Genie ® Explorer User Manual v1.01
Contents
1. 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 instrument 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 z 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 00 10 GRAPH OPTIONS Clicking on Graph Options will display the following screen WATT TTF PEEVE C2. Genie Explorer User Manual Opticene 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 Table of Contents INSTALLATION cccsceccsceccecesceceeees 3 GENIE EXPLORER ssceceeceeeess 6 Main Menu cccccecscscscscecececeaeacecs 6 New Profile aaeaaaaeaaaaaaaaanana 7 Thermal Profile 212 8 Graph Options cccccceeeeeeeeees 11 Channels sccscsecsccscaccscscoeces 12 NOTES narada zai WE LO E GEAR 12 View Active RUNS zazaeaazaaaa 13 Profile aeaaaeaaaaaaaaaaaaaananca 13 Temperature 2212201 14 Amplification 14 Amplification Rate 11111 14 ANIE ON eanne 15 Anneal Derivative 16 PE SU ene AR 16 Analysis amp Graph Options 18 ACT 1
3. 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 00 15 ANNEAL DERIVATIVE a CAU or Sese SL Desktop Duncan Gen les Thame CpliGene Enayeres FTLAME SZL gen The Anneal Derivative tab shows the plot of the derivative of fluorescence for each well Floorescence dev vaise 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 Tismo OptiGene Enzymes_RTLAMP_001 gen Annes Deratw This page shows the results in a tabular format and displays the Amplification Rate peak times and Anneal Derivative peak temperatures Version 1 00 16 ADDITIONAL TOOLS 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 wi
4. Experiment Name Profile Name ca Run Profile GEN3 1035 Temperature C 00 15 00 00 20 00 Time hh mm ss Estimated run time gt EE Minutes Seconds Advanced 4 Anneal Preheat Activation isothermal Start Temperature 98 00 oC Temperature 4500 gt e Temperature 65 00 gt End Temperature 80 00 C Minutes Duration 30 Mi Ramp Rate 0 05 H sC Sec Profiled Version 1 00 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 Time 3 gt Minutes lsothermal Temperature 65 00 c Duration 30 z Minutes Z Anneal Start Temperature 95 00 C End Temperature 50 00 C Ramp Rate 0 05 c Sec If activation is required for the enzyme then tick the Preheat Activation checkbox and set the required temperature and time Check that the Isothermal checkbox is ticked and then alter the temperature and time to suit the assay conditions If the assay requires an anneal check the Annea box and alter the start temperature end temperature and cooling ramp rate This dialogue box shows how to set an annealing curve from high to low temperatures Version 1 00 ADVANCED BOX The Advanced button shows a pop up screen showing several options which allows changes to be made to the instrument
5. SE wa Default Profile File Sets a default profile Default Profile Fie ee ce ee eens Saito reset back to the program defaults click Pernoon Pone ES Reset Default Profile Click Save to save changes to the default locations Version 1 00 21 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 II and its design is a registered trademark of OptiGene Ltd or its subsidiaries in the UK and other countries Approved V1 00 03 11 15 Initial Release V1 01 20 11 15 Updated with batch export function Version 1 00 22
6. NORMALISATION Normalisation allows all the fluorescent signals to have their background level a HE removed calculated over a specified period INormalisation of time From 60 sec To 180 Sec Z D Select by ticking the Normalisation Na PP checkbox and setting the start and end times for calculating the background level e g 60 seconds to 180 seconds Amplification 100 000 00 a MAP m THA This screenshot shows data that has not vc aa been normalised the initial signal levels are Fluorescence different for each well 20 000 00 0 00 T T T T T T T T T T 50 00 15 00 00 25 00 00 35 00 00 45 00 00 55 00 09 10 00 00 20 00 00 39 00 00 40 00 09 50 00 Time Armplificabon s 20 000 00 z zu With normalisation the levels come Fluorescence together and allow for easier analysis Version 1 00 18 PEAK DETECTION FILE Simple The software looks at the plot and assigns the peak to the highest plotted point that is above the 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 inverts the graph 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 d
