USER MANUAL
Contents
1. 14 TORON 14 RON 14 To create a new profile 15 To load a saved profile 16 Calcein detection 16 Well lt 17 ACTIVE SCREENS 18 POTO a 18 Temperature 18 ENTER 18 Anne 19 Amplification 19 ANDOA 19 19 epi 20 Stopping 20 NOTES 20 Viewing previous runs 21 CONNECTING TO A COMPUTER 23 Genie II firmware updates 26 PC SOFTWARE arseen 30 Welcome 30 Quick start buttons 30 Setting up 31 Profile 5 31 Notes 31 Wells tab essc sitae tt oen hart 32 Profile TaD menit D eden 32 Block Gradient 33 Options Dialogue Box 33 Graphs 34 Peak Classification Tab 34 Genotype 34 Run Dialogue 34 35 Observing2. 36 PLOT 36 Isothermal Tab 36 Isothermal Ratio Tab 36 Annedl 37 Anneal Derivative Tab 37 peaks 38 Results tab asse cb ants 38 Analysis and Graph Options 39 Genie ll Graph Options window 39 Peak detect options 40 Opening previous run files 41 Additional features 41 export 42 SAFETY NOTICES Please read the following notices carefully before using the Genie system The equipment supplied has been designed to consider the normal likely operation and features have been designed in to avoid risks associated with this use However to avoid any risk to the safety of the equipment operator or those in the same area as the equipment please read this chapter with care before unpacking and using the instrument If you are in any doubt as to the correct use of the equipment please contact the vendor Notices Using the instrument in a manner not specified by OptiGene Ltd 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 the surface is suitable for the weight and size of the instrument If the instrument is dropped it may cause harm The inst
3. for 0 00 mm ss for 30 00 mmss 80 Click on the wells button Description o a 005 cjs 40 0 5 10 15 20 25 30 35 Low gain for Calcein Cancel 5 A B Idle 28 Oct 2011 13 29 dj Wells Wells button will load the wells screens First Block well names amp abbreviations For The first block click the well that ff WM ___ you wish to insert a name into and DJ je type the name you wish JC 900 Fc E Re IE E Fe E e woe e fr v fv fx fol Okay continues back to the run screen ESERESESERERES F3 E3ERESESES E3 ER E38 ES E3ES LE y More switches to the second block Second Block well names amp abbreviations CO sme secomiiblodiwellnames Ls We Le Ie JLo b ewe ei Ly Lhe Le Lats 2 Ex Fev If the run is saved at this point the well names and abbreviations will also be saved as part of the profile The wells screen can be accessed at any time the instrument is running by returning to the profile screen and pressing the wells button Version 1 08 ACTIVE SCREENS Once the run has started you will be able to access the active screens Temperature Utilities Motes View Amplification Anneal Results The software will automatically go to the temperature screen however you
4. 15 5 79 Initial rate 1 Settling time 60 Measure period Jj Version 1 08 33 GRAPHS TAB The graphs tab allows the criteria for different graphs to be adjusted qu Simply click on the tabs for each graph and alter settings as you require For more information see Analysis and Graph Options Chapter This tab allows you to identify peaks for rue Tre ens T eps B n genotyping Define and enter peaks into the table and the software will automatically label matching peaks The genotype tab allows the user to define peaks which can be used for automated genotyping by the software RUN DIALOGUE BOX Version 1 08 34 5 start Run x When you click Run you will see the Instrument 9 Optigen Genie 003 start run dialogue appear This allows the user to choose which Block you Block Both y would like to run and also allows you Run IsoThermal to save the run file under a name of Data File p IsoThermal_031 genie finr your choice You can create a new folder or simply navigate to an existing folder We advise that you only save files in folders subfolders in the Genie folder under My Documents Check that you are running the assay on Block A or Block B or Both Symbols in the run name get converted to underscore i
5. All software will be installed in the following location s To install software into different location s click the Browse button and select another directory C h ti on f or n st a ti on t t a k e place Directory for Genie C Program Files OptiGene Genie s Directory for National Instruments products C Program Files N ational Instruments Version 1 08 23 License Agreement You must accept the license s displayed below to proceed NATIONAL INSTRUMENTS SOFTWARE LICENSE AGREEMENT INSTALLATION NOTICE THIS I8 A CONTRACT BEFORE YOU DOWNLOAD THE SOFTWARE AND OR COMPLETE THE INSTALLATION PROCESS CAREFULLY READ THIS AGREEMENT BY DOWNLOADING THE SOFTWARE AND OR CLICKING THE APPLICABLE BUTTON TO COMPLETE THE INSTALLATION PROCESS YOU CONSENT TO THE TERMS OF THIS AGREEMENT AND YOU AGREE TO BE BOUND BY THIS AGREEMENT IF YOU DO NOT WISH TO BECOME PARTY THIS AGREEMENT AND BE BOUND BY ALL OF ITS TERMS AND Acce pt t h e Li cense Ag reement CONDITIONS CLICK THE APPROPRIATE BUTTON TO CANCEL THE INSTALLATION PROCESS DO NOT INSTALL OR USE THE SOFTWARE AND RETURN THE SOFTWARE WITHIN THIRTY 30 DAYS OF RECEIPT OF THE SOFTWARE WITH ALL ACCOMPANYING WRITTEN MATERIALS ALONG WITH THEIR CONTAINERS TO THE PLACE YOU OBTAINED THEM ALL RETURNS SHALL BE SUBJECT TO NI S THEN CURRENT RETURN POLICY PT accept the License Agreement I do not accept the License Agr
