USER MANUAL
Contents
1. 45 Opening previous run files 47 Additional features ecceceeeee 47 TECHNICAL SPECIFICATION 50 SAFETY NOTICES Please read the following notices carefully before using Genie Il 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 there is 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 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 i2. Isothermal Amplification Made Simple Version 1 14 FPiG4 210 SIM GEM 1086 ch A B Idle 23 Aug 2012 14 13 E 9 Version 1 12 11 EMBEDDED SOFTWARE Genie II uses a touchscreen for viewing and inputting data Touch the screen gently and press the appropriate keys when required IMPORTANT Do not use a pen or any other sharp implements on the screen otherwise damage could occur GENIE I 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 Genie 12 MAIN MENU Run View Utilities Gene To begin a new run click Run Isothermal Amplification Made Simple To view profiles or previous runs click View To access the utilities click Utilities Version FPGA 21 S N GEN Q A B Idle 23 Aug 2012 11 42 4 P INITIAL SET UP When running for the first time check the time and date on the lower status bar ly A B Idle 23 Aug 2012 12 32 gy Q If either are incorrect then proceed to change the time and date The time and date settings are in the Utilities menu 13 UTILITIES 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 z Here the user is required to touch the ouch the target points target point
3. Version 1 12 BATTERY MONITOR Run View Utilities Genie Isothermal Amplification Made Simple Version 1 14 FPGA 210 S N GEN2 1086 Q A B Idle 23 Aug 2012 11 40 Q Run View Utilities Genie l Isothermal Amplification Made Simple Battery Status Charging 97 5263mAh Version 1 14 16 4V 2 1A GIN CEN2 1006 3h25min active time Q A B Idle 23 Aug 2012 12 32 Q Run View Utilities Genie Isothermal Amplification Made Simple Battery Status Battery Full 100 5415mAh Version 1 14 16 9V 0 0A Sica ee 3h31min active time l A B Idle 23 Aug 2012 13 19 Run Active View Utilities Genie Isothermal Amplification Made Simple Battery Status In Use 99 5399mAh Version 1 14 16 5V 0 1A Bene ee 3h30min active time A Amplification B Idle 23 Aug 2012 13 20 ff Q 10 The battery status can be seen but there IS NO pop up Here the pop up shows that the battery is currently charging and is at 97 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 99 Version 1 12 SCREEN BRIGHTNESS CONTROL Next to the battery icon is the brightness control ly A B Idle 23 Aug 2012 12 32 gy Q To utilise 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 Run View Utilities Genie
4. Genie ll USER MANUAL OptiGene Ltd Unit 5 Blatchford Road Horsham West Sussex RH13 5QR Tel 44 0 1403 274980 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 TABLE OF CONTENTG 0000080 SAFETY NOVICES aisosceteccepesvertctonens 3 SUPPORT orar A E 5 How to obtain SUpport eseeeeesssees 5 Supported consumables 008 5 BOX CONTENTS accros 6 SITE PREPARATION 00000cccceeeeeees 7 How to set up Genie Ilan 7 CONNECTIONS ssc dcnssssvtsccdveeaaeeonurenosnves 8 OPENING AND CLOSING THE LID 8 INSERTING TUBES ccccccceeseeeeeees 9 Batte y inesssnns 9 Battery MON tOTF cccceeeeeeeeeeeees 10 Screen Brightness Control 11 EMBEDDED SOFTWARE 000866 12 Genie ll Welcome Screen 5 12 Main Menu seces 13 Initial set Up ascessiscicedsattcccsieniveedantecess 13 LIT VSS EE page vend E PE EE 1
5. 1 O P By T Name Date modified Type wy _ Genie_I v210 RC5 28Feb2012 rbf 28 02 2012 13 29 RBF File ir oe Navigate to the extracted zip file select the file to upload and click Send If it is a firmware update the file will be an a20 file whereas if it is an FPGA software update it will be an rbf file Geniell_1_13_27Jun12 a20 X Genie software files a20 bf seq font The selected file will be uploaded to Genie II If the update was a firmware update Genie II will restart when completed If an FPGA software update was performed Genie II will require a manual restart by turning the instrument off and on with the switch on the rear of the unit The new software versions will be displayed in the bottom left hand corner of the main menu screen Version 1 12 33 VIA INSTRUMENT V1 17 amp LATER o x Jla gt Computer GEN2 1105 E 5 Search GEN2 1105 E p Organize v pe Open v Burn New folder To install the updates connect z Genie Il to a computer Navigate i amp to My Computer and open the s i enie Iv ja j j j eee ae Genie II drive The drive is named after the instruments serial number e g GEN2 1105 Copy and paste the firmware or FPGA software files onto Genie Il Geniel_1_17_26Sep12 a20 Date modified 26 09 2012 12 39 S Record file Size 1 44 MB Run View Utilities Now on Genie II click
