User Manual
Contents
1. The Temperature screen displays the measured temperatures of the blocks and the heated lids plotted against time a C Users OptiSense SL Desktop Duncan Gen files Tismo OptiGene Enzymes_RTLAMP_001 gen Profile Temperature Amplification Amplification Rate Anneal Anneal Derivative Result rz Amplification T T T T T T 00 05 00 00 10 00 00 15 00 00 20 00 00 25 00 00 30 00 00 35 00 00 40 00 00 45 00 00 50 00 00 55 00 01 00 00 Time The Amplification screen displays the fluorescence measurements for each well made during the Amplification phase plotted against time AMPLIFICATION RATE a C Users OptiSense SL Desktop Duncan Gen files Tismo OptiGene Enzymes_RTLAMP_001 gen Profile Temperature Amplification Amplification Rate Anneal Anneal Derivative Result Amplification Rate Ses D e a Coor Le Lre V 1 g testtt E wW j2 well2 v 3 well3 m l4 well4 a 5 well5 wm le well ap well7 7 la well Select 7 Weler Wel Name cal e e JS S 88 OO a el wlnio Time T T T T T T T ji ii T T 00 05 00 00 10 00 00 15 00 00 20 00 00 25 00 00 30 00 00 35 00 00 40 00 00 45 00 00 50 00 00 55 02. OO ON Oo Oo Sho oe 31 Mar 2014 12 29 549 C VIEW To view previous runs press the folder icon on the status bar 31 Mar 2014 08 41 20 C Open file _ This will display a file browser window T All Genie IIl runs are saved in the LOG folder To open click on LOG and then tick icon or double press on the folder name Version 1 05 23 Each run is stored in a folder by date order Year Month Day Each run is stored in a folder by date order Year Month Day Each run is stored in a folder by date order Year Month Day The default filename for the each run GEN3 1035_0021 gen is the instrument serial number GEN3 1035_0020 gen followed by a sequential number Touch on a file then tick icon to load a file To delete a file touch the trash can icon When the file has opened Genie III will display the profile that was run the temperature log amplification data anneal data and the results table Version 1 05 24 ZOOMING FUNCTION Zooming is available on temperature fluorescence and anneal graphs LOG GEN3 1019_0055 gen To zoom in on the area of interest touch the plot area and drag to the m WI Li UL oO pe D fa T o right and or down LOG GEN3 1019_0055 gen To zoom out touch on the plot area and drag to the left and or up Derivative FC A double press on the screen will zoom out to the full extent of the graph
3. Profile Active File Service and Options No Instruments connected OptiGene Version 1 05 31 GENIE EXPLORER DISCOVERY PANEL EA Genie Explorer opticene i 1 connected Any Genie instruments that are connected to the computer will be shown GEN3 1035 in the panel on the left side of the screen Multiple Genie instruments can be connected at the same time If any instrument is connected and not displayed click the button in the bottom left corner and the program will attempt to connect to them NEW Clicking the New button will display the following window which will allow a new experiment to be set up and run on an instrument Multiple profiles can be set up at the same time and selected via the taskbar at the bottom of the window DTEC 1 connected a Profile a hermal l ae Experiment Name Profile Name ca Run Profile GEN3 1035 Temperature C 00 15 00 00 20 00 Time hh mm ss Preheat Activation Isothermal Temperature 4500 lt Temperature 65 00 c Minutes Duration 30 Minutes ZZL Version 1 05 32 THERMAL PROFILE The Thermal Profile tab allows setting of the thermal profile that is to be used and calculates an estimated run time for the desired profile Preheat Activation If activation is required for the enzyme then 1 tick the Preheat Activa
4. button on a graph and Genie Explorer will display the graph options for that graph From this window several aspects of the graphical information can be modified SMOOTHING 3 NORMALISATION _ Normalisation From 60 sec To 190 sec Fluorescence Fluorescence 20 000 00 Z Smoothing Amplification T T T T T T T T T T 1 00 05 00 00 15 00 00 25 00 00 35 00 00 45 00 00 55 00 00 10 00 00 20 00 00 30 00 00 40 00 00 50 00 01 00 00 Time Amplification 80 000 00 s wel 00 05 00 00 15 00 00 25 00 00 35 00 00 45 00 00 55 00 00 10 00 00 20 00 00 30 00 00 40 00 00 50 00 01 00 00 Time Smoothing can be applied to all of the graphs Drag the slider or change the Points value to set the number of readings that are averaged to create a data point on the graph Normalisation allows all the fluorescent signals to have their background level removed calculated over a specified period of time Select by ticking the Normalisation checkbox and setting the start and end times for calculating the background level e g 60 seconds to 180 seconds This screenshot shows data that has not been normalised the initial signal levels are different for each well With normalisation the levels come together and allow for easier analysis Version 1 05 PEAK DETECTION Simple The software looks at the plot and assigns the peak to the highest plotted point that is above t