6. Genie ll USER MANUAL OptiGene Ltd Unit 5 Blatchford Road Horsham West Sussex RH13 5QR Tel 44 0 1403 272817 Fax 44 0 1403 271017 www optigene co uk info 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 Table of Contents SAFETY NOTICES 3 SUPPORT 5 How to obtain support 5 supported consumables 5 BOX 6 SITE PREPARATION 7 How to set up the Genie ll 7 CONNECTIONS 8 OPENING AND CLOSING THE LID 8 INSERTING TUBES 9 2r jit pr 9 Battery 10 EMBEDDED SOFTWARE 11 GENIE II Welcome Screen 11 Main Ment ec 12 Initial set UD ccce dealer ERR Os 12 UTE NET 12 Touchscreen calibration 13 Set Time and
7. If you require activation for the enzyme then tick the Preheat Activation checkbox Now set the required temperature and time for the Preheat Activation Make sure the Isothermal checkbox is ticked and then alter the temperature and time to suit your assay conditions Version 1 08 32 If you are carrying out an Anneal curve at the end of the reaction then tick v anneal the checkbox for Anneal and alter the zs THE OPE gg ec start and end temperature This f dialogue box shows how to set an End Temperature Bl 0 1 Cs e dem annealing curve from high Ramp rate iar temperature to low temperature The melt Tm peak will be a different temperature from an annealing Ta peak This is normal 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 correct temperature Isothermal To set a gradient n Temperature 63 5 Em y Set centre temperature as 63 5 C with a Duration J 20 00 mmiss gradient of 7C Black Gradient U B amp That will set from 60 C in well 1 to 67 C in well 8 OPTIONS DIALOGUE BOX If you click the options button You will see the following screen which allows changes to be made to the protocol parameters La Genie Profile options 50 Thermal O Ramp rate 1 C s Measure period
8. the profile click save and it will be saved within the directory allowing you to load it for future runs Name the profile press Okay and it will be saved within the directory allowing you to load it for future runs Version 1 08 TO LOAD A SAVED PROFILE LAMP default prof 08 09 2011 12 19 LAMP Anneal only prof 08 09 2011 12 15 65 98 80 0 05 18s Product Melt prof 08 09 2011 12 16 b A B Idle 8 Sep 2011 12 20 View Notes Utilities Preheat Amplification Anneal Preheat Amplification Anneal 2E for 0 00 mm ss for 30 00 mm ss to 80 35 C Low gain for Calcein b A B Idle 8 Sep 2011 12 21 View Notes Utilities Preheat Amplification Anneal Preheat Amplification 9C Anneal ENS to __80 c 059 lt Start Run 0 10 15 Low gain for Calcein Q A B Idle 8 Sep 2011 12 21 CALCEIN DETECTION Low gain for Calcein Low gain for Calcein From the menu on the left choose the protocol that you wish to load and press the load key The profile will be loaded and you will see the profile in the next screen To begin the run alter the profile if required and press start You will be prompted to choose Block A Block B or both If you are running experiments with Calcein rather than Fluorescein Click on the tick box for Calcein Version 1 08 WELL NAMES View Notes Utilities 5 Preheat Amplification Anneal Preheat Amplification Anneal
9. 01 Profile Isothermal Isothermal Ratio Anneal AnnealDerivative Peaks Results With Normalisation 00 00 02 00 04 00 06 00 08 00 10 00 12 00 14 00 16 00 18 00 20 00 22 00 24 00 26 00 28 00 30 00 32 00 Time 01 aj 2 PEAK DETECT OPTIONS Isothermal Isothermal Ratio Anneal 4nneal Derivative Name Anneal Derivative x axis Jj Temperature Phase Jj Anneal Y axis Jj Derivative eee None no peaks are detected Peak detect Jj Mone Smoothing 3 25 points Peak criteria Fit width 2 7 Minwidth 7 0 25 Min height 20 7000 Min ratio Jj 0 Peak markers Peak labels Isothermal Isothermal Ratio Anneal 4nneal Derivative ame Anneal Derivative axis Temperature np Simple The software looks at the peak and Phase Anneal axis Jj Derivative Normalisation from Jj tJ c assigns the peak to the highest plotted Peak detect Simple Smoothing j 25 points point Multiple peaks can be detected Peak criteria Fit width J 7 Min width J 0 25 Min height J 7000 Min ratio J 0 Peak markers Peak labels Isothermal Isothermal Ratio Anneal 4nneal Derivative Derivative M Temcersture Full The software curve fits and assigns the Phase Jj Anneal Y axis Jj Derivative omaes fon ped cl centre of a peak and can report multiple Peak detect Ful Smoothing 25 points peaks Also does sub point interpolation Peak criteria Fit widt