6. Care must be taken to ensure that objects are not obstructing the lid when trying to close it and under no circumstances should the lids be forced open or closed Version 1 12 INSERTING TUBES Each of the heating blocks has locating pins Genie II strips have holes that locate on these pins The strips will only fit in one orientation IMPORTANT Genie Il uses a proprietary tube strip that maximises optical and thermal efficiencies Other tubes and strips will not fit BATTERY Genie II has an internal rechargeable battery When Genie II is delivered the battery should be fully charged and ready for use The battery monitor is on the status bar next to the date and time hy A B Idle 23 Aug 2012 12 32 J YY 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 100 4800mA h Battery monitor pop up 16 4V 0 0A 3h 6min active time IMPORTANT Genie IIl s 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 button within the Utilities menu The LED above the display will glow brightly until the battery is fully charged At this point Genie II can be switched off using the switch on the rear
7. II User Manual 20th September 2011 2011 OptiGene Website design CEC Web Design Version 1 12 31 e To download the latest firmware click on the link and download and save 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 If Genie Il already has the latest FPGA software then only the firmware will need to be updated e f both firmware and FPGA software updates are required then update the FPGA software first followed by the firmware e If itis a firmware update the file will be an a20 file whereas if it is an FPGA software update it will be an rbf file VIA PC To install the updates connect Genie II to a computer open the Genie II software and choose Software update from the Options menu ow Genie ale 23 software update Terminal Buttons Empty window Restore default files Click Software update 0 2 0 3 Version 1 12 32 EB Genie update A pop up will be displayed If the instrument is detected the name of the Instrument OptiGene Genie 000000021090 instrument will be shown If it is not shown check the instrument is turned on and properly connected and click Find to try again Click OK Cancel Clase e HB Select files to load Lookin jj Geniell_1_13_27Jun12
8. Utilities and click Install Genie II will prompt for a file to use for the update 26 Sep 2012 13 40 Q Click on the file and click Open Genie II will then install the updated software Please wait for it to finish before trying to do anything else Q A B Idle 26 Sep 2012 13 45 T Version 1 12 34 The selected file will be uploaded to Decoding program file Genie Il Q A B Idle 26 Sep 2012 13 46 Q If the update was a firmware update Genie II will restart when completed If an FPGA software update was performed Genie II will require a manual restart by turning the instrument off and on with the switch on the rear of the unit Genie II will automatically delete the files when the update has completed The new software versions will be displayed in the bottom left hand corner of the main menu screen Version 1 12 35 PC SOFTWARE WELCOME SCREEN File Options Windows Welcome to Genie Preheat Isothermal Anneal Other From this screen there is the ability to choose to start a new experiment or review data saved from previous runs To carry out an experiment make sure that Genie II is connected to the computer and switched on To start a new isothermal run click the Isothermal button QUICK START BUTTONS The Quick Start Buttons are the buttons on the front Welcome screen Normally they state Preheat Isothermal
9. B Low gain for Calcein LOG 2012 06 28 GEN_0026 gen 5 A B Idle 23 Aug 2012 14 57 Q Profile Amplification Anneal Results Block A This shows the temperature of the block s as the experiment is progressing Temperature C Close jLOG 2012 05 12 GEN_O116 gen A B Amplification 12 Sep 2012 10 59 4 Q Run View Notes Utilities EXTEND Profile Amplification Anneal Results Block A This allows 10 minutes to be added to the Extend Amplification current phase of the run Extend lt Temperature C Yes Log 2012 08 23 GEN_0032 gen A Amplification B Idle 23 Aug 2012 17 18 Version 1 12 20 View Notes Utilities A B ADVANCE Profile Amplification Anneal Results Advances to the next phase of the run Advance to Anneal Yes 4a A B Amplification 8 Sep 2011 11 08 Run View Notes Utilities STOP Profile Amplification Anneal Results The Stop button will stop a run in progress A confirmation pop up box will prompt Yes Stop run now or No Yes Temperature C LOG 2012 08 23 GEN_0032 gen A Amplification B Idle 23 Aug 2012 17 36 Q Utilities Run Active Notes AMPLIFICATION Results Block A Anneal Profile Temperature This shows the fluorescence data that is being acquired during the amplification phase of the experiment fH a 2 Fluorescence Tine is Close N_OS78 Q A Finished B Idle 5 Sep 201