5. enie Ill User Manual Instrument Software Version v3 11 OpotiGene Unit 5 Blatchford Road Horsham West Sussex RH13 5QR United Kingdom Tel 44 0 1403 274980 Fax 44 0 1403 271017 www optigene co uk info optigene co uk If you have any feedback or comments about the instrument please email feedback optigene co uk Information in this document is subject to change without notice OptiGene Ltd assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication In no event shall OptiGene Ltd be liable for incidental multiple or consequential damages in connection with or arising from use of this document Genie IIl and its design is a registered trademark of OptiGene Ltd or its subsidiaries in the UK and other countries Table of Contents ACTIVE corcra ONES 21 SAFETY NOTICES cccccccccccccccceceeec 3 PE OU e 21 TEMPerature ccecescesceseeseenees 21 SUPPORT cecccccseccsseccssesessessssesesseessseesee 5 Amplification 1 sess eeeeeseees 22 7a ots eee ene nee ee eee 22 How to obtain support 5 PO SUNS raa 23 Supported consumables cccceecce 5 NW EEEE E EEEE EEE 23 BOX CONTENTSG cccceeeeececceeeeeeeeees 6 CONNECTING TO A COMPUTER 26 Genie IIl Software updates 29 SITE PREPARATION sceececeeceeee 7 How to set up Genie II cccee 7
6. Please read the following notices carefully before using Genie Ill The equipment supplied has been designed to be completely safe to use However to avoid any risk to the safety of the equipment operator or anybody in the vicinity of the equipment please read this chapter before unpacking and using the instrument If there is any doubt as to the correct use of the equipment contact the vendor Notices Using the instrument in a manner not specified by OptiGene may result in personal injury or damage to the instrument Always ensure that the surface on which the instrument is placed is level and stable and will not cause the instrument to topple over Ensure that the surface is suitable for the weight and size of the instrument If the instrument is dropped it may be damaged The instrument should never be lifted by its covers Always ensure that the base or sides are used as the lifting point The instrument is electrically powered Please ensure that the correct voltage settings have been applied before applying power to the instrument If in doubt consult a qualified electrician The instrument has a rating label affixed to the rear Please consult this if needed Version 1 05 Always disconnect the equipment before moving or removing any guards or covers Switch off at the mains remove the mains plug from the wall socket and remove the cable from the inlet socket on the rear The instrument carries an IP62 rating
7. 2014 15 31 s ponerse DOE UEP be displayed in the same way as E GEN2 1225 19 06 2014 15 28 32 gen 19 06 2014 15 29 19 06 2014 15 28 LogView Feb Duncan Gen E GEN2 1225 19 06 2014 15 28 51 gen 19 06 2014 15 29 19 06 2014 15 29 e Bi GEN2 1225 19 06 2014 15 14 10 gen 19 06 201415 15 19 06 2014 15 14 e ana ct ive run i GEN3 1035_19 06 2014 15 07 09 gen 19 06 201415 08 19 06 2014 15 07 e B GEN3 1035 19 06 2014 14 53 43 gen 19 06 2014 15 07 19 06 2014 14 53 a GEN3 1035_19 06 2014_15 02 58 gen 19 06 201415 06 19 06 2014 15 03 m GEN3 1035_19 06 2014_14 53 43 Copy gen 19 06 2014 15 01 19 06 2014 15 01 ex GEN3 1035 Eg gE Computer amp Local Disk C Version 1 05 44 SERVICE Clicking the Service button on the main menu will produce the following screen a r Set Date 29 09 2012 B From here it is possible to change Lal the date and time of the instrument s clock and update firmware or FPGA code on the instrument instead of using the drag amp drop method described in the instrument user manual OPTIONS The Options button allows the default locations of files to be set Profile Default location for saving profiles Data Default location for saving run files Default Profile File Sets a default profile to be used when a new run is started To reset back to the program defaults click Reset Default Profile Click Save
8. TOOLBOX Pressing the spanner icon in the taskbar will load the toolbox 31 Mar 2014 08 41 20 C BUTTONS Set up the quick start buttons on the main screen Buttons Ad Touching will allow the user to LAMP amp Anneal A browse the saved profiles on the instrument in the ASSAYS directory and assign that profile to the corresponding quick start button on the main screen To remove the buttons untick the box next to the profile name Version 1 05 13 These settings only apply when battery powered Display dim time how long the instrument waits without input before dimming the display Power Y copus Y vrees Y cars Wag Display dim level the brightness level the instrument will use after the Peper A nN POMS Bnek specified idle time Display dim level Yo Autocool Enable Standby time how long the instrument Standby time ma waits before turning off the display These settings only apply when battery powered Peltier Enable Enable active cooling of the block during a run Turning this off will save power when running on battery Autocool Enable Enable active cooling of the block after a run has finished Turning this off will save power when running on battery COLOURS The background colour and the default colours of the lines on graphs can be Colours Y Wreess Y vanes W changed here Background pR B B Click the background button or a graph number and then