10. Anneal Results This shows you the fluorescent data that is being acquired during the anneal phase of the experiment 5 A B Finished 28 Oct 2011 14 36 Run Notes Utilities RESULTS Profile Temperature Amplification Anneal i mm ss This shows you the results of the experiment A2 RE You will see the sample name and then its 3s respective amplification time and Anneal w temperature WE n b Idle 8 Sep 2011 12 31 Version 1 08 When Genie Il is running you can switch the views for Temperature Amplification Anneal and Results between block and Block B by pressing the A B button on the top menu bar STOPPING A RUN View Notes Utilities Profile Amplification Anneal Results If you need to stop a run in progress return to the Temperature Screen and Stop run now press the stop button A confirmation pop up box will prompt yes or no Amplification 8 Sep 2011 12 36 NOTES SCREEN On the notes screen you can make notes about the experiment that you are performing and they will be stored as part of the log file Version 1 08 20 VIEWING PREVIOUS RUNS To view previous runs click the view button on the top menu LOG PROFILE SCREEN Genie runs are saved in the log folder Click on log then open Amp
11. Connect to Instrument t OptiGene Genie 000000021005 Genie is detected and you click OK to accept Version 1 08 28 Select files to load Look in O Geniell 0_94 21 11 My Recent Documents e Navigate to the folder where you have extracted the downloaded zip file and choose the file to upload and click send gs My Computer File name D 94 21 11 D My Network Files of type Genie software files 20 gt The file will be uploaded Genie II will only restart after installation of a firmware file has completed It will not restart if an FPGA file has been uploaded The new FPGA code will show on the Main Menu upon a Genie II restart Version 1 08 29 PC SOFIWARE WELCOME SCREEN File Options Windows Welcome to Genie Preheat Isothermal Anneal Other From this screen you are able to choose to start a new experiment or review data saved from previous runs If you wish to carry out an experiment make sure that Genie Il is connected to the computer and switched on To start a new isothermal protocol simply click the Isothermal button QUICK START BUTTONS The Quick Start Buttons are the buttons on the front welcome screen Normally they state Preheat Isothermal Anneal and Other These buttons can be modified very easily so fre
12. M SS 5 A B Idle 8 Sep 2011 12 19 j TURN OFF Pressing turn off will place the Genie Il into standby Genie II can also be placed into standby mode by pressing the symbol Note if pressing this button during a run Genie II will not enter standby mode Normal operation can be resumed by pressing anywhere on the screen RUN LAMP default prof 29 03 2011 11 01 185 Product Melt prof 01 04 2011 09 03 65 65 98 80 0 050 When you choose run you will be LAMP Anneal only prof 04 04 2011 12 56 taken to the profile window Here you can choose to create a new profile load an existing profile or cancel and return to the menu screen Version 1 08 TO CREATE A NEW PROFILE View Notes Utilities Preheat Amplification Anneal Preheat 2G Amplification EC Anneal 9C for 0 00 mm ss for 30 00 mmss to 8c __0 05 cy w t5 O ED o Er o 3 ty er 0 5 10 15 20 Z 2 2 Low gain for Calcein 5 Idle 28 Oct 201113 29 jj View Notes Utilities Preheat Amplification Anneal Preheat Amplification 65 C Anneal SE 0 00 3 Save profile Press the New button the run screen Adjust the profile by touching the temperature box or time box that you wish to change Inputs are made using the onscreen keyboard which will appear as in the example below Once you have made the required changes press Enter and now you can save the profile Name
13. Tools Help 2 P Search lg Folders Address A x E System Tasks ue uae we 4 View system Data D De ED a Drive E Fi H pl Genie Il is now visible as a USB device programs Qe change a setting and the name appears as the Other Places instrument s serial number My Network Places My Documents E Control Panel Details 3 Computer GEN2 1005 F EIE Ld File Edit View Favorites Tools 3 gt d 2 Search Folders E Address File and Folder Tasks A Log files and Profile files can be copied QJ Make a new folder LJ from the Genie to the computer and Share this folder PROFIS vice versa Other Places 9 My Computer LA My Documents O bytes 3 My Computer Genie is now ready to be used and can be controlled from the computer Version 1 08 25 GENIE FIRMWARE UPDATES First check which versions of Firmware and FPGA are installed on your Genie They are shown in the bottom left hand corner of the Main Menu screen Run View Utilities Genie Isothermal Amplification Made Simple Version 1 05 FPGA 205 SIN GEN2 1004 A B Idle 8 Sep 2011 12 18 fj For Versions 0 99 or earlier please contact OptiGene directly for the correct upgrade files It is highly recommended to upgrade For Versions 1 00 and later go to the OptiGene website and check on the Support page if there is a newer version of firm
