Amplitronyx™ 6 Thermal Cycler - a
Contents
1. machine will begin to program When process is complete you will be prompted to click OK 7 Unplug the serial cable from the back of the cycler The machine will now auto re boot The diagnostic start up screen will confirm a successful upgrade by showing the version the first two numbers reference the front end version X XY 8 The Amplitronyx 6 is now updated and ready for use Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 26 of 30 Appendix Ill Troubleshooting Do not attempt to service your Amplitronyx 6 Thermal Cycler yourself The Nyx Technik service and support team are here to help you determine the source of any problem and the correct actions to take to resolve it If the tips below do not resolve your problem contact Nyx Technik or an authorized repair center for more detailed troubleshooting instructions Prior to contacting Nyx Technik if you are able to perform a HyperTerminal Trace see Appendix IV and to note the status of the diagnostic LED lights your problem can be addressed more quickly Diagnostic LED lights can be viewed through the vents on the left side of the machine Order of Lights top to bottom Normal Status Thermal engine online Orange blinking Fans Green solid Heated lid Red when heating off when not heating Blue when cooling Red when heating Blue2. 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 13 of 30 Program Menu From the main program menu you can write a new program by modifying an existing pre programmed template see Appendix Il or you can edit a program you have already saved Open a Program Template to Create a New Program Amplitronyx 6 contains a set of pre programmed templates for generating new programs To write a new program simply load the template similar to the program you want to create After customization your program can be saved edited or overwritten at your discretion eu TER Utilities Block To create a new program from a template select Program from the Home Screen and then Write New Stage Cycle Step Temp Options Time Options Program Use the Up and Down arrows to locate the oS ee 1 00 A desired template from the list see Appendix II Select 1 94 0 0 30 Open 2 30 2 50 0 0 30 3 1720 0 30 To make changes to the Stage Cycle Step Temp 1 72 0 5 00 Time or Options select the appropriate value button 3 1 a IED HD directly on the editing screen for whatever you wish to v change with your stylus pen Use the Up and Down arrow keys to scroll and view additional program information Program Pref Add Delete Print Save as Once a button is selected it will take you to the editing User I Standard PCR I Editi
3. A2 2001 Class B EN5502 1998 Class B and EN6100 3 2 1995 This unit satisfies the safety requirements of EN61010 1 1993 EN61010 2 1993 following the provisions and directives 73 23 EEC as amended by 93 68 EEC LVD and 89 336 EEC EMC Alteration of this unit by individuals other than those trained or certified by Nyx Technik Inc voids all conditions of the warranty and may result in electrical shock Unpacking and Inspection of the Amplitronyx 6 Thermal Cycler Carefully unpack the cycler from the shipping box and make sure it was not damaged in transit Check the contents of the box to ensure the main power cable stylus null modem cable and instruction manual have been included Save all packaging until inspection verification of condition has occurred If a return is required please contact Nyx Technik Inc at 858 320 0096 or email customerservice nyxtechnik com to request a Return Goods Authorization number A decontamination certificate will be provided by Nyx Technik and must be included with all returned units and accessories Nyx Technik is not responsible for any damage sustained in transit if the unit is improperly packaged and shipped Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 8 of 30 Introduction The Amplitronyx 6 is a high performance sub ambient thermal cycler with the widest gradient
4. Capture Text then Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 29 of 30 Appendix V Related Products Accessories for the Amplitronyx 6 Thermal Cycler Cat Description A4C Amplitronyx 4 Thermal Cycler with CombiBlock A62 Amplitronyx 6 Thermal Cycler with 0 2 ml Gradient Block A65 Amplitronyx 6 Thermal Cycler with 0 5 ml Gradient Block A63 Amplitronyx 6 Thermal Cycler with 384 Well Block A6F Amplitronyx 6 Thermal Cycler with Flat Block A6 B2 0 2 ml Thermal Block for Amplitronyx 6 A6 B5 0 5 ml Thermal Block for Amplitronyx 6 A6 B3 384 well Thermal Block for Amplitronyx 6 A6 BF Flat Thermal Block for Amplitronyx 6 A6 P Optional Printer for Amplitronyx 6 Electronyx Horizontal Electrophoresis Systems Cat Description EH7 Electronyx Mini 7x7cm amp 7x10cm UV Tray 2x8 sample combs loading guides and dams EH8S Electronyx Speed Mini 8x10cm UV Tray 2x8 sample combs 1 5mm and casting dams EH10 Electronyx Midi 10x7cm amp 10x10cm UV Tray 2x16 sample combs loading guides and dams EH15 Electronyx Midi Ultra 15x7cm 15x10cm amp 15x15cm UV Tray 2x20 sample combs loading guides and dams EH20 Electronyx Maxi 20x10cm 20x20cm amp 20x25cm UV Tray 2x20 sample combs loading
5. Time Elapsed 0 19 also show if the program is in lid heating or holding mode Time Remaining 1 09 Estimated ion 13 35 Progi The screen will also show whether you are running in j Running TUBE PLATE OR SLIDE mode based on the temperature control option you have set Verify that this text matches the type of plastic you are using if not stop the program through the Run Options Menu and correct the temperature control mode Open Run Options Menu User Standard PCR Running The Run Progress Clock provides a large visual estimation of your program progress The green shade represents the portion of the program that has been completed It will also show a text of the current running mode such as Lid Heating Running or Hold The Estimated Completion Time will be accurate provided the main clock has been set prior to beginning the run see page 20 Run Options Submenu View Current Program Settings Selecting this option allows you a read only view of the currently loaded program its temperature control setting and other parameters If you need to make changes select Edit Current Program from the main Program menu Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 20 of 30 View Real Time Chart The real time chart shows a graphic representation of what the thermal cycler
6. guides and dams EH26 Electronyx Screen 26x16cm 26x24cm amp 26x32cm UV Tray 6x28 sample combs loading guides and dams Electronyx Mini 10 x 10 cm Vertical Electrophoresis Systems Cat Description EV10G Electronyx MiniPAGE Gel Unit 10x10cm incl Tank and lid Glass Plates with bonded 1mm thick spacers 2x12 sample combs cooling pack dummy plate and Casting Base EV10C Electronyx MiniPAGE Capillary Tube Unit 10x10cm incl Tank and lid glass capillary tubes blanking ports cooling pack 2D combs 2D spacers EV10B Electronyx MiniPAGE Blot Unit 10x10cm incl Tank and lid 3 cassettes 6 fiber pads and cooling pack Electronyx MiniPAGE Blot Insert Module includes 3 cassettes amp 6 fiber pads Converts EV10C to EV10 BI EV10B Electronyx MiniPAGE Gel Insert includes internal gel insert glass plates with bonded 1mm thick EV10 Gl spacers 2x12 sample combs cooling pack dummy plate and Casting Base Converts EV10C to EV10G EV10 Cl Electronyx MiniPAGE 2D Capillary Tube Gel Insert Module includes glass tubes and blanking ports Converts EV10B to EV10C Electronyx Maxi 20 x 20 cm Vertical Electrophoresis Systems EV20G Electronyx MaxiPAGE Gel Unit 20x20cm incl Glass Plates with bonded 1mm thick spacers 2x24 sample combs cooling pack dummy plate and Casting Base EV20C Electronyx MaxiPAGE Capillary Tube Unit 20x20cm incl Tank and lid glass capillary tubes blanking ports cooling pack 2D combs 2D spacers