9. To install in this folder click Next To install to a different folder enter it below or click Browse eae Choose a location for the installed program Install Genie Explorer for yourself or for anyone who uses this computer Everyone Just me Confirm Installation The installer is ready to install Genie Explorer on your computer Click Next to start the installation Confirm to start the installation Pr Genie Explorer Genie Explorer is being installed Please wait The installer will copy all necessary files to the computer Cae Co Version 1 05 27 m je Genie Explorer Installation Complete Genie Explorer has been successfully installed Click Close to exit Once the installation is complete exit by clicking Close Please use Windows Update to check for any critical updates to the NET Framework Close A Genie instrument can now be connected to the computer When connected via USB and switched on the Genie instrument will appear as a USB drive and will be accessible from Genie Explorer Version 1 05 28 GENIE III SOFTWARE UPDATES It is recommended to keep the software on Genie IIl up to date Upgrading may improve performance and add new features to Genie III There are two types of software on Genie Ill the firmware and the FPGA software The current versions of firmware and FPGA software that are installed on Geni
10. be switched off using the switch on the rear Genie l Opticene Power off Yes Mo WALII aan USB serial Version 3 06 re 2 FPo4 406 SIN GENS 1029 Note If this button is pressed during a run Genie III will not enter standby When in standby normal operation can be resumed by pressing anywhere on the screen Version 1 05 BATTERY MONITOR LAMP amp Anneal Anneal oe The battery status can be seen but ares there is no pop up 31 Mar 2014 08 52 209 LAMP amp Anneal Anneal Here the pop up shows that the BE Battery Status battery is currently charging Charging 2841 mah 16 0 2 5A ih 48min active time 21 Mar 2014 08 53 210C LAMP amp Anneal Anneal Here the pop up shows that the BE Battery Status battery is fully charged Battery Full 3633 mAn 16 7 0 04 2h 19min active time 31 Mar 2014 10 11 349 C LAMP amp Anneal Anneal Here the pop up shows that the Battery Status instrument is discharging Discharging 2845 mAh 15 6 2 54 ih 48min active time 21 Mar 2014 08 53 210C Version 1 05 10 SCREEN BRIGHTNESS CONTROL Next to the battery icon is the brightness control 31 Mar 2014 08 41 20 C Touch the icon and a slider will appear on the right hand side of the screen Move the slider to the desired position Press the icon again to remove the slider Gene l opis LAMP amp Anneal It is not recommended to set the br
11. firmware or FPGA software files onto the Genie III drive Now on Genie III select the Toolbox touch the Utilities tab and press Update Genie III will prompt for a file to use for the update Touch on the file and touch Open Genie III will then install the updated software Please wait for it to finish before trying to do anything else If the update was a firmware update Genie III will restart when completed If an FPGA software update was performed Genie III will require a manual restart by turning the instrument off and on from the switch on the rear of the unit Genie III will automatically delete the files when the update has completed 30 Version 1 05 GENIE EXPLORER In addition to standalone operation Genie instruments can be run and completely controlled by a computer and the results data then stored and analysed The software that supports remote operation is called Genie Explorer and is included on the OptiGene USB memory stick that is included with the Genie instrument installation instruments are in chapter 6 Disclaimer Genie Explorer is an additional tool and should not be used for patient care or clinical analysis To run Genie Explorer double click on the icon on the desktop or run from the Start Menu MAIN MENU When the program has loaded the first screen that will be displayed is the main menu where there are several options New
12. pop up box will prompt Yes Temperature C z5 a0 35 20 Time mins GEN3 1013_0005 gen x ee AMPLIFICATION This shows the fluorescence data that is being acquired during the amplification phase of the experiment welll well2 wells well4 wellS Fluorescence tF well well Se a a S well ANNEAL well This shows the fluorescence derivative data E that is being acquired during the anneal phase of the experiment ie co an well4 am wellS Derivative Fle an well 30 gz well 56 tata Temperature 72 MULTIPLE CHANNEL OPTIONS Genie IIl uses two different channels depending on the profile being run These buttons allow either the first or second channel to be selected The graphs will update by pressing the relevant button on the Amplification and Anneal pages Version 1 05 22 GEN3 1013_0005 gen Anneal Y Resuts Wag SELECTION OF GRAPHS welll Pressing the well name on either the Amplification or the Anneal page cycles well4 ie co on o the state if the related curve on the graph well between normal highlighted and off well I well well Derivative FEC an 31 Mar 2014 09 33 63 C GEN3 1013_0005 gen RESULTS This shows the results of the experiment Each sample name is shown along with amplification time and anneal temperature
13. to save changes to the default locations Version 1 05 45 GENIE III TECHNICAL SPECIFICATION Operational Block with 4 zone independent digital PID and heated Temperature control method lid Sample number Single strip of 8 tubes Samplevoiume aso Physical Sze BRULEE NRE HY MUTT XGS x35 Weight 1 75 kg 4 Ib Operating temperature OCC Storage temperature 20 C 7F0 C Environmental protein PER Interfaces Positioning GPS Wireless data 1 etooth2 0 Wireless data 2 Wi Fi Wiredasta 8820 Electrical Bateyype LiiumPoymer Battery capacity 40 Wh External supply 19 VDC 46 OptiGene Unit 5 Blatchford Road Horsham West Sussex RH13 5QR United Kingdom Tel 44 0 1403 274980 Fax 44 0 1403 271017 www optigene co uk info optigene co uk If you have any feedback or comments about the instrument please email feedback optigene co uk Information in this document is subject to change without notice OptiGene Ltd assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication In no event shall OptiGene Ltd be liable for incidental multiple or consequential damages in connection with or arising from use of this document Genie IIl and its design is a registered trademark of OptiGene Ltd or its subsidiaries in the UK and other countries V1 03 10 11 14 Addition