10. Block A an ao To zoom in on the area of interest drag to the right and or down Fluorescence F S on a 30k Tans tins Close Version 1 12 25 Run Active Notes Amplification Utilities Profile Temperature Anneal Results Block A an To zoom out drag to the left and or up F BSS Fluorescence Time mins Close A double press on the screen will zoom out to the full extent of the graphs Version 1 12 26 CONNECTING TO A COMPUTER Genie II is a standalone instrument however for software updates and other applications it will need to be connected to a computer IMPORTANT Do not plug Genie II into the computer before installing software The PC software can be installed from the USB drive included with Genie Il To begin the Genie II USB drive should be plugged into a computer a a SWA Yl 4 Open the USB drive in My Computer t Oy Manual venion Price ket ML2 pat Geriel Tint Geti DP at Gere 203 Genie 0 203 exe 0 nab 110 pat Open the folder Genie 0 2 O 3 install and double click Setup exe Follow the onscreen instructions OptiGene isothermal Amplification Made Simple All software will be installed in the following location s To install software into a different location s click the Browse button and select another directory Ch o O S e a o c ati O n f o r i n st a ati
11. Start Temperature S 98 C Estimated run time 38 13 mm ss E Preheat Activation 95 C for 10 s Duration 30 00 mmiss End Temperature 80 Ee Block Gradient J 0 Re Ramp rate J 0 05 C s Version 1 12 38 Preheat Activation 95 C for 10 5 a Isothermal Temperature 65 i Duration 30 00 mmiss ai Block Gradient 0 i vanea 3 Start Temperature 99 ie a End Temperature so a Ramp rate O 1 Cys ww BLOCK GRADIENT If activation is required for the enzyme then tick the Preheat Activation checkbox and set the required temperature and time Check the Isothermal checkbox is ticked and then alter the temperature and time to suit the assay conditions If the assay requires performing an anneal check the Anneal box and alter the start and end temperature This dialogue box shows how to set an annealing curve from high to low temperatures Note A melt T peak will be a different temperature from an annealing T peak This is normal 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 Temperature 63 5 fa r Duration 30 00 mm s5 a Block Gradient a OPTIONS DIALOGUE BOX Example of setting up a gradient Set centre temperature as 63 5 C witha gradient of 7 C Th
12. be updated to show the Finishe new time Extend Advance To advance to the next phase press the Advance button and Advance it will stop the current phase and go onto the next stage specified Stop l Stop This will stop the run in progress DO NOT press unless it is required for the run to stop Export The results can be exported into a txt file This allows importing of data into Microsoft Excel or other spread sheet software Version 1 12 47 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 spread sheet for additional end user manipulation oJ Genie Run KHV1 tRNA_Dilution_series genie Profile Isothermal Isothermal Ratio Anneal Anneal Derivative l Peaks Results 10E7 KHY1 tRNA 7 10E6 KHY1 tRNA 77 10E5 KHY1 tRNA 77 10E4 KHVI tRNA 7 10E3 KHY1 tRNA 77 10E2 KHVI tRNA 57 ii The example below shows if the 10E1 KHV1 tRNA A eo em 7 Isothermal graph is exported it will export time versus fluorescence for each well akan T 7 T 7 i T 7 T T 7 1 00 00 03 00 06 00 09 00 12 00 15 00 18 00 21 00 24 00 27 00 30 00 32 00 Time ET e a m The data exported is the data from that graph if changes are made to the graph for analysis purposes then the graph will need to be re exported for the changes to be reported The following table
13. o n t o t a k e place Directory for Geniell Directory for National Instruments products C Program Files amp 86 National Instruments Version 1 12 27 OptiGene Isothermal Amplification Made Simple NATIONAL INSTRUMENTS SOFTWARE LICENSE AGREEMENT E INSTALLATION NOTICE THIS IS 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 A h L A BECOME A PARTY TO THIS AGREEMENT AND BE BOUND BY ALL OF ITS TERMS AND CONDITIONS CLICK THE APPROPRIATE BUTTON TO CANCEL THE INSTALLATION PROCESS cce pt t e License 8 reemen t 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 Agreement do not accept the License Agreement wees am OptiGene Isothermal Amplification Made Simple EPEE Cannot install NI VISA 5 0 3 higher version already installed Run Time Support higher version already installed Adding or Changing Geriell Files The installer will display the processes being performed Click the N
14. type a name 2Sampe2 UC I pl More switches to the second block a f2 3 4 5 le 7 We 9 Yo r Okay returns back to the run screen ee with changes made Leet caf z xe liv fe fw lim Le Cancel returns to the run screen with CAP ELS Es ee ee ee no changes made Second Block well names amp abbreviations Weis sens a erio CO weiss swenis CO owen Seeond bioekwellnames Lee eee es et tee Reed as ee es Las BOB GS El El TS 9 io Lote Lom 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 returning to the profile screen and pressing the Wells button Version 1 12 19 ACTIVE Once the run has started the Active screens which are no longer greyed out will be Temperature accessible Notes Utilities Amplification Anneal Results The software will automatically go to the Temperature screen initially The other screens can be accessed using the tabs below Active Run Notes Utilities PROFILE Profile Temperature Amplification Anneal Results Preheat C ze Amplification C Anneal C Th h h fi h Is snows the profile that Is running for mmiss for mmi ss to aoc p 8 Description o at __0 05 C s gt S 2 a o a zs oO a v a o