7. into your computer HyperTerminal Procedure 1 Right click on the My Computer icon and go to Properties Click the hardware tab then device manger Under Ports COM amp LPT expand the listing so you can see the USB serial converter Remember the COM number as you will need this in the steps to follow 2 Open the HyperTerminal program on the computer by clicking on the Start button Choose Programs than Accessories then Communications then HyperTerminal 3 Choose an icon and name it APX Click OK When the next window opens select the COM number you saw in step 1 from the dropdown menu called Connect Using Click OK 4 When the next window opens under Bits per Second select 57600 and under Flow Control select none Leave all other fields at the default values Click OK 5 In order to capture the readout into a file that can be sent by email on the top menu bar of the HyperTerminal program select Transfer and then Capture Text In the pop up window create a filename for the HyperTerminal readout Click Start 6 Start the run on the thermal cycler that results in an error or problem You should see lines of numbers appearing on the screen Let the machine run all the way through the program or until it stops automatically with an error 7 On the top menu bar of the HyperTerminal program select Transfer then
8. is doing within the context of the entire program The 2 D chart is shown with time represented on the X axis and temperature represented on the Y axis Each step is differentiated by the duration of the amp Run Program Utilities Block dwell time temperature and its sequence in the program The screen is partitioned vertically in Current Program Chart i i r Stage Cycle Step Temp Options Time Options straight lines to represent the dwell time points r a Gee E Gk ae between steps The X axis represents the dwell time periods of all the steps in programmed sequence spanning left to right A step or more specifically the dwell time span in a step is represented by parallel lines The left line will be the start point and the right line will be the endpoint of a step and consequently start point of the next step lt gt User Standard PCR Running A line graph spanning the entire chart shows the Temp vs Time at any given point The running step will be represented by a green line segment while the rest of the graph will be represented in black For stages containing multiple cycles the green line cycles through the same portion of the chart The chart shows the progress of actual ramping or cooling and shows both a color and time change green of a line segment spanning two time points representing the most current step the program is running Also the thickness of the line at the gra
9. of temperature control and regulation When using the temperature probe it is necessary to use dome capped PCR tubes not flat topped ones to ensure the heated lid comes down evenly Simulated Tube Control In Simulated Tube Control algorithms take into account the heat transfer properties of the plastic tube the spatial difference between the temperature probe and the block and the specific heat capacity and volume of your sample Simulated tube mode reads the temperature from the block and an algorithm takes into account the time required to heat your sample volume in conjunction with those other variables This method of temperature control is driven by calculation instead of by temperature probe Typically the reaction and cycling times are slightly longer to incorporate this offset Simulated Plate Control This is the same control method as Simulated Tube Control but is employed when using multi well plates It is extremely important NOT to use this method for tubes Simulated Slide Control This is the same control method as Simulated Tube and Plate Control but is employed when using an in situ block also called a flat block and glass slides Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 10 of 30 Getting to Know the Amplitronyx 6 External Layout Front of unit Push button cover release
10. when cooling Red when heating Blue when cooling Red when heating Blue when cooling Red when heating Thermal block zone 1 Thermal block zone 2 Thermal block zone 3 Thermal block zone 4 Software amp Programming Symptom Possible Cause You may be in a sub menu Press the back Unable to select one of the main menu buttons arrow repeatedly until the main menu tabs are selectable If heating block was removed and replaced Program appears frozen without turning off the power the machine must be reset by powering off and on again Re calibrate touch screen under Utilities Advanced Features Display Setup Screen inaccurate or unresponsive Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 27 of 30 Tubes amp Plates Symptom Possible Cause What often appears as melting can actually be the result of a deformation due to too much pressure applied by the heated lid Ensure the temperature control setting is not on Sim Plate if you are using tubes Tubes appear melted Plastic may not be rated up to 120 C Adhesive from lid labels or tape can melt and stick to the heated lid Do not use lid labels or tape on the tops of tubes Ensure that the Sim Plate temperature control option is selected or the correct amount of pressure
11. will not be applied to seal the plate Multi well plates not sealed properly Ensure that the sealing film or tape used is rated to withstand up to 120 C Problems during Run Symptom Possible Cause If changes are made to a program and the program is re saved with the same name the changes will not be sent to the main computer unless the program is re loaded To check the Running program does not seem to match parameters actually being read by the cycler saved program during the run open the Run Options Menu and select View Current Program Settings If the settings show the original program stop the running program and Load Another Program from the Run Options Menu Ensure that there is some kind of tube or plate in the cycler If no reaction vessel is present there is no buffer between the lid while it is heating and the block while it is chilling and the lid will not be able to reach the correct temperature The threshold for the heated lid is 25 1 C If a step is programmed to 25 0 C or lower the heated lid turns off After the machine finishes the 25 0 C cycle it will go into lid heating mode again which means the block will go Lid heating appears in the middle of a cycle down to 4 C to hold the tubes while the lid turns back on and heats up Once the lid is fully heated the block temperature will rise from 4 C to the next programmed temperature To avoid this delay ensure that all