14. 0 Isothermal Ratio shows the amplification take off time during the Amplification phase Isothermal Ratio peak time is similar to the C or C values in QPCR assays Genie Explorer can detect the trace peaks and report them automatically To access the graph options click Settings on the graph and a side panel will appear 39 Version 1 05 LF IIE ES Select the Peak detection option None Simple or Full and check the default peak criteria The peak threshold minimum value of peak can be adjusted to ensure that all valid peaks are identified while others are not The Anneal tab shows the plot of the fluorescence measurements for each well made during the Anneal phase plotted against temperature Version 1 05 ANNEAL DERIVATIVE SL Desktop Duncan Gen files Tismo OptiGene Enzymes_RTLAMP_001 gen The Anneal Derivative tab shows the plot of the derivative of fluorescence for each well made during the Anneal phase plotted against temperature Select the Peak detection option None Simple or Full and check the default peak criteria The peak threshold minimum value of peak can be adjusted to ensure that all valid peaks are identified while others are not This pag
15. EPARATION HOW TO SET UP GENIE III Genie Ill has been designed to be used at point of care and so not necessarily in a laboratory When it is being used the instrument should be placed on a level and stable surface and the surfaces surrounding the instrument must be clear of obstructions at all times Care must be taken not to unduly restrict the air at the outlet vents at the rear Restricting airflow may impede operation and could affect performance Electrical points should be close to the instrument to avoid injury from trailing wires Genie III is rated to IP62 which means that it is splash proof but only when the lid on top and the lip on the back are closed It is recommended that the instrument is kept away from sinks and other wet areas when running Version 1 05 CONNECTIONS Genie Ill is ready to use straight out of the box without any external connections It can be operated standalone taking power from its internal battery In order to charge the battery or to use Genie IIl with a computer some connections must be made Connect the power supply plug into the back of the instrument and then attach the power cable to the supply Located at the rear of the instrument is an on off power switch When in the on position Genie III will power up and progress through its checks USB TO PC POWER INLET POWER SWITCH OPENING amp CLOSING THE LID Press the button on the front of the unit and the lid should ope
16. GENIE EXPLORER c cceceeeeeees 31 CONNECTIONS eccerre 8 Main MenU sseeesssesssssrrrrrrrrrrrrrrreeeees 31 Opening amp Closing the Lid 00 8 Genie Explorer Discovery Panel 32 Inserting TUDES ccccccccccccccccccceccccecccce 8 NEN a 32 Thermal Profile aaneen 33 BaO y sesen 9 Graph Options sssessseeeeeeeseenesne 36 Channels sence scvessccesceescsatecczenseecaces 37 Battery MOMItOL sesssessesseessesseesseen 10 NOLE a tt riconc eivnia sean oectene 37 Screen Brightness Control 11 ACUVE corratier 38 Profile senseca 38 USER INTERFACE se Bel Weide coskoro rinos 12 Temperature ee nT eet ee 39 Amplification cecce 39 Main MenU cccccccceccececescecceaeecs 13 Amplification Rate csccesc cssscssesesss 39 TOGIDOX sensin 13 Anneal eee 40 BUON eee beaseietenatcsceaemtensennss 13 Anneal Derivative eee 41 A 14 RESUIC savecsoudesosiviesvessevdebseavcsnenaensses 41 Ge 910 gcse ene nen eee ae 14 Analysis amp Graph Options 43 Wireless cccsccccsceecsceccescecscoeces 15 Utilities sssrin 15 l EE EE 44 Touchscreen calibration 15 Date and Time ccecceceececeeeees 16 BO CC a 45 ESE E E E A ene 17 ODEON er 45 Quick Start cece ceceeceececeeceees 17 Profile Screen 17 GENIE IIl TECHNICAL SPECIFICATION To create a new profile NG E E E EE E 46 To load a saved profile 19 SAFETY NOTICES
17. This means it is protected from total dust ingress and protected from water spray less than 15 degrees from vertical This only applies when the lid on the top and the lip on the back are closed If fluids are spilt on the instrument when the lid is open they may cause damage and cause an electrical hazard If a spill occurs remove power from the instrument Do not touch the instrument or any fluid flowing from it while it is connected to the mains supply Always follow local health and safety guidelines Normal safe local operating standards should be applied at all times The warnings above are for guidance only Please consult the instrument supplier if there is any doubt Disconnection Method Genie Ill is disconnected by removal of incoming mains power source to the unit Following disconnection the unit should be left for a period of at least 5 minutes before any internal assemblies are removed or examined When in use the heating block and heated lid are hot so allow to cool before touching the surfaces Safe removal of fluids from Genie III will depend on the chemistry used This will also require knowledge of the fluids used in the system to adhere with local health and safety and COSHH regulations If in doubt consult the person responsible for the equipment in the laboratory Cleaning Method The Genie II can be disinfected using the following procedure which can be used as a safety measure if this equipm