15. 2 13 46 gi Q Version 1 12 21 Run Active Notes Utilities Anneal Profile Temperature Amplification Results Block A ANNEAL This shows the fluorescence derivative data that is being acquired during the anneal phase of the experiment FPO Derivative N Run Active Notes Utilities AJB Temperature Amplification Anneal RESULTS This shows the results of the experiment The sample name and its respective amplification time and anneal temperature are displayed 78 GEN Q A Finished B Idle 5 Sep 2012 13 49 gi Q A B Whilst Genie Il is running the display can switch the views for Temperature Amplification Anneal and Results between block A and block B by pressing AJB the A B button on the top menu bar Data for both blocks together is displayed by cycling through the A B button When displaying both graphs together block A data is shown with solid lines whilst block B data is shown with dashed lines Version 1 12 22 NOTES On the Notes screen notes about the experiment that is being performed can be added and will be stored as part of the log file View Utilities experiment 3 date 5 september babs We Is ls JL Le Ls le JL ma _ ew Le ie LL Le Le ais tele le JU UE EJ OBEnmoOOoOnR eee ewe em d Cancel VIEW To view previous runs press the View button on the top menu t Run Active Note
16. 4 Touchscreen calibration 14 Set Time and Date 15 TUG POND a scrneassconiaenvaceneess 15 PRIN e enceessnteeuceseecs 16 profile SCREEN cccccseseeeeeeeee 16 To create a new profile 16 To load a saved profile 17 ACTIN E S 20 PrOTIG casccicincedusatadsanidoucsiesstedeontates 20 TEMperature csccsccsscsscseceees 20 Amplification ccccceeecceeeeeeeeees 21 ANDE aer unonssaceteeenannes 22 RESUS nnne 22 AD a ene ee 22 NOTE eee 23 VIE W ee E 23 CONNECTING TO A COMPUTER 27 Genie Il Software updates 31 AT a Ce ann ee nr A A 32 Via Instrument v1 17 amp Later 34 PC SOFTWARE ccececcececeececeecess 36 Welcome SCreen ccsccsceccsceceeeess 36 Quick start bUuttons cee eee ee eeee 36 Setting UP a rUn cccecceeceseeeeeeeeeeees 37 Profile Screen 37 NOTES sanninna 37 PISS AS e 38 LS See 38 Profile cccescscciauinsiacwevdeniecnandeimnctases 38 EE 0 e E en ree 40 Peak Classification ceceeeee 40 Genotype sssssssssssssssessssrsresseressee 41 Observing a FUN ceeccceeseeeeeeeeeeeees 42 POM Cec ccccsheecan es cece n cio ne es 42 ISOtHerMal cccscecceceecscecesceees 42 Isothermal Ratio ccceceeceees 42 Annede aae 43 Anneal Derivative 43 Peaks onanera A Aa 44 ResUl ean S 44 Analysis and Graph Options 45 Genie Graph Options
17. Anneal and Other These buttons can be modified very easily so frequently used experiments or profiles can be stored as a button and be run right from the welcome screen e Save the run file then click Options on the welcome screen and click Buttons e Type inthe name for the button and tell the program where the profile file is located e The Welcome screen should then be updated with the new button Version 1 12 36 SETTING UP A RUN PROFILE SCREEN Opening a profile allows modification of all of the experiment parameters J Genie profile Iso Thermal Notes Assays Wells Profile Graphs Peak classification Genotypes Run e Enter information here about the type of experiment N ot e S Experiment Name IsoThermal Experiment Notes AS S a y S e Wells e Profile details File 4 C Documents and Settings Steve Application Data OptiGene Genie Isothermal expt e Graphs e Peaks Classification e Genotypes Click upon the desired tab to view or modify settings It is recommended that users work through the tabs in order i e Notes Assays Wells and Profile in order to add all necessary information before starting a run EJ Genie profile Experiment 1 Notes Assays Wells Profile Graphs Peak classification l Genotypes Run Enter information here about the type of experiment Experiment Name Experiment 1 Experiment Notes T
18. a Ta paaa peaks for genotyping Define and C a enter peaks into the table and the software will automatically label matching peaks Version 1 12 40 GENOTYPE i Genie profile Isothermal Notes Assays Wells Profile Graphs Peak classification Genotypes Run This table defines which peaks must or must not be present for each genotype and which can be ignored T h e G e n oty p e t a b a OWS t h e u S e r eH to define peaks which can be used for automated genotyping by the software RUN DIALOGUE BOX Start Run J On clicking Run this box will appear Instrument E Optigene Genie TiGmEN1 003 Block CA B Both of the run file It is advised to save files Run Mame IsoThermal in folders subfolders in the Genie II Data File 4 IsoThermal_031 genie directory in My Documents This allows selection of which block is being used and also options for saving Note If only 8 wells are being used the option to select Both will be greyed out In order to use both blocks change the setting in the Wells tab to 16 wells Note Symbols in the Run name will get converted to underscores in the file name Note If a filename is not entered the software will generate one from the run name and a unique number and save it in the default directory 2 Genie profile 28 09 10_NDM_LAMP Notes Assays Wells Profile Graphs l Peak classificatio