14. aks and genotypes Version 1 08 38 ANALYSIS AND GRAPH OPTIONS GENIE II GRAPH OPTIONS WINDOW Click the settings button and it displays the Genie II Graph Options window From this window several aspects of the graphical information can be modified There are four tabs on this page and each tab allows the user to check and modify settings appropriate for that tab i e Isothermal Isothermal Ratio Anneal amp Anneal Derivative Isothermal Isothermal Ratio Anneal Anneal Derivative Mame Isothermal X axis J Time t E Phase 3 Isothermal Y axis Fluorescence EI Normalisation allows all the fluorescent Normalisation v from J 120 to 240 signals to be normalised back grounded Peak detect J None Smoothing J 0 points Peak criteria over a defined period of time Fit width J 0 Min width Jj 0 Min height J 0 Min ratio 2 0 Peak markers _ Peak labels Tick the normalisation checkbox and then set the time for normalisation from say 60 Normalisation Ig 1 UL seconds to 240 seconds Then click Okay Lo Genie Run Malf_ primer _test_set1_ set2_ 001 Profile Isothermal Isothermal Ratio Anneal Anneal Derivative Peaks Results The screenshot below shows data that has not been normalised the fluorescent signals are different for each well and look untidy Version 1 08 39 Genie Run MalB_primer_test_seti_set2_ 0
15. can access other screens using the tabs below active View Notes Utilities PROFILE C Preheat Amplification Anneal Preheat 65 Amplification 65 Anneal 98 for 0 00 mm ss for 30 00 mm ss to This shows you the profile that is running Low gain for Calcein Q A B Idle 28 Oct 2011 13 29 View Notes Utilities TEMPERATURE This shows you the temperature of the block s as the experiment is progressing Extend Advance 5 Finished 8 Sep 2011 10 57 Utilities AJB Notes EXTEND Profile Amplification Anneal This allows 10 minutes to be added to the Amplification phase by clicking the button Extend Amplification Yes Advance A B Amplification 8 Sep 2011 11 16 Version 1 08 View Notes Utilities Ee eS ANNEAL Profile Profile Temperature Amplification Anneal Results Anneal Results Advances the programme from amplification to the Anneal phase by clicking the button Advance to Anneal Yes A B Amplification 8 Sep 2011 11 08 Utilities AJB Results Block A View Notes Profile Temperature AMPLIFICATION This shows you the fluorescent data that is being acquired during the amplification phase of the experiment Q A B Finished 28 Oct 2011 14 34 amp Run View Notes Utilities ANNEAL Profile Temperature Amplification
16. eement LY Genie tart Installation Review the following summary before continuing Adding or Changing Genie Files 4 2 Run Time Support The software will inform of the processes being performed Click the Next button to begin installation Click the Back button to change the installation settings j Overall Progress 16 Complete Overall progress Installation Complete The installer has finished updating your system Installation complete click Finish IE Version 1 08 24 You must restart your computer to complete this operation If you need to install hardware now shut down the computer If you choose to restart later restart your computer before running any of this software System must be restarted Genie can now be connected to the computer When connected via USB and switched on the Genie II will appear as a USB device Device driver software will be installed from the Genie Il Installing device driver software USB Composite Device 4 Ready to use Genie C Searching Windows Update USB Mass Storage Device af Ready to use OptiGene Genie II USB Device off Ready to use Devi ce D rive r nsta ati on Obtaining device driver software from Windows Update might take a while Skip obtaining driver software from Windows Update Computer Seles gt File Edit View Favorites