18. a will bring up this window allowing selection of the channels to be used Version 1 05 20 ACTIVE Once a run is started the software will go to the screens can be accessed using the tabs Lowa 2014 04122 GEN3 1035_0019 gen x Amplification Temperature 2 20 Time mins Li 2014 03 31 GENS 1029_0005 gen x 65 0 C Temperature tT 20 Time mins z5 a0 35 Li 2014 03 31 GENS 1029_0005 gen f amo Y area Y resus Wig Amp 65 0 C Advance Temperature tC Stop 20 25 Time mins Lie 2014 03 31 GENS 1029_0005 gen f amo Y anea Y resus Ve Amp 65 0 C Temperature C 20 Time mins z5 a0 35 21 Mar 2014 09 21 21 Temperature screen initially The other PROFILE This shows the temperature profile that is running At the top of this screen there is a text box to edit the run description a button to add notes about the run and a button to save the profile TEMPERATURE This shows the current temperature of the block as the experiment is progressing EXTEND This adds 10 minutes to the current phase of the run ADVANCE Advances to the next phase of the run Preheat to Amplification or Amplification to SH neal Version 1 05 Ls 2014 03 31 GENS 1029_0005 gen ee STOP 65 0 C The Stop button will abort a run in progress Exten A confirmation
19. al features added to main SUL software V1 04 01 04 15 Added disclaimer about Genie Explorer V1 05 17 09 15 Added instrument cleaning guidelines SUL and feedback email address Version 1 05 47
20. ate a new profile If there are many profiles scroll down by dragging on the window Version 1 05 TO CREATE A NEW PROFILE Channels Amplification 25 20 Time mins LAMP amp Anneal prot 1h LAMP amp Anneal prof OF fo4 e014 11 47 Anneal prot O7 fo4 2014 11 47 18 x v Press the New button on the profile screen Click the graph to adjust the profile by touching the appropriate temperature or time box Once the required changes have been made pressing the tick button will accept the changes Clicking the cross in the top corner will cancel any changes Pressing the play icon will accept the changes and prompt the user to start the run To set a thermal gradient across a block enter a range of temperatures in the Amplification temperature box The range of temperatures should be entered separated by a hyphen as shown below Pressing the save icon will save the profile Name the profile press the tick button and it will be saved within the PROFILE directory in the on board memory allowing it to be loaded for future runs Saving into the ASSAYS directory will allow the profile to be set up as a quick start button on the main menu Version 1 05 TO LOAD A SAVED PROFILE Temperature C Amplification Cancel 7 Apr 2014 11 48 36 C Anneal prof OF f04f2014 11 47 LAMP amp Anneal prot OF 04 2014 11 47 Amplification 20 Time mins Amplificat
21. drag the cursor on the E i as colour chart to select a colour VA The two small coloured boxes on the right show the colour that is currently Green 77 Blue 93 set Cur and the default Def colour Pressing on either will set the colour Version 1 05 14 WIRELESS Buttons Power Colours Wirel arm X 14 Apr 2014 12 03 26 C 4 GPS WiFi amp Bluetooth Ticking the corresponding box will turn this feature on Click the View button next to GPS and the status will be shown giving universal identities of time latitude longitude and the current satellites being used WiFi and Bluetooth features are currently in development UTILITIES Buttons Power Colours Wireless F Utilities x Touchscreen Date amp Time Touchscreen This will start the touchscreen calibration see below Date amp Time Set the time and date within the instrument Update Allows updating of the instrument software See Chapter 6 TOUCHSCREEN CALIBRATION Touching anywhere on the screen with Touchscreen calibration Touch screen to start 15 the exception of Test or Skip will invoke the touchscreen calibration To check the sensitivity of the screen press Test Any point pressed on the screen will then be marked Version 1 05 Touchscreen calibration Touch the target points Calibrate the touchscreen by touching the target points shown on the screen the stylus shou
22. e III are displayed in the bottom left hand corner of the main menu screen LAMP amp Anneal Anneal Other 21 Mar 2014 08 52 200C e To download the latest firmware visit the OptiGene website http www optigene co uk Click on Support and click on the appropriate link on the right hand side of the page and download the zip file e Open the zip file and extract the contents to a new folder The contents of the folder will include the latest firmware FPGA software and this manual e fGenie III already has the latest FPGA software only the firmware will need to be updated e f both firmware and FPGA software updates are required update the FPGA software first followed by the firmware e If it is a firmware update the file will be a mot file whereas if it is an FPGA software update it will be a rbf file Version 1 05 29 ele aaa KJ eles gt Computer GENN 001 E gt Search GENN 001 E 2i I Organize v Share with v Burn New folder LOG PROFILE Genie N_N_01_r c3_23Jull3 mot Buttons Power Colours Wireless Touchscreen Battery Test Time amp Date Update PROFILE Genmell COC 3 06 re _24Mlari4 mot To install the updates connect Genie Ill to a computer Navigate to My Computer and open the Genie III drive The drive is named with the instrument serial number e g GEN3 1001 Copy and paste or drag the