19. al Isothermal Ratio l eer ARRES T E which pale to display and Se e ct t h e P e a k d ete ct O pti O n N O n e p ow the data is processed I Simple or Full check the default Phase J Isothermal Y axis JRatio Normalisation from o 0 to oj olis Peak detect Ful Smoothing 5 points Peak criteria A T an as JF The peak criteria allow the software to Minrato J o display the peaks in the results table Peak markers l Peak labels J Peak criteria and click Okay Okay k Genie Run E coli 0104 dilution series with tRNA water jol Settings i 85k 80k 75k The Anneal tab plots the fluorescence of each well versus Finished Extend by 10 minutes temperature in an annealing curve on7roauwrtA wn Stop i x lt 10E7 KHV1 tRNA e ean A7 The Anneal Derivative tab shows 10E4 KHVI tRNA 7 es awian A the derivative fluorescence of each 10E2 KHV1 tRNA WY a well plotted against temperature Derivative thereby giving the data as a peak 0 80 81 82 83 84 85 86 87 88 89 90 9 92 93 94 95 96 97 98 99 100 Temperature C E 4 gt l Version 1 12 43 k Genie profile 28 09 10_NDM_LAMP If the Peak detect box is set on lc p Simple or Full then the peaks will f Derivative i el be displayed in the results table Check that the peak criteria are c
20. at will set well 1 to 60 C well 2 to 61 C etc through to 67 C in well 8 Version 1 12 The Options button shows a pop up screen showing several options which allows changes to be made to the protocol parameters Lo Genie Profile options Iso Thermal oa TE neds Ramp rate J 1 C s Measure period J 15 R Initial rate 1 CS Settling time J 60 Measure period 0 iaa o e ey S T 2 Genie profile 28 09 10_NDM_LAMP 4 lol x Notes l Assays Wells l Profile Graphs l Peak classification l Genotypes l Run l The Graphs tab allows the parameters for different graphs to be Isothermal l Isothermal Ratio l Anneal l Anneal Derivative l This table defines which graphs to display and how the data is processed Name Isothermal Xaxis time Phase isotherm Y axis O Fluorescence Normalisation V from gf 120 to J z0 s Peak detect dinone Smoothing J o points Peak criteria adjusted Click on the tabs for each graph and Fit width ol 0 Min width 6 0 Min height A a Min ratio o 0 Peak markers l alter settings as required Peak labels J For more information see section Analysis and Graph Options a Genie profile Iso Thermal Notes Assays Wells Profile Graphs Peak classification Genotypes Run This tab allows identification of This table identifies peaks for genotyping Each peak found is identified by the First matching entry in the table e ee ee a
21. c s box Inputs are made using the onscreen keyboard which will appear Temperature C as a pop up as in the example below O Low gain for Calcein D mee womans a 9 View Notes Utilities Preheat Amplification Anneal Preheat 4 Amplification 65 c Anneal 98 c Once the required changes have been for 0 00 mm ss for EE mm ss to 80 ec made pressing Enter will cause the onscreen keyboard to disappear and parerrrgrnrnzrraAmTEa the profile can now be saved Lew ee Le Ee Le batts Oot eb bE LE ler bb JL bb bE IL Ee J OCG Version 1 12 Save profile Seen ee Clicking Save will save the profile 18S Product Melt prof 01 04 2011 09 03 LAMP Anneal only prof 04 04 2011 12 56 Name the profile press Okay and it will be saved within the Profiles directory on the on board memory allowing it to be loaded for future runs To set a 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 Amplification i Amplification ce Anneal for 30 00 mm ss to shown below TO LOAD A SAVED PROFILE standard lamp with anneal prof 23 08 2012 14 17 From the profile screen choose the profile to be loaded and press the 65 98 80 0 05 Load key The profile will be loaded and details will be displayed on the next screen b A B Idle 23 Aug 2012 14 18 Q Ve
22. cal health and safety and COSHH regulations If in doubt consult the person responsible for the equipment in the laboratory Version 1 12 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 Il 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 II tubes pack size 50 strips OP 0008 500 Genie II tubes pack size 500 strips Version 1 12 BOX CONTENTS The following is a list of contents in the box for Genie II Genie Il instrument Power supply Power lead USB connection lead USB memory stick containing Genie II software and this manual as a PDF file 20x Genie II tubes optional Sample preparation blocks optional Version 1 12 SITE PREPARATION HOW TO SET UP GENIE I The laboratory bench should be level and stable The instrument should be
