15 72 0 72 0 01 00 02 00 00 15 i L Accept pT S y wE j no An arrow will appear that will point by default to the temperature step directly before the final step in the loop Use the lt 4 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 22 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific F1 F2 F3 F4 YES F5 NO lt gt Saving a protocol Thermo Fisher Scientific Operation Saving a protocol No action 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 adde
25. entific directly Save all packing material in case you need to return the Arktik Thermal Cycler for maintenance Setting up the Arktik Thermal Cycler 1 Remove all components from the packaging 2 Install the Arktik Thermal Cycler in a protected location where no one can step on or trip over the power cord and where the power cord remains accessible if the unit needs to be unplugged 3 Place a 96 well block 384 well block or a 48 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 4 Plug the power cord into the back of the Arktik Thermal Cycler 5 Insert the power cord into the power outlet Thermo Scientific Arktik Thermal Cycler User Manual 15 Installation Compatible vessels Caution To prevent risk of shock or damage to the instrument it is very important that the power supply be first connected to the Arktik Thermal Cycler before plugging it into the wall a Caution Always use a grounded power outlet and power cord to provide power to a Arktik Thermal Cycler A 6 Turn on the power switch on back of the instrument Compati ble vessels The Arktik Thermal Cycler is compatible with both standard vessels and Thermo Scientific UTW ultra thin wall reaction vessels 16 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fis
26. gent component tubes only when needed e Uncap and close tubes 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 Cond itions for This section describes the environmental requirements of the Arktik Thermal Cycler proper 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 le
27. he Arktik Thermal Cycler issesrcsssenennsstebinneusettgasteneanes 15 CompatiDIe yensels maiie e A 16 Oprati o Moroeni lene eee eed neal anitd 17 Installing blocks in the Arktik base Unit eee eeeeeeeeeeeeeneeeeeeees 17 Opening and closing the Arktik blocks eee eeeeeeeeneeeeeneeeeenees 18 Main ICU ace Ss rin eo oeestaidcat cece a r A N a ered 18 Creare anew DLO OCO sees cats teases tesa tuincaeh Cesacied ipsa tetas ieeuniee 19 BASIC Pror l eaaa E E E E 19 Entering advanced programming Options ssssesssesssressressseesere 20 Gradiehtsetup DEMU renie E 21 Farine a Cy ClO loopren a pro sauod eae ses 22 Modilying acy cling lOO Peann wists ine areieeeteereeieea 22 Adding hew cycling lO0porsreseri ia a EEE AT 22 Savine a Protocoles a a E Giemsa 23 Editing a Protocol eeren S 25 Mapasine TOL EG sce a E Sw as nae alo ee te 26 Cerina d Mele ias 6 al gaan ee etn reer err errant E Smt ert eer 26 Rinne A protoco Ret enero ener en eerie tne cen re rere ee eee re eres 27 Running protocols with the 48 dual block eee ee eeeeseeeeeneeee 29 Thermo Scientific Arktik Thermal Cycler User Manual 7 Contents IVEOU IE OLIN A TAO ong ss shuesesenistsntie sd O 30 Chapter 5 MOONS ME ionainn 33 NIAC TO SECS a E E E A E E eeu ctatees 33 E a EEE EEA E A E E A EE AEE A E E T EE ANTEE 33 PO O a O a macarons 34 TOG EE E ENEE PE NEEE N EESE E AES E EE deneeaee 35 S16 101 0 6 ee P ERE Rent ir er eee enn RE Pe Re nee ee mente O en iene een 36
28. her Scientific Chapter 4 Operation The operation of the Arktik Thermal Cycler is described below Installing blocks in 1 Make sure that the Arktik base unit is turned off the Arktik base unit n 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 pE 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 SSS SSS SIY SS SS il il in Ill iil co ill iii fh i al i Il il il il es l il yl il 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 Main menu F1 RUN F2 NEW F3
29. ing a file from a USB flash drive Local User List RECENT SHARED t Page 1 of 1 pack VIEW To export the selected file press COPY F4 Local File List test Page 1 of 1 pack COPY 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 j Page 1 of 1 Back TO TO vew To import the selected file press COPY F4 38 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Thermo Fisher Scientific Tools Menu USB link File List Page 1 of 1 pack COPY the Arktik giving the option to overwrite the existing file a Note A message will be displayed if the same folder file already exists on 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 Note Ifthe USB flash drive is not inserted the NO DISK CONNECTION message will be displayed A
30. ing and remove Figure 6 10 pa oq Figure 6 10 Opening the fuse block assembly Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 41 Maintenance Disposal of the instrument 3 Replace the blown fuse s with the same type 8 0 A Figure 6 11 D gr ACINLET Il Figure 6 11 Fuse block assembly 4 Place the fuse holder back into the slot and push it until it clicks 5 Plug in the instrument and turn it on Disposal of the Ifthe Arktik Thermal Cycler is exposed to potentially infectious t t biological samples toxic or corrosive chemicals or radioactive chemicals Instrumen waste management of the complete instrument must be carried out to ensure that there is no risk of contamination Follow laboratory and country specific procedures for biohazardous or radioactive waste disposal 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 X Warning The used lithium Li battery is regulated waste and must be local authorities concerning take back of electronic equipment and K Dispose of the instrument according to the legislation stipulated by the 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