23. e by checking the corresponding tick box Clicking on the Notes button allows experimental notes to be entered and saved as part of the profile Version 1 05 37 ACTIVE On starting a run Genie Explorer will display the Active window The status icon of the Genie instrument which is running will change showing red labels for the blocks that are active The taskbar at the bottom allows selection of the different running profiles If multiple channels are being used each channel will show as a different tab Genie Explorer 1 l i 1 connected a9 GEI 035 22 34 Block A z J A a Run Profile WA GEN3 1035 T 2 v E f pd o a E o E 00 20 00 Time hh mm ss HE oer There are several tabs available to display the thermal profile and measured readings from the run i e Profile Temperature Amplification Amplification Rate Anneal Anneal Derivative and Result a GEN 2 1045 Block A B Amplification Rate Anneal Anneal Derivative Result Run Profile Temperature C The Profile screen shows the run wms 002000 a profile settings Time hh mm ss Version 1 05 38 TEMPERATURE Temperature Temperature C well Block ALID 1 Block ALID 2 00 02 00 Time hh mm ss
24. e shows the results in a tabular format and displays the Amplification Rate peak times and Anneal Derivative peak temperatures Version 1 05 ADDITIONAL TOOLS dulenee RARAS From left to right the buttons are Save The results will be saved to a gen file for subsequent access from either the instrument or software Save Profile The profile currently being run will be saved Stop This will stop the run in progress Skip To advance to the next phase press the Skip button Extend If more time is required on the current phase press the Extend button and the run will extend by 10 minutes A confirmation box will pop up every time Extend is pressed and the run profile will be updated to show the new time The buttons below the graphs can be used to zoom in and out of the graph in different directions The Reset button will return the graph to its original state From left to right the buttons are Save to Text will save the raw data toa comma separated txt file for import into a spreadsheet application such as Microsoft Excel Save to Image will save the current graph to a jpg file Report will display all of the results of the experiment in an organised report form which can be printed or saved These buttons allow the data to be saved in different formats Version 1 05 42 ANALYSIS amp GRAPH OPTIONS Click the Settings
25. ent as normal OPEN Any saved profiles from either Genie Explorer or a Genie instrument can be run from Genie Explorer Navigate to the profile file select it and all the parameters will be loaded in RUN Pressing Run will start the experiment On clicking Run this box will appear This allows selection of which block is being r aJ Select Block used and also options for saving of the run file The default location for saving the files is set within Genie Explorer and can be changed in Options If the Genie instrument only has one block then only block A will be selectable Version 1 05 35 GRAPH OPTIONS Clicking on Graph Options will display the following screen RUI UE za LEEEEE EE TEEPE Choose either 8 Wells one block or 16 Wells two blocks Genie Ill only supports 8 wells It is also possible to enter well names change plot colours set line styles and to select which wells are visible on the results display The tabs allow the parameters for all graphs to be adjusted Click on the tabs for each graph and alter settings as required For more information see section Analysis and Graph Options Version 1 05 CHANNELS If the Genie instrument supports multiple channels such as the Genie III the Channels button will be available Select which channels are to be used in the profil
26. ent is routinely exposed to bio hazardous materials 1 Wipe all outside surfaces of the Genie II with a 10 bleach solution 2 After 10 minutes wipe all the same surfaces with a 70 ethanol solution CAUTION Do not allow any of the liquid solutions to enter the wells as this can cause damage Version 1 05 SUPPORT HOW TO OBTAIN SUPPORT For the latest services and support information go to http www optigene co uk support htm IMPORTANT When directed to do so contact OptiGene Ltd to schedule maintenance or calibration of a Genie IIl instrument IMPORTANT If a Genie III instrument is kept in a very cold environment the battery will not begin charging until the internal temperature has reached 15 C SUPPORTED CONSUMABLES IMPORTANT Genie Ill uses a proprietary tube strip that maximises optical and thermal efficiencies Other tubes and strips will not fit IMPORTANT Forcing non supported consumables will cause damage to the instrument and invalidate the warranty IMPORTANT The shape of the tubes is such that they will only fit in one way round The locating pins on the block have corresponding holes in the strips Version 1 05 BOX CONTENTS The following is a list of contents in the box for Genie III Genie IIl instrument Power supply Power lead USB connection lead Stylus USB memory stick containing Genie Explorer and this manual as a PDF file Version 1 05 SITE PR