12. 0 Maximum steps per stage 10 Gradient software 36 range from 30 C 80 C Max programmed dwell time Infinite Hold Pause function Yes Temp increments decrements Yes Time increments decrements Yes Ramp rate limiting Yes Auto restart function Yes Run end time calculation Yes Temperature control options Block control active tube control simulated tube control simulated plate control and simulated slide control Working Conditions Temperature Ambient 12 C 32 C Relative humidity Up to 80 Power requirements 533W at 115 230V a c 10 and 50 60Hz Physical Characteristics Dimensions W x D x H 10 x 10 3 4 x 10 inches 25 x 27 4 x 25 cm Shipping Weight 26 Ibs 12 kg Nyx Technik Inc 6191 Cornerstone Court E Ste 103 San Diego CA 92121 Phone 858 320 0096 Xd Fax 858 320 0022 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 9 of 30 Temperature Control The Amplitronyx 6 offers five temperature control options 1 Block Control 2 Active Tube Control 3 Simulated Tube Control 4 Simulated Plate Control and 5 Simulated Slide Control Depending on the interchangeable block present in the chassis some of these options may not be available if they do not apply Temperature control options allow the user to establish the source from which actual temperature values are drawn These mechanisms ensure confidence in the accurat
13. 03 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 14 of 30 Edit Temperature Using the stylus select the temperature parameter to edit Using the keypad enter a temperature between 4 99 C in increments of 0 1 C If lt 4 C is entered the default of 4 C is stored if gt 99 C is entered the default of 99 C is stored Select Store Temp to save and return to the editing screen or select the Back button to exit the screen and return without editing the temperature Entering a Temperature Gradient A maximum gradient range of 36 C can be achieved across the 0 2 ml and 0 5 ml blocks with the temperature Temperature Gradient limits between 30 C and 80 C To set a gradient select Column Number the button in the Options column next to the temperature 1 2 3 4 s e 7 elo fro 1 12 in the step to which you want to apply the gradient From 50 7 51 4 52 8 54 9 57 2 59 1 60 9 62 8 65 1 67 2 68 6 69 3 the Temperature Option Menu Select Temperature Temperature C Gradient This will take you to the Temperature Gradient l Edit Screen If you are unable to select Temperature 50 0 Set caen Store Gradient Gradient you may already have an Gradient Clear increment decrement option set for this temperature It is euu Ss kenge SERENA possible only to program either a temperature gradient or an increment decrement Go back to the User Standard Editing increm
14. 4 1 sec 2 30 2 55 1 sec 3 72 1 sec 1 72 2 min 3 1 2 4 Hold RT 1 Step Template Temp Temp Time Stage Cycle Step C Options Time Options 1 p 1 90 5 min 2 42 60 min 2 1 1 90 10 min Ice Bucket Template Temp Temp Time Stage Cycle Step C Options Time Options 1 1 1 4 Hold Ligation Template Temp Temp Time Stage Cycle Step C Options Time Options 1 1 1 15 Hold Digest Template Temp Temp Time Stage Cycle Step C Options Time Options 1 1 1 37 Hold Nyx Technik Inc 6191 Cornerstone Court E Ste 103 San Diego CA 92121 OX NYXTECHNIK Phone 858 320 0096 Fax 858 320 0022 www nyxtechnik com Rev 011311_1 59 Page 25 of 30 Appendix II Amplitronyx 6 Front End Software Upgrade Procedure 1 Plug the serial cable provided in the accessory pack into the back of your PC and the powered off Amplitronyx 6 Thermal Cycler 2 Open executable User Interface Software Uploader 3 Click on OPTIONS and then COMUNICATIONS set baud rate to 57600 and comport to auto 4 Click on FILE and select OPEN in the open target program file window locate file NATCXXY hex after opening numbers and letters will appear on the top left and across the bottom of the screen 5 Turn on the thermal cycler Blue text will appear on the top right of the screen If blue text does not appear turn the cycler off and on again If there is still a problem check the serial cable connections 6 Click TARGET then AUTO
15. 5 7 diag adjustable color touch screen Ventilation for power supply Connector for main power cable USB diagnostic port for hyperterminal Serial port for printer or for uploading front end software Dual fans Initial Set Up Connect the unit to a grounded power outlet using the provided power cable and turn on the power using the switch on the Sei Sn ver 1 09 back The Self Diagnostic Program screen appears indicating ses the unit is checking the status of its internal systems and Coarant RARS components When a system component passes its diagnostic Thermal Engine Tasting test an OK will appear to the right of the corresponding Block component If any system fails FAILED will appear on the GUI Controller screen One possibility for receiving this message is an Power Supplies incorrectly installed block Make sure the block is correctly installed and sits flush in the unit Reboot the machine by turning the power off and on again and wait to see if FAILED reappears If you still get FAILED please contact Nyx Technik Inc IDagosita Aur Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYX ECHNIK www nyxtechnik com Rev 011311_1 59 Page 11 of 30 Home Screen When all systems pass the Self Diagnostic Program the Home Screen will appear The Home Screen is the point from which all navigation beg
16. EV20B Electronyx MaxiPAGE Blot Unit 20x20cm incl Tank and lid 3 cassettes 6 fiber pads and cooling pack Electronyx MiniPAGE Blot Insert Module includes 3 cassettes amp 6 fiber pads Converts EV10C to EV20 Bl EV10B Electronyx MiniPAGE Gel Insert includes internal gel insert glass plates with bonded 1mm thick EV20 GI spacers 2x12 sample combs cooling pack dummy plate and Casting Base Converts EV20C to EV20G EV20 Cl Electronyx MaxiPAGE 2D Capillary Tube Gel Insert Module includes glass tubes and blanking ports Converts EV10B to EV10C Nyx Technik 6191 Cornerstone Court E Ste 103 San Diego CA 92121 Phone 858 320 0096 Fax 858 320 0022 www nyxtechnik com Inc OX NYXTECHNIK Rev 011311_1 59 Page 30 of 30 Electronyx Semi Dry Blotting Systems Cat Description ESD10B Electronyx Mini Semi Dry Blot Unit 10x10cm System ESD20B Electronyx Maxi Semi Dry Blot Unit 20x20cm System Ituminyx Transilluminators Cat Description 12126B Illuminyx UVB Transilluminator Wave Length 302nm Tube 6 X 8W Filter Size 21 X 26cm ID2126AB IIluminyx Dual UVA UVB Transilluminator Wave Lengths 302 365nm Tube 5 X 8 6 X 8W Filter Size 21 X 26cm IWLCP Illuminyx White Light Conversion Plate Photonyx Gel Documentation Systems Cat Description P8F Photonyx Gel Documentation System P8F l2126B Photonyx Gel Documen
17. K www nyxtechnik com Rev 011311_1 59 Page 12 of 30 Entering Data 4 moam Keyboard To make a selection on the keyboard use the stylus to press the desired character your selection will appear on the line above the keyboard Use the BACK button to remove letters right to left and Q W ERT YU I O P One character at atime Select Enter when finished Z X C V B N M Back Enter Numeric Keypad AT Peron ona Ta Time Entry This standard keypad allows you to enter numeric values The Back 00 00 8 9 Arrow to the right of the number 9 will remove numbers right to left one at a time Use the HOLD button to program an infinite dwell Sueccimel 4 5 6 time such as a 4 C HOLD Select Store button to save the entered numeric value Mins Secs 5 HoD O Plastic Consumables Tubes and Plates In order for the heated lid to apply the correct pressure for your tubes or plates you MUST select the appropriate temperature control setting before starting When using individual or strip tubes do not group them all together but instead space them out across the block as to equalize the pressure of the heated lid Printing Options A printer for the Amplitronyx 6 Cat A6 P can be purchased as an accessory item Once attached it is possible to print program parameters including all options notes temperature control method gradient table and block type Nyx Technik Inc Phone 858 320 0096