17. fication efficiency and curve shape This allows the ratio method to achieve a v vl vi vi EVI ET a highly reliable determination along with quantitative evaluation Isothermal Ratio is unaffected by drifting fluorescent baseline un normalised baseline and odd jumps in the amplification plot due to bubbles in a tube etc Version 1 08 36 Genie ll software can detect the peaks and call them automatically J Genie profile 28 09 10_NDM_LAMP Isothermal Ratio Isothermal Jra J o J s J 7 Mnwith f 0 25 Min height 5 Select the Peak detect option None Simple or Full check the default Peak criteria and click Okay The peak criteria allows the software to call the peak in the results table ra Genie Run E coli 0104 dilution series with tRNA water pm The anneal tab plots the fluorescence of each well versus temperature in a annealing curve Sm S gt gt gt gt gt lt lt lt lt SIL SL x The Anneal Derivative tab shows the derivative fluorescence of each well plotted against temperature thereby giving the data as a peak Version 1 08 37 i Genie profile 28 09 10_NDM_LAMP If the Peak detect box is set on Q emexue Simple or Full then the peaks will be Jemes Ca displayed in the results table Check that the peak criteria are set K Ge
18. h J 7 Min width J 0 25 Min height J 7000 Min ratio J 0 Peak markers Peak labels mm Version 1 08 40 OPENING PREVIOUS RUN FILES To view previously run data simply go to File Log and open the file you require Files are saved by default in a Genie folder in My Documents The run file is encrypted Options Windows L Profile Import Replay 59 The requested file will be loaded back into Exit the software and you will be able to analyse the data as required Extend If you are running an isothermal assay and find more time is required press the extend button and the run will extend by 10 minutes If the button is pressed 3 times it will extend the run by 3 x 10 minutes Finished A box will pop up every time Extend is pressed and the Run profile will be updated to show the new time Extend Advance if you are happy that the amplification has completed and you Advance would like to go to the annealing curve you can press the advance button and it will stop the isothermal phase and go onto the next stage specified Stop Stop Stop will stop the run in progress DO NOT press unless you want the run to stop Export Version 1 08 41 Export when you have finished the analysis you can export the results into a txt file Simply name and save the file This allo
19. instrument e Power supply Power Lead e USB connection Lead e Manual PDF version on memory stick e USB memory stick Version 1 08 SITE PREPARATION HOW TO SET UP THE Genie The laboratory bench should be level and stable The instrument should be placed centrally on the lab bench and the surfaces surrounding the instrument must be clear of obstructions at all times Care must be taken not to unduly restrict the air inlet at the rear of the instrument and the outlet vent at the front of the instrument must not be covered Restricting airflow by placing objects in front of these areas will impede operation and significantly affect performance Electrical points should be close to the instrument to avoid injury from trailing wires It is recommended that the instrument is kept away from sinks and other wet areas Genie II is an electrical instrument and care should be taken not to operate if there is a risk of water damage Version 1 08 CONNECTIONS Once un packed Genie 11 is ready for use Connect the power supply plug into the back of the instrument and then attach the power cable to the supply Located to the rear of the instrument is an on off power button switch to on and Genie II will power up and progress through its checks POWER IN OPENING AND CLOSING THE LID To open and close the instrument lid to add or remove samples gently lift the lid and it should open upwards Close the lid by
20. ion 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 blocks and heated lid are hot please allow to cool before touching the surfaces Safe removal of fluids from the Genie II 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 COSH regulations If in doubt consult the person responsible for the equipment in the laboratory Version 1 08 SUPPORT HOW OBTAIN SUPPORT For the latest services and support information go to www optigene co uk support htm IMPORTANT When directed to do so contact OptiGene to schedule maintenance or calibration of the Genie II instrument SUPPORTED CONSUMABLES IMPORTANT Genie Il uses a proprietary tube strip that maximise optical and thermal efficiencies Other tubes and strips will not fit IMPORTANT Forcing non supported consumables will cause damage to the instrument and invalidate warranty IMPORTANT The shape of the tubes is such that they will only fit in one orientation The locating pins on the block have corresponding holes in the strips Catalogue number ISO 001 Isothermal Master Mix OP 0008 50 Genie tubes pack size 50 strips OP 0008 500 Genie II tubes 500 strips pack size Version 1 08 BOX CONTENTS Following is a list of contents in the Box for Genie II Genie Il