27. he Threshold value Multiple peaks can be detected Full The software performs more complicated analysis of peaks above the Threshold value Multiple peaks can be detected Invert Invert inverts the graph FILE To view previously run data go to the main menu and click the File button Then click on either a Genie instrument or PC to browse for a run file Files are saved as gen files by default in the folders specified in Genie Explorer Options or in the Log folder on a Genie instrument The run file is encrypted N Genie Explorer ad Spo See Open om lt b Users gt OptiSense SL AppData Local OptiGene GenieExplorer Results 4z Search Results 2 e The requested file will be loaded a DropboxPersi Name Date modified v Date ize Ere GEN3 1035_10 07 2014_14 22 34 gen 10 07 2014 14 24 10 07 2014 14 22 e a n d a n a lys S of t h e d a t a C a n b e D eee E GEN2 2004 04 07 2014 13 46 03 gen 04 07 201413 49 04 07 2014 13 46 ie 4 E GEN3 1035_04 07 2014_13 29 15 gen 04 07 2014 13 34 04 07 2014 13 29 lebsite e W GEN2 2004_04 07 2014 12 05 28 04 07 2014 12 12 04 07 2014 12 05 f d T h fi 1 d d asta a apn OAU want 03 07 2014 12 18 19 06 2014 15 31 p e r O r m e l e W l O a a n a es m GEN3 1035_26 06 2014_09 23 13 gen 26 06 2014 09 35 26 06 2014 09 23 W GEN2 1225_19 06 2014 15 30 54 19 06 2014 15 32 19 06
28. ightness at 100 for long periods of time as this will significantly decrease battery life Anneal Other USB serial Version 3 06 rc 2 FPGA 406 SIM GENS 1029 Version 1 05 11 USER INTERFACE Genie III uses a touchscreen for viewing and inputting data Touch the screen gently and press the appropriate keys when required The touch screen can be operated while wearing protective gloves or by using the stylus included with the instrument IMPORTANT Do not use a pen or any other sharp implements to touch the screen GENIE IlI WELCOME SCREEN When switching on the LED above the screen will be amber in colour Wait for the light to change to green then touch the screen to access the main menu Version 1 05 12 MAIN MENU To Start a predefined run touch the name of Genie OptiGene the assay and it will begin Alternatively LAMP amp Anneal touch Other to create a new profile or open a saved profile Anneal To view profiles or data from previous runs touch the folder icon J on the status bar Other USB serial Version 3 06 rc 2 FPG4 406 SIN GEN3 1029 To access the toolbox touch the spanner icon 31 Mar 2014 08 52 20 C gy SY yd on the status bar IMPORTANT When running for the first time check that the time and date on the status bar are correct These can be changed from the Utilities screen in the toolbox 31 Mar 2014 08 41 20 C
29. ion Cancel 20 Time mins Pressing one of the quick start buttons on the main menu will pop up a preview of the profile and give the user the choice to start edit or cancel the run Alternatively press the Other button and a file browser will be displayed Choose the profile to be loaded and press the Open button A preview graph will appear and allow the user to start edit or cancel the run Pressing Edit will open the main profile screen Changes can be made as required To begin the run press the play icon A prompt will be displayed Select Start to run or Cancel to abort Version 1 05 WELL NAMES Channels To assign names to the block wells Amplification click on the well names area 25 20 Time mins To change a well name press on the text box and type a name and abbreviation if desired Next switches to the next name and saves the current well name Pressing the cross returns back to the run screen with no changes made to that well Pressing the return button on the keyboard returns to the run screen with changes saved If the profile is saved at this point the well names and abbreviations will also be saved as part of the profile The well names screen can be accessed at any time the instrument is running by clicking on the Results tab and clicking anywhere on the well names column CHANNELS Touching the Channels are
30. ld be used for this It is also possible to run the touchscreen calibration when the instrument first starts Press and hold down on the welcome screen for 5 seconds to initiate DATE AND TIME Date click in the white box for date and enter in the format DD MM YY Time click in the white box for time and enter in the format HH MM SS Press Set to save or click the cross to cancel Version 1 05 16 RUN On Genie Ill there are two ways to start a run either quick start by touching one of the predefined profiles saved on the instrument or by creating a new profile Predefined profiles can only be selected for quick start if they are saved in the ASSAYS directory in the instrument file system QUICK START LAMP amp Anneal Anneal Other 31 Mar 2014 08 52 2000 g PROFILE SCREEN Anneal prof OF f04f2014 11 47 LAMP amp Anneal prot OF 04 2014 11 47 17 Up to four saved profiles can be shown on the main screen to allow quick starting of an assay The four profiles are selected from the Buttons page in the Toolbox Pressing one of buttons on the main menu will pop up a preview of the profile and allows the user to start edit or cancel the run To create a new profile press the Other button on the main screen This allows access to any predefined profiles or creation of a new one Cancel to return to the main menu Press the tick to select a file or to cre