18. Menu Power Failure Response The Amplitronyx 6 can be programmed to either continue Cont running your program in the event of a power interruption or to stop Select Cont to resume the run in the event of a power interruption or Reset to abandon the program if the power is interrupted Choose Store to return to the Advanced Features submenu Set Adjust Current Time Setting the current time allows the Estimated Time of Completion for a run to be accurate Select Adjust and use the Up and Down arrows to adjust the time When finished select Done Choose Store to return to the Advanced Features submenu Set Adjust Current Date Select Adjust and use the Up and Down arrows to adjust the date The US format of month day year will appear unless you select EU to follow day month year When finished select Done Choose Store to return to the Advanced Features submenu Reset Memory Option Selecting this option will erase all data in stored programs and is generally not necessary Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 22 of 30 Block Setup Menu Information about the heating block is stored on this screen If desired you can change the Block Name by pressing the button labeled A6 and using the keypad that opens Display Setup Menu Calibrate Touch S
19. NYXTECHNIK Amplitronyx 6 Thermal Cycler Operating Manual Cat A62 Amplitronyx 6 Thermal Cycler with 0 2 ml Gradient Block Cat A65 Amplitronyx 6 Thermal Cycler with 0 5 ml Gradient Block Cat A63 Amplitronyx 6 Thermal Cycler with 384 Well Block Cat AGF Amplitronyx 6 Thermal Cycler with Flat Block Rev 011311_1 59 6191 Cornerstone Court E Ste 103 San Diego CA 92121 Phone 858 320 0096 Fax 858 320 0022 www nyxtechnik com Rev 011311_1 59 Page 2 of 30 Contact Information Nyx Technik Inc Global Headquarters 6191 Cornerstone Ct East Suite 103 San Diego CA 92121 Phone 858 320 0096 Fax 858 320 0022 Worldwide Distribution Email customerservice nyxtechnik com to be put in touch with your local dealer Internet URL www nyxtechnik com Email customerservice nyxtechnik com Service Questions No matter where you are in the world our San Diego office is here to help you one on one Regardless of where you purchased your thermal cycler please contact us directly for personal support and quick turnaround time Please review pages 25 27 in this manual for important troubleshooting information In order to provide excellent service it is critical to send all of the following information in your inquiry Serial number of chassis found on the back of the instrument Serial number of thermal block found on the bottom of the block Software version found on the startup screen Protocol
20. ant to alarm If an option button next to a step that is not at the end of a stage is selected the alarm will sound at the end of the stage After pressing the Option button select either On or Off for stage sound Select Store Options to save and return to the main screen where a red oval will appear in the options box to indicate the alarm option has been set To save these settings select Save As to save as a new program or Save to overwrite the existing program Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 16 of 30 Saving a New Program After customizing the template to your protocol save the changes as a new program name After a new program is saved it can be accessed from the Program Menu The Amplitronyx 6 holds 200 programs The number of programs available for storage can be determined by the number of Empty placeholders in the file menu To save a program select Save As in the lower right corner of the Template Editing screen This will take you to the Program Files Menu Select Save As a second time Using the keypad enter the desired name of the program and press Enter Verify the new program exists in the menu and select it to ensure the program has the correct settings Edit a Stored Program Select Edit Saved Program on the Program M
21. creen After selecting Calibrate Touch Screen the screen becomes a solid color and a small circle appears Using the stylus pen carefully press in the middle of the circle Once the input is registered the circle will move to another part of the screen Using the stylus pen carefully press the middle of the second circle When instructed select anywhere on the screen to complete the calibration process Adjust Contrast Use the Up and Down arrows to adjust and select Done Reset Lid Travel If the thermal cycler power is turned off while a program is running instead of being correctly stopped through the Run Options Submenu the heated lid will remain in the down position To retract the heated lid select Reset Lid Travel and wait for the motorized mechanism to engage raise and then stop This option is unavailable if the thermal cycler is running a program Block Menu Information regarding your block name and format is found on this read only screen Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Appendix I Pre programmed Protocol Templates Page 23 of 30 Standard Template Temp Tem z Time Stage Cycle Step C Op
22. decreasing of temperature in a stage For example if you have 4 cycles in a stage with a starting temperature of 55 C and an auto increment set at 0 5 C the temperature of the step after 4 iterations will be 57 C Conversely if the decrement is set at 0 5 C the temperature after 4 iterations will be 53 C Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 15 of 30 To set a temperature increment or decrement select the button in the Options column next to the temperature in the step to which you want to apply the changes From the Temperature Option Menu Select Auto Increment Decrement This will take you to the editing screen If you are unable to select Auto Increment Decrement you may already have a gradient option set for this temperature It is possible only to program either a temperature gradient or an increment decrement Go back to the temperature gradient editing screen and Clear the gradient values to be able to select Auto Increment Decrement Set Ramp Rate Limit For a particular temperature it is possible to slow down the rate at which the machine arrives at the set temperature Once Set Ramp Rate Limit is selected you will see a confirmation of the stage and step you are adjusting The default value is MAX in C second Using the up and down arrows the ramp rate can be reduc
23. dient step represents the width of the gradient as measured along the Y axis Pause Current Program Selecting this option allows you to pause the running program When you are ready to begin the program again enter Resume Program Pausing the program will release the heated lid pressure to allow access to samples and resuming the program will re apply the pressure initially selected in the Program Preferences screen Stop Current Program Selecting this option allows you to stop the running program The fans will continue to operate until the cycler cools down Load Another Program Selecting this option brings up the list of stored programs Using the Up and Down arrows select the program you want to load and press Open The new program name will now be displayed in the status bar at the bottom of the screen View Current Program Settings This option allows a read only view of the currently loaded program its temperature control setting and other parameters If changes are necessary exit the Run Menu and move to the Program Menu Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 21 of 30 Incubate The Amplitronyx 6 allows for quick set up of timed or infinite incubation for protocols such as restriction digests and ligation reactions in either individual or strip tubes The temperature control me