23. ext button to begin installation Click the Back button to change the installation settings x OptiGene Isothermal Amplification Made Simple Overall Progress 87 Complete The installer will copy all necessary files to the computer cia ne Coote Version 1 12 28 oOo OptiGene Isothermal Amplification Made Simple Genie Il Driver installation On Windows 7 and Vista manual installation of the Geniell driver is required When the installation is complete it will Locate Start All Programs OptiGene Win 7 Geniell driver Right click and select Install display information about the device driver On Windows XP the driver file is installed automatically installation for Genie II To close the window click Finish o You must restart your computer to complete this operation Once the installer has finished the f you need to install hardware shut down the computer If i E a a a a apt computer may require a restart to complete software the installation process Close any programs and save any open files before restarting Genie II can now be connected to the computer When connected via USB and switched on Genie II will appear as a USB device The driver will automatically install on Windows XP however on Windows 7 and Vista manual installation of the Genie II driver may be required 2S di Masa i ii Sets et es I Jo Hisa Install T te S
24. f needed Version 1 12 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 there is any doubt Disconnection Method Genie II 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 blocks and heated lid are hot please allow to cool before touching the surfaces Safe removal of fluids from Genie II will depend on the chemistry used This will also require knowledge of the fluids used in the system to adhere with lo
25. ghest plotted anion Ej simple Smoothing s 25 points point Multiple peaks can be detected Fit width J 7 Min width J 0 25 Min height J 7000 Min ratio 0 Peak markers Peak labels _ Isothermal Isothermal Ratio Anneal Anneal Derivative Full The software curve fits and assigns the Name Anneal Derivative x axis A Temperature Phase z3 4nneal axis zy Derivative A J centre of a peak and can report multiple Normalisation _ From A o to zi oe g j peaks It also performs sub point Peak detect S Full Smoothing J 25 points Peak criteria interpolation Fit width F 7 Min width J 0 25 Min height 3 7000 Min ratio J o Peak markers _ Peak labels _ Version 1 12 46 OPENING PREVIOUS RUN FILES To view previously run data go to the main menu and click File gt Log and navigate to the file required Files are saved by default in a Genie II folder in My Documents The run file is encrypted Ls Genie a Ed Options Windows Profile P Import Replay The requested file will be loaded back into Exit the software and analysis of the data can be performed as required O a ADDITIONAL FEATURES Profile Options Extend If more time is required on the current phase press the Extend Motes e button and the run will extend by 10 minutes A box will pop up every Nil time Extend is pressed and the run profile will
26. his is where you can make notes relevant to the experiment being performed Any experimental notes releva nt to the assay being run can be noted here File 4 C Documents and Settings StevetApplication Data OptiGene Genie New expt Version 1 12 37 ASSAYS Genie profile Isothermal Notes Assays Wells Profile Graphs Peak classification Genotypes Run This it a list of assay types you may be using in the experiment They are used to define assay specific peak classification etc This is a list of assay types that may be used in the experiment They are used to define assay specific peak classification 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 Choose if the experiment is using 8 or name assay colour pont ue ne o vene fmol e a 16 wells default is 8 There is the ability to enter well names change plot colours line styles and choose to make the sample visible on the results display or not PROFILE L Genie profile Iso Thermal Notes Assays Wells Profile Graphs Peak classification Genotypes Run The Profile tab allows setting of the thermal profile that is to be used and calculates an estimated run time for the desired profile Basic vf Isothermal Anneal m Temperature J 65 EG
27. n Genotypes Run Run Name 28 09 10_NDM_LAMP The Run tab is an experiment Started Ended Instrument Operator 28 09 2010 11 13 46 28 09 2010 11 52 36 OptiGene Genie I GEN1 003 l nfo rmat on screen It d iS p ays t h e Run Notes profile name when the profile was run and what instrument it was run on It allows input for the operator s name RunFile 4 E Documents and Settings My Documents Genie 28_09_10_NDM_LAMP_001 genie a n d t h e a b i ity to a d d ex p e ri m e n t e notes Version 1 12 41 OBSERVING A RUN PROFILE The Profile screen allows observation of the temperatures of the blocks and the heated lids plotted against time It acts as a thermal record of the run TT III The Isothermal screen allows observation of the fluorescence of each well plotted against time ISOTHERMAL RATIO Isothermal Ratio shows the amplification take off time in a robust manner Isothermal Ratio peak time is equivalent to the C or C in qPCR a A A A A A A A kon x5 assays Version 1 12 42 The Genie II software can detect the peaks and report them automatically To access the graph options click Settings and select the Graphs tab and select the corresponding graph a Genie profile 28 09 10_NDM_LAMP Notes l Assays Wells Profile Graphs l Peak classification l Genotypes Run Isotherm