31. mperature before it starts to take readings LOW GAIN This option is mainly for use if the user is running experiments with Calcein The range of values is between 0 and 7 Some guidelines on values are 0 Normal use Default 4 Low gain for use with Calcein 7 Lowest gain BLOCK GRADIENT The Block Gradient facility enables a gradient to be set across the blocks This is especially useful when setting up assays for optimisation of the amplification temperature Version 1 05 34 Example of setting up a gradient Set temperature of the midpoint of the block as the temperature of the Isothermal stage on the Temperature Profile screen Mid Point Temperature C 7 Then set the temperature range for the Block Gradient 0 o block by adjusting the Block Gradient parameter For example if the midpoint temperature is set to 63 5C and the gradient is set to 7 C that will set well 1 to 60 C well 2 to 61 C etc through to 67 Cin well 8 SAVE Profiles can be saved in order to repeat experiments Clicking the Save button will store the profile on the computer The default location is set within Genie Explorer and can be changed if desired Any saved profiles from Genie Explorer can also be copied to a Genie instrument s internal memory and run directly from the instrument Copy the saved profile to the Profile folder on the Genie instrument and then access it on the instrum
32. n upwards Close the lid by lowering and pressing down firmly Care must be taken to ensure that objects are not obstructing the lid when trying to close it and under no circumstances should the lid be forced open or closed INSERTING TUBES IMPORTANT Genie IIl uses a proprietary tube strip that maximises optical and thermal efficiencies Other tubes and strips will not fit IMPORTANT The shape of the tubes is such that they will only fit in one way round The locating pins on the block have corresponding holes in the strips Version 1 05 BATTERY Genie Ill has an internal rechargeable battery When Genie III is delivered the battery should be fully charged and ready for use The battery monitor is on the status bar next to the block temperature reading 31 Mar 2014 08 41 20 C To see more details on the battery press the battery icon and the monitor will appear as a pop up in the bottom right hand corner of the screen To remove the pop up press on the status bar indicator again Battery Status Charging 3397 mAh 16 6Y 1 04 2h 10min active time Battery monitor pop up IMPORTANT Genie IIl s internal battery will only charge when the instrument is plugged into mains electricity and the instrument is switched on Genie III can be shut down using the power button in the bottom left corner The LED above the display will glow brightly until the battery is fully charged At this point Genie III can
33. s Version 1 05 25 CONNECTING TO A COMPUTER Genie Ill is a standalone instrument however for software updates data upload and analysis it will need to be connected to a PC running Microsoft Windows XP Vista 7 Disclaimer Genie Explorer is an additional tool and should not be used for patient care or clinical analysis IMPORTANT Do not plug any Genie instrument into the computer before installing Genie Explorer Genie Explorer can be installed from the USB drive included with any Genie Instrument wm See Welcome to the Genie Explorer Setup Wizard The installer will quide you through the steps required to install Genie Explorer on your computer WARNING This computer program is protected by copyright law and international treaties Unauthorized duplication or distribution of this program or any portion of it may result in severe civil or criminal penalties and will be prosecuted to the maximum extent possible under the law Open the USB drive in My Computer Run the file Genielnstall msi Follow the onscreen instructions A prompt may appear requesting installation of NET Framework 4 0 This must be installed prior to installation Follow the link to the Microsoft download page http www microsoft com en gb download details aspx id 17718 Version 1 05 26 Select Installation Folder The installer will install Genie Explorer to the following folder
34. tion checkbox and set GC l l the required temperature and time Time 3 gt Minutes sothermal Check that the Isothermal checkbox is ticked Temperature 65 00 C and then alter the temperature and time to Duration 30 n suit the assay conditions 7 Anneal If the assay requires an anneal check the Start Temperature 95 00 C Annea box and alter the start temperature End Temperature 80 00 2C end temperature and cooling ramp rate This dialogue box shows how to set an annealing Rate 0 05 c Sec Ramp C Sec curve from high to low temperatures Version 1 05 33 ADVANCED BOX The Advanced button shows a pop up screen showing several options which allows changes to be made to the instrument control parameters Preheat Isothermal Ramp rate 1 00 C Sec Ramp rate 1 00 K ClSec Mid Point Temperature pE Measure period 15 Sec Block Gradient 0 C Anneal Low Gain Initial rate 1 00 C Sec Settling time 60 Sec Measure period 0 gt Sec RAMP RATE The Ramp rate specifies how fast the heating will occur It can be set for the three different phases independently MEASURE PERIOD The Measure period is the interval between measurements of fluorescence and is measured in seconds It can be set for both the isothermal and anneal phases SETTLING TIME The Settling time is the time that the instrument will wait once it has reached the desired annealing te
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