21. lification 8 Sep 2011 12 34 j 2011 11 10 13 11 09 07 11 06 08 11 06 07 Each run is stored in a folder by date 11 05 10 11 05 06 O rd er 11 05 03 11 04 28 11 04 26 Q A B Idle 28 Oct 2011 13 16 LOG 11 06 17 GEN 0070 GEN 17 06 2011 15 49 IsoThermal 25 65 98 80 0 050 GEN_0067 GEN _0068 _0069 Each run is then stored numerically in sequential order 0 Idle 8 Sep 2011 11 00 1 08 21 Notes Utilities Anneal Amplification Results Temperature gt GEN 0067 GEN GEN 0068 GEN GEN 0069 GEN Please wait for the file to load and Loading file Please wait then you will be able to view the data b A B Idle 8 Sep 2011 12 50 8 You are now able to view the profile that was run the temperature log the amplification the anneal and the results table Version 1 08 22 CONNECTING TO A COMPUTER Genie Il is a standalone instrument however for software updates and other applications you may wish to connect to a computer IMPORTANT Do not plug Genie II into the computer before installing software The PC software is preloaded on the USB stick Insert USB memory stick into computer Labview Software FULL INSTALL Version 22 File Edt Favortes Tools Choose Set up installer Genie Destination Directory Select the primary installation directory
22. lification Made Simple Version 1 05 SIN GEN2 1026 5 A B Idle 1 Sep 2011 18 09 4 Run View Utilities Genie Isothermal Amplification Made Simple Battery Status Charging 62 3832mAh Version 1 05 15 6V 1 8 FPGA 205 SIN GEN2 1026 b Idle 1 Sep 2011 18 10 4 View Utilities Genie Isothermal Amplification Made Simple Battery Status Battery Full 10096 4800mAh Version 1 05 17 1V 0 0A SIN GEN2 1026 o Idle 1 2011 18 29 Run View Utilities Genie Isothermal Amplification Made Simple Battery Status In Use 99 4797mAh Version 1 05 17 0V 0 2 SIN GEN2 1026 b Idle 1 Sep 2011 18 30 8 The battery status be seen but there 15 no pop up Here the pop up shows that the battery is charging 6296 Here the pop up shows that the battery is fully charged The pop up shows that the instrument is in use and the battery is at 9996 Version 1 08 EMBEDDED SOFIWARE The Genie Il uses a touchscreen for viewing and inputting data Simply touch the screen gently and press the keys required IMPORTANT Do not use a pen or any other implement upon the screen otherwise damage could occur WELCOME SCREEN When switching on the LED above the screen will be amber in colour wait for the light to change to green then simply touch the screen to access the main menu Genie Em Version 1 08 MAIN MENU Ru
23. lowering gently Care must be taken to ensure that objects are not obstructing the lid when trying to close it and under no circumstances should you force the lids open or closed Version 1 08 INSERTING TUBES You will notice that each of the heating blocks has locating pins The Genie II strips have holes that locate on these pins the strips will only fit in one orientation IMPORTANT Genie uses a proprietary tube strip that maximises optical and thermal efficiencies Other tubes and strips will not fit BATTERY The Genie has an internal rechargeable battery The battery is fully charged and ready for use The battery monitor is on the status bar next to the time and date A B Idle 1 Sep 2011 18 30 To activate the battery monitor press the battery icon and the monitor will appear as pop up To remove the pop up simply press on the status indicator Battery Status Charging 100 4800mAh Battery status pop up 16 4V 0 0A 3h 6min active time IMPORTANT The Genie internal battery will only charge when the instrument is plugged into mains electricity and the instrument is switched on Genie II can then be shut down using the turn off command within the utilities menu The LED will glow brightly until the battery is fully charged At this point Genie II can be switched off using the switch on the rear Version 1 08 BATTERY MONITOR Run View Utilities Genie Isothermal Amp
24. n View Utilities To begin a new run click run Genie 1 Isothermal Amplification Made Simple To view profiles or previous runs click view To access the utilities click utilities 23 uou OPS m 1004 A B Idle 8 5 2011 12 18 j INITIAL SET UP When running for the first time check the time and date on the lower status bar A B Idle 1 2011 18 30 J If either are incorrect then proceed to change the time and date The time and date settings are in the utilities menu UTILITIES Run View Touchscreen To access the utilities screen click the Sate utilities tab on the menu bar you are then given several options Turn off 5 A B Idle 8 Sep 2011 12 18 Version 1 08 TOUCHSCREEN CALIBRATION Touchscreen calibration Touch screen to start Touching anywhere on the screen with the exception of Test or Skip will invoke the touchscreen calibration Touchscreen calibration Touch the target points Here you are required to touch the target points shown on the screen this will calibrate the touchscreen Clear To check the sensitivity of the screen press test Touchscreen Test Any point now pressed on the screen will be displayed Version 1 05 5 Version 1 08 SET TIME AND DATE Click in the white box for date and enter the date The date should be in Set Date and Time the format DD MM YY Click in the white box to enter the time The format should be HH M