7. control parameters Preheat Isothermal Ramp rate 1 00 C 5Sec Ramp rate 1 00 K ClSec Mid Point Temperature pE Measure period 15 ec Block Gradient 0 H C Anneal Low Gain Initial rate 1 00 CiSec 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 temperature 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 O 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 00 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 SBS Da Tens C Then set the temperature range for the Block Gradient 0
8. 18 Version 1 00 Select Installation Folder The installer will install Genie Explorer to the following folder To install in this folder click Next To install to a different folder enter it below or click Browse z Choose a location for the installed program Install Genie Explorer for yourself or for anyone who uses this computer Everyone 6 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 Ce es Version 1 00 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 00 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
9. 225 19 06 2014 15 28 51 gen 19 06 201415 29 19 06 2014 15 29 GEN File 12KB an i GEN2 1225 19 06 2014 15 14 10 gen 19 06 20141515 19 06 2014 15 14 GEN File 37KB ar E GEN3 1035_19 06 2014_15 07 09 gen 19 06 2014 15 08 19 06 2014 15 07 GEN File 14KB Boi M GEN3 1035 19 06 2014 14 53 43 gen 19 06 201415 07 19 06 2014 14 53 GEN File 60 KB a i GEN3 1035 19 06 2014 15 02 58 gen 19 06 2014 15 06 19 06 2014 15 03 GEN File 34 KB Local Disk E GEN3 1035 19 06 2014 14 53 43 Copy gen 19 06 2014 15 01 19 06 2014 15 01 GEN File 59KB GEN3 1035 E 4 m 19 The requested file will be loaded and analysis of the data can be performed The file will load and be displayed in the same way as an active run Version 1 00 SERVICE Clicking the Service button on the main menu will produce the following screen From here it is possible to change the date and time of the instrument s clock and update firmware or FPGA code on the instrument instead of using the drag 8 drop method described in the instrument user manual BATCH EXPORT Clicking the Batch Export button on the main menu will allow the user to export amplification data from multiple log files into a single comma separated value CSV file X Date modified Type 19 11 2015 14 20 File folder 19 11 2015 14 20 File folder Genie Explorer will ask for a filename and location as to where to save the CSV file a Compliance
10. 9 SOV CO soda k AZ daw iGO 20 Batch Export cccccccsssecceeeeseeeeeeees 20 Default Directory Options 21 INSTALLATION The Genie range are standalone instruments however for software updates data upload and additional analysis it will need to be connected to a PC running Microsoft Windows XP Vista amp 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 Home WODO lotu Welcome to the Genie Explorer Setup Wizard D sg The installer will guide 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 ar 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 177
11. Temperature C 00 20 00 Time hh mm ss H Blaos 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 all GEN2 1045 Block A B RE zwy e Aika a SOS Run Profile The Profile screen shows the run profile settings Version 1 00 13 TEMPERATURE The Temperature screen displays the measured temperatures of the blocks and the heated lids plotted against time Temperature C 00 02 00 Tite hhimmm ss sh ALsers OpliSenue S1 DesetoziDunzan Gen filer TamztOprGene Enzymes RTLAMP DL gen The Amplification screen displays the fluorescence measurements for each well made during the Amplification phase plotted against time OREDO bee TOO UGO OOS w WU 01 0200 Time AMPLIFICATION RATE 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 00050 MiM MISA 002000 MFO 03000 023502 MAM 004506 MAM MEM lire 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 Version 1 00 14