24. e fulfillment of strict protocol guidelines and in the accuracy of end products The temperature control setting is also the only means by which the Amplitronyx 6 knows what kind of vessel tube plate or slide is present and therefore what level of pressure to apply when closing the lid It is critical to set the appropriate temperature control parameter prior to beginning a run Block Control Block Control is the most common and basic temperature control mechanism in which the block itself is the basis of absolute temperature values The thermal cycler begins and ends a stage when the block reaches and maintains the set temperature value for the programmed time Active Tube Control Temp Probe Active Tube Control noted as Temp Probe in the software utilizes a thermistor covered in an epoxy sheath sealed in a thin walled PCR tube A volume of mineral oil equal to that of the intended reaction volume is added by the user to the tube The thermistor probe registers the temperature of the oil and begins ends a stage when that value has reached the set temperature The temperature is tracked continuously and checked against the set temperature This continuous feedback loop facilitates responsive and accurate temperature regulation Active Tube Control is a more accurate means of temperature control than Block Control It adjusts for the temperature offset between the heating block and sample thus creating a representative method
25. e or loss of time or materials incurred through the servicing of this unit by an untrained or unauthorized individual will invalidate the warranty The Amplitronyx unit is protected by two 2 8A 250V fuses and is suitable for operation at both 110V and 220V The Nyx Technik Inc warranty does not cover the replacement of fuses under any circumstance Nyx Technik Inc reserves the right to update Amplitronyx specifications without prior notice in order to implement improvements and provide our customers with superior products Product Returns All returns must be pre authorized by a Nyx Technik Inc representative in San Diego CA USA Once a return has been authorized a RGA Return Goods Authorization number is assigned and must be referenced in all correspondence related to the return No refunds credits or repairs will be issued for products returned without an RGA number Items ordered in error and returned unused in the original packaging with a RGA number are subject to a 20 restocking fee Product Replacement A replacement product will be shipped in the event that an instrument is deemed by Nyx Technik Inc to be an out of box failure In all other circumstances instrumentation will be repaired and returned Please record the following information which will be needed for all service requests Serial Number of Chassis Serial Number of Thermal Block Software Version Date of Purchase PCR Disclaimer The Am
26. ed from the maximum of 3 C second down to 1 C second in 0 1 degree increments Edit Time Using the stylus select the time parameter to edit Time settings are programmed in increments of 1 second as follows MINS SECS 00 00 For example an entry of 1 2 0 is 1 minute 20 seconds HOLD is infinite until user intervention and is useful for hot start applications or 4 C holds after incubations Entering Extended Time per Cycle This feature allows you to extend specific steps within a cycle in increments of seconds This is often recommended for amplification of longer templates Based upon the entered time increment every successive cycle will add the entered value to each enabled step For example a 10 second step with a 5 second increment will add 5 seconds to each step in additive succession If there were 30 cycles in this example the 1 cycle would be 10 seconds the 2 cycle would be 15 seconds the 3 cycle would be 20 seconds etc To enter an extended time increment Select the Option button to the right of the Time in the desired step Use the Up and Down arrow keys to program in seconds the extended time per cycle Select Store Options To save these settings select Save As to save as a new program or Save to overwrite the existing program Program a Stage Alarm To set an alarm to sound at the end of any protocol stage select the Option button to the right of the final time for the stage you w
27. ent decrement editing screen and Clear the values to be able to select Temperature Gradient Select Set next to the text Gradient Start C enter the starting temperature Select Store Temp to save the gradient temperature starting point Select Set next to the text Gradient Range C enter the temperature range 36 C or less Select Store Temp to save gradient range To save the gradient when finished press Store Gradient Bun Program tities Bi Upon successful entry of a gradient a RED OVAL appears in the Options button adjacent to the Temp Shae Gyles Sieh Feria Op tenes Tene Options button and the range will be displayed on the Temp al Ee Ee ee 1 00 A button for that step 1 94 0 0 30 2 30 2 50 70 0 30 In order to save these settings select Save As This will aml 720 0 30 take you to the Program Files Menu If you select Save 1 720 5 00 As you will be prompted to enter a program name and 3 1 the program will automatically be placed into the next za o HOLD z empty slot You can manually place the program where you want on the program list if you select an empty slot Program Pref Add Delete Print Save as first followed by Save As To overwrite an existing User I Standard Editing program select the program from the list and select Save Entering a Temperature Increment Decrement This feature allows for successive increasing or
28. enu and locate the program you wish to edit Select Open to proceed to the Program Editing Screen Edit your program as necessary You may either overwrite the current program with edits or you may save the program under a different name using the Save As button In this way an existing program acts as a pre programmed template for a new program If you wish to overwrite the current program select Save instead of Save As You will be prompted to confirm you want to overwrite the original program Navigating away from the editing screen without saving a new program or writing over an existing program will prompt a warning that your changes will not be applied Select YES to dismiss and not save the current changes This will take you to the Program Menu Select CANCEL to return to the editing screen and save your changes Delete a Stored Program From the Program Menu choose Edit Saved Program Select the program then select Delete You will be prompted to confirm you want to delete the original program Select YES to delete or Cancel to return to the Edit Saved Program screen Program Preferences Submenu From the main editing screen where the program appears select the Program Pref button in the lower left hand corner From the Program Preferences screen you will be able to e Set the appropriate temperature control method e Change the heated lid option if desired e Add text based notes to