28. nds to 240 seconds Then click Okay ie Run MalB_primer_test_seti_set2_ 001 Profile Isothermal Isothermal Ratio Anneal Anneal Derivative Peaks Results This screenshot shows data that has not been normalised the fluorescent signals are different for each well i i i i i i i i T i i i i i i 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 HE w a Genie Run MalB_primer_test_seti_set2_001 Profile Isothermal Isothermal Ratio Anneal Anneal Derivative Peaks Results With normalisation the starting points line up and allow for easier analysis 5k 1 T j 1 1 1 j 1 T 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 Hw z Version 1 12 45 PEAK DETECT Isothermal Isothermal Ratio 4nneal 4nneal Derivative Name Anneal Derivative x axis F Temperature 7 CA z Phase z Anneal axis J Derivative None no peaks are detected Normalisation _ from J 0 to 3 o ee Peak detect d None Smoothing ry 25 points Peak criteria Fit width 7 Min width 0 25 Min height J 7000 Min ratio o Peak markers L_ Peak labels _ Isothermal Isothermal Ratio Anneal Anneal Derivative E ne e 5 Simple The software looks at the peak and Normalisation from 0 to o c assigns the peak to the hi
29. opied from Genie II to the computer and vice versa Genie II is now ready to be used and controlled from the computer Version 1 12 30 GENIE Il SOFTWARE UPDATES It is recommended to keep the software on Genie II up to date Upgrading may improve performance and add new features to Genie Il There are two types of software on Genie Il the firmware and the FPGA software The current versions of firmware and FPGA software that are installed on Genie II are displayed in the bottom left hand corner of the main menu screen Run View Utilities Genie Isothermal Amplification Made Simple Version 1 14 gt FPGA 210 S N GEN2 1086 MBIde Ang OD g G For Versions 0 99 or earlier please contact OptiGene Ltd directly for the correct upgrade files It is highly recommended to upgrade For Versions 1 00 and later go to the OptiGene Ltd website and check on the Support page if there is a newer version of firmware available htttp www optigene co uk support htm e Google P ft 5 OptiGene Isothermal Amplification Made Simple Support Home About Us Genie II firmware Products Applications Click here to download the latest Genie II firmware v1 08 Contact Us PC application Distributors Click here to download the latest version of Genie II PC application v0 2 0 3 News Events Genie IT User Manual gt Support Click here to download the latest Genie
30. ore bie carne A BE eters iua or b mgka niakardi This is performed by locating the file It can ah besii Pees Cee Cnr i Sani be p A Banh MAAR MIH D aiy ma Listapaha be found by clicking Start gt All Programs gt r iaaa pa OptiGene gt Win 7 Geniell driver Right click tt ee D kiip Cana Taa P P h bia ar kisra E Casp m aai on the file and click Install amp biai i eae era tere ar eE oak bir uer Ean Pay PF ree he bin hiat D han sa Pamir bm User kkinl et ed ed oe irii db bira Mgr ere b Maida bet eet j Hesir bree tae ke Perna peat a my A Ogee LI ad OptiGene Ciaisie a Genie Explorer Tinara HQ Geniell Win7 Geniell driver is ik Core ara er Bedarra rt a ie a Pusan T d Bahri Ue j Reri erase G fhri Version 1 12 29 TT a x emm e w gt Computer gt gt Search Computer p Organize AutoPlay Eject Properties 4 Hard Disk Drives 1 w Local Disk C i a 4 Devices with Removable Storage 2 Genie ll is now visible as a USB drive in My Computer and the name appears as the instrument s serial number gt Network Location 2 GEN2 1090 E Space used WL Removable Disk Space free 250 MB ere Sax Keele gt Computer GEN2 1090 E Search GEN2 1090 E pl A NAA m H 7 l Organizey Sharewith v Burn New folder LOG PROFILES SYSTEM Log files and profiles can be c
31. orrectly set n Genie Run KHV1 tRNA_Dilution_series genie This page shows the results in a Tahoma Rabo as 10ES EVERA 10480027 45 Toor EES e ea Ee ee ee Isothermal Ratio AS__ 10 3 KHYI4tRNA has jume SS thor fa Tie anna a oazies foao ors Tamas peaks for the different profiles used within the experiment the position of peaks the peak width and height Semen Abbr Peaks l haaa aaa aaa aa A eaa e This page shows the results in a tabular format and displays the peaks and genotypes Version 1 12 44 ANALYSIS AND GRAPH OPTIONS GENIE II GRAPH OPTIONS Click the Settings button and it displays the 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 NORMALISATION Isothermal Isothermal Ratio Anneal Anneal Derivative Name Isothermal x axis J Time O EE O CEE Normalisation allows all the fluorescent ooa oO CE eE signals to be normalised back grounded no CNN o over a defined period of time Fit width J 0 Min width J 0 Min height 0 Min ratio 0 Peak markers L_ Peak labels _ Tick the Normalisation checkbox and then set the time for normalisation E g 60 Normalisation Do7 maa _240 i seco