12. e File name Tests Save as type esv Ce Hide Folders Genie Explorer will then ask the user to select the files to be m s 1 exported eo m Date modified m GEN2 1175_12 08 2015_09 54 24 gen 12 08 2015 10 35 JB gt aa Select as many files as required and i GEN3 1033_29 06 2015_15 35 29 gen 29 06 2015 15 36 GEN3 1033_29 06 2015_15 31 39 gen 29 06 2015 15 34 le R 1 fi GEN3 1033_29 06 2015_15 29 47 gen 29 06 2015 15 30 t h e n C IC k O pe n m GEN3 1033_29 06 2015_15 27 59 gen 29 06 2015 15 28 le s m GEN3 1033_29 06 2015_15 25 50 gen 29 06 2015 15 26 E GEN3 1033_29 06 2015_15 18 41 gen 29 06 2015 15 19 m GEN3 1033_29 06 2015_15 05 15 gen 29 06 2015 15 05 i GEN3 1033_29 06 2015_14 56 58 gen 29 06 2015 15 03 je i GEN3 1033_29 06 2015_14 53 58 gen 28 06 2015 14 55 T h f e s A GEN3 1033_29 06 2015_14 45 12 gen 29 06 2015 14 53 le e l es WI a uto m at l ca y O p e n l n i GEN3 1033_29 06 2015_14 12 37 gen 29 06 2015 14 13 e A GEN3 1033_29 06 2015_13 33 16 gen 29 06 2015 13 39 moro ay ss Genie Explorer When the final file has loaded the CSV file will be complete Version 1 00 20 DEFAULT DIRECTORY OPTIONS The Default Directory Options button allows the default locations of files to be set Profile Default location for saving profiles Default Directory Data Default location for saving run files Profile
13. efault in the folders specified in Genie Explorer Options or in the Log folder on a Genie instrument The run file is encrypted File name Experiment File gen ected rei le 4 Al Genie Explorer os w 5 e cene ee a m BABS u l a 1 OptiGene 1 connected l Users OptiSense SL AppData Local OptiGene GenieExplorer Results 44 Search Results Pp Organize New folder M DropboxPers Name Date modified Date Type Size a Build Record 5 EJ z R s E GEN3 1035 10 07 2014 14 22 34 gen 10 07 2014 14 24 10 07 2014 14 22 GEN File 18 KB m 3 E GEN2 2004_04 07 2014_13 46 03 gen 04 07 2014 13 49 04 07 2014 13 46 GEN File 84 KB Beas E GEN3 1035_04 07 2014 13 29 15 gen 04 07 2014 13 34 04 07 2014 13 29 GEN File 40 KB B tents Bi GEN2 2004 04 07 2014 12 05 28 gen 04 07 201412412 04 07 2014 12 05 GEN File 169 KB a za a GEN2 1225 19 06 2014 15 31 09 gen 03 07 2014 12 18 19 06 2014 15 31 GEN File 16 KB Bi reb ll GEN3 1035 26 06 2014 09 23 13 gen 26 06 2014 09 35 26 06 2014 09 23 GEN File 50 KB a fe is aj GEN2 1225 19 06 2014 15 30 54 gen 19 06 201415 32 19 06 2014 15 31 GEN File 20 KB Done E GEN2 1225 19 06 2014 15 19 59 gen 19 06 201415 31 19 06 2014 15 20 GEN File 182 KB mie M GEN2 1225 19 06 2014 15 28 32 gen 19 06 2014 15 29 19 06 2014 15 28 GEN File 15 kB pa E GEN2 1
14. hoose either 8 Wells one block or 16 Wells two blocks Genie Il 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 00 11 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 profile 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 00 12 VIEW ACTIVE RUNS On starting a run Genie Explorer will display the Active Run 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 a Genie Explorer m ji Di EN 1 connected Profile Temperature Amplification Amplification Rate Anneal Anneal Derivative Result Run Profile
15. 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 Profile View Open Profiles View Active Runs File Service Batch Export and Default Directory Options Ge er E OptiGene Version 1 00 GENIE EXPLORER DISCOVERY PANEL EA Genie Explorer Optcere i Any Genie instruments that are connected to the computer will be shown in the panel on the left side of the screen Multiple Genie instruments can GEN3 1035 be connected at the same time If any instrument is connected and not displayed click the scan for instruments button in the bottom left corner and the program will attempt to connect to them NEW PROFILE Clicking the New Profile 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 ea Genie Explorer OODE E
16. ll stop the run in progress a OE 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 OQ Q oo zoom in and out of the graph in different VA 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 00 17 ANALYSIS amp GRAPH OPTIONS Click the Settings 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 Smoothing Smoothing can be applied to all of the graphs A 0 Drag the slider or change the Points value to Points set the number of readings that are averaged to create a data point on the graph
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