25. n the file name If you do not give a file name the File name is created from run name unique number in the target directory RUN TAB Genie profile 28 09 10 LAMP Notes Assays Wells Profile Graphs Peak classification Genotypes Run 128 09 10 The run tab is the experiment Started Ended Instrument Operator 28 09 2010 11 13 46 28 09 2010 11 52 36 OptiGene Genie I GEN1 003 information screen It displays the run Run Notes name profile running and run date It allows you to input the operator name make experimental notes RunFile E Documents and Settings My DocumentslGeniel28 09 10 NDM LAMP D01 genie Okay Version 1 08 35 OBSERVING A RUN PROFILE TAB When running the profile screen allows you to observe the temperatures of the blocks and the heated lids plotted against time It acts as a thermal record of the run ST TT TTT TTI ISOTHERMAL TAB When running the Isothermal screen allows you to observe the fluorescence of each well plotted against time BEEESEEEEEEEEREEE ISOTHERMAL RATIO TAB Isothermal Ratio peak time is equivalent to the Ct or Cq in qPCR assays Our method identifies a consistent point within the exponential region without user intervention This amplification ratio generates several measurements of amplification including time of crossing and relative measures of ampli
26. nie Run KHV1 tRNA_Dilution_series genie Profle Isothermal Isothermal Ratio Anneal Anneal Derivative Peaks Results This page shows the results in a Name width Height d vidX2 Relative Class A DS NS NN ET CONUS NN tabular format and dis la S the TsothermalRatio 2_ 10E6 KHVIHRNA 9 25 0 05316 030 005514 L91 amp S 100 _ play Ce Dips Joe Hae T thermal Rato AS 1063 KNER 1542 iss 85086 peaks for the different profiles TsothermalRatio 6_ lOE2 KHVIHRNA 2242 0 02183 000 0 01726 908226 100 NENNEN Anneal Derivative AL 10E7 KHVIHRNA 89 72 1429 0 20 1 4008 4 1 100 Anneal Derivative 2_ l E amp KHVIHRNA 89 66 1 2616 4 020 12338k4 172 5 100 Anneal Derivative _ 10E5 KHVI tRNA 89 55 1322644 0 25 1 293644 1707 5 100 Anneal Derivative A4_ 10E4 KHVIHERNA 89 56 1 267E 4 0 25 1 239644 1 664E 5 1 000 Anneal Derivative AS_ 10E3 KHVI tRNA 89 55 1 307 0 5 1 279E 4 1 6616 5 Anneal Derivative A6_ 10E2 KHVIHtRNA 89 55 1 317E 4 0 25 1 2888k4 1 6806 5 1 used within the experiment the position of peaks the peak width d height and height This page shows the results in a tabular format and displays the pe
27. quently run experiments can be stored as a button and run right from the welcome screen Simply save your run file as you need it then simply go to Options on the welcome screen and click buttons Then type in the name you wish to call that run and tell the button where the run file is located The Welcome screen should then be updated with your new button I Version 1 08 30 SETTING UP A RUN PROFILE SCREEN In this screen you are able to modify all the experiment parameters Genie profile Iso Thermal e Notes Notes Assays Wells Profile Graphs Peak classification Genotypes Run Enter information here about the type of experiment e AS S a y S Experiment Mame IsoThermal Experiment Motes e Wells e Profile e Graphs File 4 C Documents and Settings StevelApplication Data OptiGene Genie Isothermal expt 2 Peaks Classification e Genotypes Simply click upon the tab in which you want to add information into We recommend however that you work through the tabs in order Notes Assays Wells and Profile This will allow you to add all the information necessary before starting the run NOTES TAB 1 Genie profile Experiment 1 Notes Assays Wells Profile Graphs Peak classification Genotypes Run Enter information here about the type of experiment Experiment Name Experiment 1 Experiment Notes This is where you can make notes relevant to the experiment being pe