32. 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 12 CONNECTIONS Genie II is ready to use straight out of the box without any connections as it can be used as a standalone instrument and has an internal battery However to charge the battery or to use Genie II 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 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 y Pii a USB POWER IN OPENING AND CLOSING THE LID To open and close the instrument lid s in order to add or remove samples gently lift the lid and it should open upwards Close the lid by lowering gently
33. rsion 1 12 17 View Notes Utilities C Preheat Amplification Anneal Preheat C Amplification 3e Anneal for 0 00 mm ss for 30 00 mmiss to aoc Alterations can be made if desired To begin the run press Start Description __ o at _0 05 C s m 2 ad v a 5 0 o a E o p Low gain for Calcein PROFILE New Q A B Idle 23 Aug 2012 14 19 Q View Notes Utilities E Preheat Amplification Anneal Preheat C Amplification C 65c Anneal 8 A prom pt will ask whether the a to _____80 c experiment is to be run on block A Description at 0 05 C s block B or both 30 35 CJ Low gain for Calcein PROFILE standard lamp with anneal prof Q A B Idle 23 Aug 2012 14 25 Q CALCEIN DETECTION This option is if the user is running experiments with Calcein rather than Fluorescein Low gain for Calcein Click on the tick box when using Calcein Version 1 12 18 WELL NAMES View Notes Utilities a Preheat Amplification Anneal Preheat oC Amplification 3G Anneal a for 0 00 mm ss for _30 00 mm ss to 80 c To assign names to the wells click on Description 0 at __0 05 c s_ the Wells button By 25 30 35 E Low gain for Calcein PROFILE New Q A B Idle E Aug 2012 14 19 Q First Block well names amp abbreviations Well Name Abbreviation Well Name Abbreviation To change a well name press on the js 1 Sample 4 C s L_ well and
34. s Utilities AJB iS 2012 This will display a folder browser window A B Idle 23 Aug 2012 17 48 c Version 1 12 23 PROFILE Q A B Idle 5 Sep 2012 13 30 Q 2012 23 Aug 2012 17 48 23 Aug 2012 17 49 Q 23 Aug 2012 17 51 Q 5 A B Idle 24 All Genie Il runs are saved in the LOG folder Click on LOG then Open Alternatively double clicking on the folder name will open the folder 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 Version 1 12 LOG 2012 08 23 de Bil GEN_0032 gen 23 08 2012 17 42 GEN_0031 gen GEN_0030 gen Each run is then stored numerically in sequential order 0 A B Idle 23 Aug 2012 17 52 j T LOG GEN_0578 GEN 01 06 2012 13 11 TinLF ChemMod LAMP GEN_0074 GEN GEN_0055 GEN 2012 Click on a file then Open and wait for the file to load Loading file Please wait Q A Finished B Idle 5 Sep 2012 15 15 9 Q When the file has opened Genie II will display the profile that was run the temperature log amplification data anneal data and the results table ZOOMING FUNCTION Zooming is available on temperature fluorescence and anneal graphs Utilities Run Active Notes Amplification Profile Temperature Anneal Results
35. s shown on the screen this will calibrate the touchscreen To check the sensitivity of the screen press Test Touchscreen Test Any point now pressed on the screen will be displayed Version 1 14 5 Version 1 12 14 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 MM SS Q A B Idle 23 Aug 2012 14 16 TURN OFF Pressing Turn Off will place Genie II into standby Genie II can also be placed into standby mode by pressing and holding the symbol on the lower status bar Note If this button is pressed during a run Genie II will not enter standby Normal operation can be resumed by pressing anywhere on the screen Version 1 12 15 RUN PROFILE SCREEN standard lamp with anneal prof 23 08 2012 14 17 Pressing Run will take the user to the ones profile screen Here the user can choose to create a new profile load an existing profile or cancel and return to the main menu Q A B Idle 23 Aug 2012 14 18 Q TO CREATE A NEW PROFILE View Notes Utilities _ Preheat Amplification Anneal Press the New button on the profile Preheat 40 c Amplification _65 C Anneal __98 C screen Adjust the profile by touching for__2 00 mms ee the appropriate temperature or time Description oo at __0 05
36. shows what data is exported for each graph Profile Graph Isothermal graph Export time versus fluorescence for each well Isothermal Ratio graph Version 1 12 48 Anneal graph Export temperature versus fluorescence for each well Anneal Derivative graph Peaks graph Export the Well Name Peak Position Value Width Weight d Y dX Relative and Class for each well Results graph Version 1 12 49 TECHNICAL SPECIFICATION Version 1 12 50 OptiGene Ltd Unit 5 Blatchford Road Horsham West Sussex RH13 5QR Tel 44 0 1403 274980 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 12 51
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