31. ing directly at the Arktik Thermal Cycler system 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 Merele GSS enre EA AA ER 3 How to use this user manual senneseeneseensssossecssesreseerssecrssecrsesrese 3 FOP MOE nornai ossa a aaa a eae 3 S E A E E E A T A E E eee 4 Electromagnetic weri renc Eei ears chee ceseecentiet ee 5 Good laboratory Practices recoil ieus ee Ea E neeen eas 5 Generalehemical warming seisoin i i a E ei 5 General biohazard Warni i o eacee a E 5 Conditions tor Proper se einiorcasiesiiapenis inie eee 6 Absolute environmental requirements sssssssssesssseresssresssresseseeeo 6 Recommended working conditions sssssssessssssssssesssesssressrerseresees 6 PPNOW aa A Noe 6 Arktik Thermal Cycler Overview ccsssssssessssssssessesneeeeeaes 9 Arktik Thermal Cycler Main Parts cscsssssssssssessesessesseeees 11 TOMO WIC We casa sten cos aten onan ecencaassa te EEE EEA 11 PRCA MCW oeae ar a a aa baawnneea tease eseueiee seas 11 Instrument user interface c cccssescccssccccceccccsscececssccccscceeeeescenees 12 nter hanged ble BlOCKS scsec vice ta that E E eMac tatnite 12 NTU Cel ACTON naaa diataactaaest a coraaeeaceettate near 15 iRveruetugelell baler Rea ere eer ReR TE E a ea 15 Setting up t
32. lock allowing versatile use of the cycler You control the Arktik Thermal Cycler through a simple instrument user interface Graphical representation of a cycling routine makes navigation convenient The integrated USB port enables protocol transfer Figure 1 1 Arktik Thermal Cycler Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 9 Arktik 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 Front view The front view of the Arktik Thermal Cycler is shown in Figure 2 2 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 at iri Locking handle j id PRUROUE Ethernet port F UUU Uni ul Hl F i Power switch gt e y o l W ULE Power socket Fuse Figure 2 3 Arktik Thermal Cycler rear view Thermo Fisher Scientific Thermo Scientific Arktik Thermal Cycler User Manual 11 Arktik Thermal Cycler Main Parts Instrument user interface Instrument user The user interface of the Arktik Thermal Cycler is shown in Figure 2 4 inte rface Alphanumeric keypad o Display oe e Block shift key for dual blocks Enter ke F1 F5 b gt ba asce e
33. n F4 BACK Returns to the previous screen F5 No action Cursor actions A W Highlights the folder for selection protocol is saved to a folder final confirmation will be presented A Note A protocol may not be saved to the RECENT folder Before a xe FOLDERS i SHARED Page 1 of 1 Save file in SHARED YES YES amp RUN BACK Function key actions F1 YES Saves the protocol file to the selected folder and returns to the Main menu 24 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific F2 YES amp RUN F3 F4 BACK F5 Editing a protocol F1 START F2 EDIT F3 Thermo Fisher Scientific Operation Editing a protocol Saves protocol file to selected folder and proceeds to the Running a protocol step see Running a protocol on page 27 No action Returns to the previous screen No action Note Ifa 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 graphical representation of the protocol 60 0 01 00 02 00 00 15 30
34. on key actions Terminates the run after confirming with the user Pauses the run on the present temperature step or the next step if Thermo Scientific Arktik Thermal Cycler User Manual 31 Operation Monitoring a run ramping When paused this option becomes RESUME F3 NEXT Skips to the next step F4 STATUS Toggles to the Status screen F5 MAIN Returns to the Main menu 32 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific Diagnostics Thermo Fisher Scientific Lid Chapter 5 Tools Menu Select TOOLS F5 in the Main menu no TooLS DIAGNOSTICS LOG FILES USB LINK 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 Highlight LID and press OPEN F1 Thermo Scientific Arktik Thermal Cycler User Manual 33 Tools Menu Diagnostics ne DIAGNOSTICS LID SENSORS CLOCK SOUND
35. ot the instrument performance This user manual also describes 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 X e gt e These symbols are intended to draw your attention to particularly important information and alert you to the presence of hazards as
36. ssions nor for any damages resulting from the application or use of this information This manual supersedes all previous editions Remark on screenshots and product images Screenshots and product images may differ from your system depending on the product and firmware versions No liability for consequential damages Thermo Fisher Scientific shall not be liable for any direct or consequential damages whatsoever arising out of the use or inability to use this product Power failure The system requires uninterrupted power supply in order to operate correctly Thermo Fisher Scientific has no responsibility whatsoever for system malfunctions arising from power failures Cat No N11467 October 2013 Manufacturer Thermo Fisher Scientific Oy Ratastie2 P O Box 100 FI 01621 FINLAND Intended users How to use this user manual For more information Thermo Fisher Scientific About This User Manual The Thermo Scientific Arktik Thermal Cycler can be used for example 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 Troublesho
37. 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 successive 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 60 0 01 00 02 00 00 15 30 Set from 60 0 C to 90 0 C
38. vel performance and have the fewest problems adhere to the environmental requirements described here A Absolute The Arktik Thermal Cycler is rated to operate reliably in the following environmental environmental conditions Avoid extremes of these environmental ranges to best preserve the long term performance and life span of the requirements ot nent 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 reliability when the working conditions are as close to standard 9 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 blow
39. ws Status screen when running Not used Accesses global settings or diagnostic routines 18 Thermo Scientific Arktik Thermal Cycler User Manual Thermo Fisher Scientific SWITCH Creating a new protocol Basic protocol Thermo Fisher Scientific Fl ADD F2 DELETE F3 OPTION F4 BACK F5 SAVE Operation Creating a new protocol Switches 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 graphical 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 72 0 72 0 60 0 01 00 02 00 00 15 30 ADD DELETE OPTION BACK SAVE Function key actions Adds a temperature step to the right of the highlighted step or allows the addition of aGOTO 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 progr

N11467 ver 1.2 Arktik Thermal Cycler User Manual

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