28. rformed If you click the notes ta b this allows you to make any experimental notes relevant to the assay you are running File C Documents and Settings Steve Application DatalOptiGenelGenielNew expt Version 1 08 31 WELLS TAB L Genie profile Iso Thermal Notes Assays Wells Profile Graphs Peak classification Genotypes Run 8 wells 16 wells Define the name and contents of each well and how it is displayed on the graphs PROFILE TAB E Genie profile Iso Thermal Notes Assays Wells Profile Graphs Peak classification Genotypes Run Anneal Start Temperature J 98 C Isothermal Temperature J 65 BE Basic x options 38 13 mmiss E Preheat Activation Estimated run time E Duration 7 30 00 mmiss End Temperature J 80 Block Gradient j 0 Ramp rate J 0 05 5 95 for 10 s Preheat Activation ri 95 C For J 10 5 Isathermal Temperature 65 ENS Duration 2 30 00 mmiss Block Gradient 0 ES This tab allows you to input specific sample information Choose if you are running 8 or 16 wells default is 8 You have the ability to enter names change plot colours line styles and choose to make the sample visible on the display or not The Profile tab allows you to set the thermal profile that you wish to use and gives you an estimated run time for your desired profile
29. rument 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 08 Always disconnect the equipment before moving or removing any guards or covers Switch it off at the mains outlet remove the mains plug from the wall socket and remove the cable from the inlet socket on the rear While every effort has been made to protect the inside of the instrument against splashes the instrument carries no IP rating If fluids are spilt over the instrument they may get inside and cause a dangerous situation with respect to the voltage within the enclosure If a spill occurs that may pose a danger remove power from the instrument Do not touch the instrument or any fluid flowing from it while it is connected to the live mains supply Always follow local health and safety guidelines Normal safe local operating standards should be applied in general terms The items above are for guidance and are not a definitive list Please consult the instrument supplier if you are in any doubt Disconnection Method The Genie Il is disconnected by removal of incoming mains power source to the unit Following disconnect
30. s graph Export the Well Name Peak Position Value Width Weight Relative and Class for each well Results graph Version 1 08 OptiGene Ltd Unit 5 Blatchford Road Horsham West Sussex RH13 5QR Tel 44 0 1403 272817 Fax 44 0 1403 271017 www optigene co uk info 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 Version 1 08 44
31. ware available Version 1 08 26 www optigene co uk support htm 3 Google f ur E P optiGene Ltd Isothermal Amplification Made Simple Support Home About Us Genie II firmware Products Applications Click here to download the latest Genie II firmware v1 08 Fita De PC application Distributors Click here to download the latest version of Genie II PC application v0 2 0 3 News inf Events Genie II User Manual Support Click here to download the latest Genie II User Manual 20th September 2011 2011 OptiGene Website design CEC Web Design Click on the link and download and save the zip file Open the zip file and extract the contents to a new folder The contents of the new folder will include this guide and the latest firmware and FPGA code If your Genie already has the latest FPGA code then you only need to upgrade the firmware code If you need to upgrade both the FPGA code and the firmware code then upgrade the FPGA code first followed by the firmware code using the Genie software on your computer To install code updates Connect your Genie I to your computer open the Genie software on your computer and choose software update from the options menu Version 1 08 27 ER Genie Seema Windows Software update Terminal Buttons Empty window Restore default Files Click on software update 0 2 0 3 Genie update m
32. ws you to import the results into Excel or other spread sheet programmes EXPORT FUNCTION The Export function allows that data from each graph can be individually exported as a tab delimited txt file that can be imported into a spreadsheet for additional end user manipulation En Genie Run KHV1 tRNA_Dilution_series genie Profile Isothermal Isothermal Ratio Anneal Derivative Peaks Results 10E7 KHV1 HtRNA 10E6 KHY 1 tRNA 10 5 KHY 1 tRNA 10 4 KHY 1 tRNA 10E3 KHY 1 tRNA 10E2 KH 1 tRNA 10 1 KHY 1 tRNA 10 0 1 Lu yu c E Hu 1 i i i i i i i i i i i 00 00 03 00 06 00 09 00 12 00 15 00 18 00 21 00 24 00 27 00 30 00 32 00 i Time Bl B 238 3 194 8 m m 160 3 110 6 91 83 127 3 125 6 5 83 The data exported is the data from that graph if changes are made to the graph for analysis Settings The example below shows that if you export the Isothermal graph it will export time versus fluorescence for each well adi purposes then the graph will need to be re exported for the changes to be reported 42 Version 1 08 FOR EACH GRAPH Profile Graph Isothermal graph Export time versus fluorescence for each well Isothermal Ratio graph Anneal graph Export temperature versus fluorescence for each well Anneal Derivative graph Peak
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