29. ins and you can always return by repeatedly selecting the Back Arrow at the top left of the display Program Tab Select this tab to edit or write Run Tab new programs Select this tab to navigate through and ultimately ru programs saved in the units memory Utilities Tab Select this tab to explore the advanced features menu Back Tab Select this tab to go back in order through visited screens until you reach the home screen The back tab is inactive on the home screen Block Tab Select this tab to view information about the block currently installed Status Bar Indicates the program currently loaded in the run queue and the overall status of the instrument Using the Touch Screen The stylus pen is the recommended method for interfacing with the Touch Screen Avoid using objects that can puncture or damage the Touch Screen Every button on the LCD screen is encased in an active box to indicate a successful selection To make a selection use the tip of the stylus to lightly press the button of choice on the screen When a selection has been made successfully the unit will make a beeping sound and the button will appear as though it has been pressed If the touch screen does not respond accurately to your touch calibrate the touch screen under Utilities Menu Advanced Features Display Setup Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYX ECHNI
30. k Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 7 of 30 Cleaning Blocks should be cleaned regularly to ensure proper thermal transfer Cotton swabs a non abrasive cloth or wipe and isopropyl alcohol or ethanol should be used to properly clean the block Always allow the block to cool to below 50 C and disconnect the unit from its power source before attempting to clean the block Touch screens should be cleaned with the same products used to clean computer monitors and wiped dry with a non abrasive cloth or wipe Never use water and do not allow dirt to accumulate around the edges of the screen The touch screen is durable but can be damaged if improperly used and or maintained Never use sharp objects including fingernails to make selections on the touch screen The stylus provided with the Amplitronyx should be used to make any and all selections on the touch screen Damage to the screen resulting from cleaning or operation procedures not listed in this section will be termed misuse and will not be covered by the warranty Working Environment The Amplitronyx Thermal Cycler should be operated in environments with ambient temperatures between 12 C and 32 C with a relative humidity not exceeding 80 The unit should be operated at 115 230V A C 10 and 50 60Hz This unit satisfies the EMC requirements of EN61326 1997
31. ng screen Add Delete a Stage New stages are automatically added directly below the selected stage A selected stage is indicated by a highlight or change in button color To add an additional stage select the stage that is one above your desired insertion point Select Add The added stage will contain the default template values of 30 seconds at 45 C Customize by following the steps above To delete a stage select the stage you want to remove and press Delete You can program a maximum of 10 stages per program Add Delete a Step New steps are automatically added directly below the selected step A selected step is indicated by a highlight or change in button color To add an additional step select the step that is one above your desired insertion point Select Add The added step will contain the default template values of 30 seconds at 45 C Customize by following the steps above To delete a step select the step you want to remove and press Delete You can program a maximum of 10 steps per stage Edit Cycle Number Using the stylus select the cycle paramater to edit Using the keypad enter a number of cycles between 1 and 99 If no number is stored a default of 1 is recorded Select Store Cycles to save and return to the main editing screen or select the Back button to exit the screen and return without editing the cycle number Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 1
32. ngs To save select Save As to save as a new program or Save to overwrite the existing program Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 19 of 30 Run Menu Critical Notes about Temperature Control e Be sure you have selected the appropriate method of temperature control for your consumable plastic tubes or plates See page 9 for more information e If you have selected the Temp Probe temperature control option be sure the temperature probe has the same amount of mineral oil as your reaction size and is securely connected to the block The probe must be placed in the well indicated by the arrow on the block to ensure the probe wiring is not damaged When using the temperature probe it is important to use dome capped tubes instead of flat tubes to ensure an even amount of contact pressure between the heated lid and the sample area Start Current Program The Current Program is the one named in the status bar at ess Run Program Utilities Block the bottom of the touch screen A program listed here is z Running TUBE considered to be Loaded When Start Current ree Program is selected the loaded program begins oo a id SEMPR aa Te immediately and the word Running appears to the right of the program name at the bottom This run status field will
33. now the Amplitronyx 6 10 External Layout 10 Initial Setup 10 Home Screen 11 Using the Touch Screen 11 Entering Data 11 Keyboard 12 Numeric Keypad 12 Plastic Consumables Tubes and Plates 12 Printing Options 12 Program Menu 13 Open a Program Template to Create a New Program 13 Add Delete a Stage 13 Add Delete a Step 13 Edit Cycle Number 13 Edit Temperature 14 Nyx Technik Inc 6191 Cornerstone Court E Ste 103 San Diego CA 92121 NYXTECHNIK Phone 858 320 0096 Fax 858 320 0022 www nyxtechnik com Rev 011311_1 59 Page 4 of 30 Entering a Temperature Gradient 14 Entering a Temperature Increment Decrement 14 Set Ramp Rate Limit 15 Edit Time 15 Entering Extended Time per Cycle 15 Program a Stage Alarm 15 Saving a New Program 16 Edit a Stored Program 16 Delete a Stored Program 16 Program Preferences Submenu 16 Set Appropriate Temperature Control Method 17 Activating Deactivating Heated Lid Operation 18 Add Text Based Notes to your Program 18 Run Menu 19 Start Current Program 19 Run Options Submenu 19 View Current Program Status 19 View Real Time Chart 20 Pause Current Program 20 Stop Current Program 20 Load Another Program 20 View Current Program Settings 20 Incubate 21 Utilities Menu 21 Advanced Features Menu 21 Cycler Setup Menu 21 Power Failure Response 21 Set Adjust Cu
34. plitronyx can be used for a variety of purposes including the Polymerase Chain Reaction PCR PCR is a technology protected by patents held by Hoffman LaRoche Inc and F Hoffman LaRoche Ltd Licenses are available for the use of the procedures outlined in the patents protecting PCR The terms of licensing agreements are dictated by the intended applications of the protected process and vary depending upon the country in which the technology is used Users interested in using the Amplitronyx in PCR related applications are encouraged to contact the PCR Licensing Manager at Hoffman LaRoche Inc Hoffman LaRoche Inc Contact Information United States 510 814 2970 Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 6 of 30 Safety and Operation Information Please read this user manual before attempting to operate or install any component of your Amplitronyx Thermal Cycler If you are unsure how to operate or set up any element of your thermal cycler please contact Nyx Technik or an authorized dealer It is important to observe and follow all safety precautions Any damage or loss resulting from use that does not follow these precautions will not be covered under the 24 month warranty A Voltage A built in voltage sensor allows Amplitronyx to function in various voltage formats anywhere in the world This de
35. program steps are at 25 1 C or greater Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Machine does not get past lid heating mode Rev 011311_1 59 Page 28 of 30 Appendix IV HyperTerminal Diagnostic Procedure In order to properly diagnose any problems with your Amplitronyx Thermal Cycler please follow the instructions below to establish a HyperTerminal connection with the machine to log the necessary data Drivers for Windows 2000 A Go to www nyxtechnik com and download the FTDI USB Driver Installer Windows 2000 B Turn on the thermal cycler After it has booted up and is at the home screen plug a USB cable into the rear port of the machine A cable is not provided but is the same A B type as found ona USB printer C Plug the other end of the USB cable into your computer which should prompt you to install the downloaded driver Direct Windows to the file you downloaded to install Drivers for Windows XP A Go to www nyxtechnik com and download the FTDI USB Driver Installer Windows XP B Open and run the downloaded driver file to install it C Turn on the thermal cycler After it has booted up and is at the home screen plug a USB cable into the rear port of the machine A cable is not provided but is the same A B type as found on USB printers etc Plug the other end of the USB cable
36. range available Easy to use programming is facilitated via the large color Liquid Crystal Display LCD touch screen and program progress can be checked at a glance with the large on screen timer The auto pressure heated lid allows superior sealing of tubes and multi well plates ensuring negligible sample evaporation Multiple program options and reaction formats provide exceptional flexibility and the low price and wide range of features provide superior value for any laboratory Amplification reactions take place under tightly regulated thermal conditions where samples are guaranteed to stay at the programmed temperature for the entire length of the step The heated lid minimizes condensation within the sample tube and the thermal block interior is protected from condensation by unique double seal construction Amplitronyx 6 Specifications Sample Blocks Capacity 0 2 ml Gradient Block 96x 0 2ml tubes or 1x 96 well plate 0 5 ml Gradient Block 54x 0 5ml tubes Programming 384 Well Block 1x 384 well plate Flat Block 4 slides Temperature 4 C 99 C Heating rate Up to 3 C sec Cooling rate Up to 2 C sec Uniformity 0 4 C within 15 sec Material Nickel plated aluminum Heated Lid Temperature Modes Auto Off and User Adjustable Pressure Electromechanical adjustment Display Input 5 7 diag touchscreen color Number of programs 200 Maximum program stages 1
37. rrent Time 21 Set Adjust Current Date 21 Reset Memory Option 21 Block Setup Menu 22 Display Setup Menu 22 Calibrate Touch Screen 22 Adjust Contrast 22 Reset Lid Travel 22 Block Menu 22 Appendix I Pre programmed Protocol Templates 23 Appendix II Front End Software Upgrade Procedure 25 Appendix III Troubleshooting 26 Appendix IV HyperTerminal Diagnostic Procedure 28 Appendix V Related Products 29 Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 www nyxtechnik com NYXTECHNIK Rev 011311_1 59 Page 5 of 30 End User Warranty The Amplitronyx Thermal Cycler is for research use only Nyx Technik Inc guarantees the Amplitronyx thermal cycler has been thoroughly tested and meets all specifications published by Nyx Technik The Amplitronyx warranty covers defects in materials and workmanship as well as return shipping The warranty for the thermal block is one year from the date of delivery The warranty for the thermal cycler chassis is three years from the date of delivery The warranty is only valid if the unit and included accessories are used and maintained according to the instructions outlined in this manual Nyx Technik Inc will not accept liability for loss or damage if the unit is not operated according to the instructions published in this manual Only personnel trained by Nyx Technik Inc should attempt to service the Amplitronyx Any damag
38. ssure between the heated lid and the sample area Reaction Temperature Vessel Control Option 96 well Plate Simulated Plate Control 384 well Plate Simulated Plate Control 0 2 ml Tubes Simulated Tube Control Temp Probe Active Tube Control or Block Control 0 5 ml Tubes Simulated Tube Control Temp Probe Active Tube Control or Block Control Slides Simulated Slide Control From the main editing screen where the program appears select the Program Pref button in the lower left hand corner 4o o Rmo Program Oiane Bock Toward the top of the Program Preferences screen you will see buttons marked Block Temp Probe Sim iii aii Tube and Sim Plate Select the method appropriate to your plastic reaction vessel If Sim Tube or Sim Plate are selected use Up and Down arrows to enter reaction Block Temp Probe Sim Tube Sim Plate Heated Lid Operation volume in microliters If Temp Probe is selected 00 A v Of Auto Adi ensure the temperature probe is connected to the block Choose Store Settings To save these settings select 3 AW Save As to save as a new program or Save to Son Opora pen overwrite the existing program 4 Jeet tEh lkaarg Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 www nyxtechnik com NYXTECHNIK Rev 011311_1 59 Page 18 of 30 Activating Deactiva
39. tation System with 12126B P8F ID2126AB Photonyx Gel Documentation System with ID2126AB P16FU2020 Photonyx Ultra System with 20cm x 20cm transilluminator P16FU2030 Photonyx Ultra System with 20cm x 30cm transilluminator P16FU2530 Photonyx Ultra System with 25cm x 30cm transilluminator P16C2020 Photonyx Chemi System with 20cm x 20cm transilluminator P16C2030 Photonyx Chemi System with 20cm x 30cm transilluminator P16C2530 Photonyx Chemi System with 25cm x 30cm transilluminator P16CS2020 Photonyx Chemi Super 16 System with 20cm x 20cm transilluminator P16CS2030 Photonyx Chemi Super 16 System with 20cm x 30cm transilluminator P16CS2530 Photonyx Chemi Super 16 System with 25cm x 30cm transilluminator Accessories P8F P Photonyx Thermal Printer for P8F systems P16 P Photonyx Digital Thermal Printer for P16 systems P16 3FS 3 Position filter slide P16 7FW 7 Position filter wheel P SYBRG58F SYBR Green 58mm Filter for slide P16 SYBRG72F SYBR Green 72mm Filter for wheel Nyx Technik Inc 6191 Cornerstone Court E Ste 103 San Diego CA 92121 Phone 858 320 0096 Fax 858 320 0022 www nyxtechnik com OX NYXTECHNIK
40. thod is automatically set to Block when using this shortcut Because the temperature control method and therefore the heated lid pressure is not adjustable by the user this quick program method is not recommended for use with multi well plates To incubate in plates create a formal program and be sure to select Sim Plate as your temperature control method Select Incubate from the Run Menu and then set the incubation temperature using the numerical keypad Select Store Temp to save and return to the setup screen Select Set Incubation Time and use the keypad to enter HR MN 00 00 For example an entry of 1 2 0 is 1 hour and 20 minutes Select Store Time to return to the setup screen If you want the Amplitronyx 6 to make an audible sound when the incubation is complete turn the End Signal On Otherwise turn it Off Select Start Incubation when ready Once Start Incubation is selected the current temperature reaches set point The Clock Display will initially display Incubating while the unit reaches the set temperature and will then change to a representative clock face indicating time remaining When incubation is set to HOLD instead of for a specified time the Clock Display reads Incubation Hold throughout the incubation As long as the incubation temperature is 25 1 C or greater the heated lid will remain on Utilities Menu Advanced Features Menu Cycler Setup
41. ting Heated Lid Operation When set to Auto the heated lid will be automatically set to the ideal temperature based on the cycling temperatures in the program Use of the Auto setting is the best way to ensure that condensation does not occur in the reaction tubes If required by your specific protocol the heated lid can be either adjusted or turned off From the main editing screen where the program appears select the Program Pref button in the lower left hand corner To turn off the heated lid select the Off button under the title Heated Lid Operation To adjust the heated lid between 99 C 110 C select the Adj button and enter the desired value using the arrows Be aware that if you set the lid temperature too low condensation may occur in your reaction tubes Once selection is complete choose Store Options To save these settings select Save As to save as a new program or Save to overwrite the existing program Add Text Based Notes to your Program From the main editing screen where the program appears select the Program Pref button in the lower left hand corner Select the Notes button in the lower right corner then select Accept to keep the existing text or choose Edit Add to change or add text using the keyboard Select Enter on the keypad screen when you are finished adding notes Select Accept to return to the Program Preferences screen and Store Setti
42. tions Time Options 1 1 1 94 1 min 1 94 30 sec 2 30 2 55 30 sec 3 72 30 sec 3 P 1 72 5 min 2 4 Hold Gradient Template Tem Tem Time Stage Cycle Step coy Options Time Options 1 1 1 94 1 min 1 94 1 min 2 30 2 50 60 10 C gradient 30 sec 3 72 30 sec 3 1 72 5 min 2 4 Hold Hot Start Template Tem Tem F Time Stage Cycle Step coy orice Time Options 1 1 1 94 1 min 2 95 Hold 1 94 30 sec 2 30 2 50 60 10 C gradient 30 sec 3 72 30 sec 3 1 72 5 min 2 4 Hold Touchdown Template Tem Tem z Time Stage Cycle Step coy Opti ee Time Options 1 1 1 94 1 min 1 94 30 sec 2 20 2 65 Increase 0 5 C each cycle 30 sec 3 72 30 sec 1 94 5 min 3 10 2 55 30 sec 3 72 30 sec 1 72 5 min 4 1 2 4 Hold Nyx Technik Inc 6191 Cornerstone Court E Ste 103 San Diego CA 92121 OX NYXTECHNIK Phone 858 320 0096 Fax 858 320 0022 www nyxtechnik com Rev 011311_1 59 Page 24 of 30 Long Template Temp Temp Time Stage Cycle Step C Options Time Options 1 1 1 94 2 min 1 94 10 sec 2 10 2 65 30 sec 3 68 10 min 1 94 10 sec 3 20 2 65 30 sec 3 68 10 min Extend 20 sec each cycle 4 P 1 68 7 min 2 4 Hold Rapid Cycle Template Temp Temp Time Stage Cycle Step C Options Time Options 1 1 1 94 2 min 1 9
43. vice must be plugged into a grounded socket with the provided power cord A Explosive Materials Amplitronyx should not be exposed to explosive or highly reactive substances or used in an explosive or highly reactive environment A Liquids amp Condensation Liquids of any kind should never enter the inside chassis of the unit Exposure of the internal workings of this machine to any liquid may cause electrical damage failure or loss AN Heat The Amplitronyx sample block can reach a temperature of 99 C The heated lid operates at temperatures exceeding 100 C Care must be taken when handling this unit and its accessories to prevent accidental burns Do not place flammable materials near the block or heated lid while the unit is running Allow the unit to cool prior to removing replacing or adding sample tubes to and from the block Ensure all plastics and other substances placed in the block of this unit are stable at temperatures up to and possibly exceeding 120 C Ventilation Ensure adequate ventilation around the thermal cycler This unit requires a minimum of 1 foot between the rear of the instrument and any walls or partitions User Maintenance Only personnel trained by Nyx Technik Inc should attempt to service Amplitronyx Thermal cyclers Any damage or loss of time or materials incurred through the servicing of this unit by an untrained or unauthorized individual will invalidate the warranty Nyx Techni
44. you are trying to run all times and temperatures Complete detailed description of all problems symptoms and concerns e Finally if you are able to perform and send a HyperTerminal Trace page 27 and to note the status of the diagnostic LED lights page 25 your problem can be addressed more quickly How to get help Click the Thermal Cycler Service Request link on the Support page at www nyxtechnik com 2008 2010 Nyx Technik Inc All rights reserved No part of this user guide may be reproduced or transmitted in any form or by any means electronic or mechanical for any purpose without prior written permission of Nyx Technik Inc Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 3 of 30 Contents End User Warranty 5 Product Returns and Replacements 5 PCR Disclaimer 5 Safety and Operation Information 6 Voltage 6 Explosive Materials 6 Liquids amp Condensation 6 Heat 6 Ventilation 6 User Maintenance 6 Cleaning 7 Working Environment 7 Unpacking and Inspection of the Amplitronyx 6 7 Introduction 8 Amplitronyx 6 Specifications 8 Temperature Control 9 Block Control 9 Active Tube Control Temp Probe 9 Simulated Tube Control 9 Simulated Plate Control 9 Simulated Slide Control 9 Getting to K
45. your program Nyx Technik Inc Phone 858 320 0096 6191 Cornerstone Court E Ste 103 Fax 858 320 0022 San Diego CA 92121 NYXTECHNIK www nyxtechnik com Rev 011311_1 59 Page 17 of 30 Set Appropriate Temperature Control Method You must select a temperature control method see page 9 in accordance with the consumable plastic used for each experiment The pressure applied by the heated lid is determined by what kind of consumable you have told the Amplitronyx 6 is present using the Temperature Control selection For example in Sim Plate mode more lid pressure is applied to provide an adequate seal e Block Control although always available as a reference point for comparing protocols between cyclers is not always the most accurate temperature control method and will not allow the heated lid to apply the pressure needed to adequately seal plates e Using the incorrect Temperature Control method for tubes or plates can result in malfunctions such as melted or deformed plastic or incomplete sealing e f you select the Temp Probe temperature control option be sure the temperature probe has the same amount of mineral oil as your reaction size and is securely connected to the block The probe must be placed in the well indicated by the arrow on the block to ensure the probe wiring is not damaged When using the temperature probe it is important to use dome capped tubes instead of flat tubes to ensure an even amount of contact pre
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