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Gentier Real-Time PCR System

Figure E-2. Instrument software – Experiment File interface

Interface Introduction & Parameter Descriptions

Experiment File Displaying Area

: display the pre-existed experiment files or file folders

within the instrument system, as shown in figure E-2.1.

Figure E-2.1 Experiment File tab - Experiment file display area

▶

User can press the icon of a certain experiment file or file folder in the experiment file display

area to open it.

Summary of Contents for Gentier 48E

Page 1: ...I Gentier Real Time PCR System Gentier Real Time PCR System User Manual Xi an TianLong Science and Technology Co LTD Bring Technology to Life ...

Page 2: ...anical nor electronic nor translated into any other languages without the express written permission of XATL Co Ltd Every effort has been made to ensure that all the information contained in this manual is correct at the time of publishing However XATL Co Ltd reserves the right to make any changes necessary The contents of this manual are subject to change without prior notice at any time and the ...

Page 3: ...g fluorescent dyes or labeled probes and converts them to comparative quantitative readouts of DNA or reverse transcribed RNA Special Declaration Before installing and operating the Gentier instrument please read this manual carefully observe the warnings and non recommended functions Also bear mind the potential scope for misuse it is advisable to draw attention to the possible consequences User ...

Page 4: ...s it is prohibited to stack more than 4 layers for the storage and transportation of packages Recycle indicates the packaging materials are recyclable Safty Labels on Gentier Instruemt Label Description Biohazard indicates that a certain area of the Gentier instrument can be easily contaminated with biological reagents or samples Reminding user to timely disinfect this area keep necessary precauti...

Page 5: ...s Serial Number indicates the serial number of this instrument Manufacturer indicates the manufacture of this instrument Caution indicates the caution of this instrument Manufacture Date indicates the manufacture date of this instrument Consult Instructions for Use indicates the consult instructions for the use of this instrument Separate Collection for this Equipment indicates that this instrumen...

Page 6: ...it may results in instrument damage or abnormal function even constitutes a personal injury hazard Conventions Used in User Manual Convention Meaning Ordered list Procedure steps must be performed follow the list order Double Click A Click A on the application software Click A B Click B in menu A on the application software Press A Press A key on the instrument system sofware Italic Bold Refers to...

Page 7: ...y damage even personal injury Reminding please pay attention to the descriptions with Caution Reminding Prohibit symbols and the safety labels on the instrument and transport package I General Instrument Safeties and Precautions Caution no person except the XATL Co LTD professional engineers are allowed to open the instrument to replace any component or to debug the Gentier instrument Caution do n...

Page 8: ...y touch the sample block and the hot lid while the instrument is still running they may generate enough heat to cause serious burns Please wait the sample block to return to idle temperature before opening the top lid III Electrical Safeties and Precautions Prohibit the voltage of Gentier instrument can cause harms to human body please cut off the power supply before opening the instrument shell a...

Page 9: ...roper fuse tube may lead to circuit system damage Please check and make sure that the fuse tube has been properly installed before switch on the instrument Caution before replacing the fuse tube please cut off the instrument power supply unplug the power plug and use a screwdriver to pry open the fuse box Then substitute the old fuse tube with an equal one IV Environmental Safeties and Precautions...

Page 10: ...area with appropriate detergent to avoid the spreading of contaminant prevent the laboratory or instrument from biohazards Biohazard please comply with the local or national applicable regulations to complete the disposal of waste samples and contaminated materials Biohazard user should consider the abandoned Gentier instrument as biological contaminated material and comply with the local or natio...

Page 11: ...cters 5 3 2 Software Characters 5 3 3 Reagent Specifications 6 3 4 Consumable Specifications 6 B GENTIER INSTRUMENT INSTALLATION 7 1 UNPACKING INSTRUCTIONS 7 1 1 Unpacking Steps 7 2 WORKING ENVIRONMENTAL REQUIREMENTS 9 2 1 Instrument Space Requirements 9 2 2 Instrument Power Requirements 9 3 INSTRUMENT INSTALLATION 10 3 1 External Device Connection 10 3 2 Application Software Installation 10 3 3 C...

Page 12: ...TWARE OPERATION 89 1 BOOT SCREEN MAIN MENU INTERFACE 89 2 INSTRUMENT SOFTWARE OPERATION AREA 91 2 1 Experiment File 91 2 2 Run Setting 94 2 2 1 Temperature Setting 95 2 2 2 Fluorescence Setting 105 2 3 Run Monitoring 106 2 4 Result Anlysis 109 2 5 General Setting 111 2 5 1 Instrument Sub tab 111 2 5 2 Configuration Sub tab 113 2 5 3 Service Sub tab 115 F INSTRUMENT CLEANING AND MAINTENANCE 116 1 I...

Page 13: ...r Flow 118 2 2 Maintain Stable Power Supply 118 2 3 Maintain Instrument Cleanliness 118 2 4 Replace Fuse Tube 119 3 TRANSPORTATION OR RETURN TO FACTORY 119 3 1 Instrument Disinfection 119 3 2 Product Packaging 120 4 TROUBLESHOOTING 122 G AFTER SALE SERVICE COMMITMENTS 124 1 WARRANTY SERVICE 124 2 RESPONSE TIME 125 3 CONTACT INFORMATION 125 ...

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Page 15: ... in fields of immunology molecular biology forensic science genetics archeology zoology phytology etc 2 Product Constitute and Instrument Structure 2 1 Product Constitute The Gentier real time PCR system is mainly consisted of control system power system temperature control system detection system man machine interface system and instrument shell etc Among them the temperature control system inclu...

Page 16: ...ent 4 Power air vent 5 Power socket 6 Fuse tube box 7 Power switch 8 12 USB interface 9 Internet access 13 Hot lid 14 Sample block 15 Touch screen 3 Product Introduction 3 1 Instrument Parameters and Characters 3 1 1 Instrument General Parameters Instrument Specification Dimension 400mm L x 260mm W x 260mm H Weight 11kg ...

Page 17: ...10 C 30 C Relative humidity 20 85 non condensing Atmospheric pressure 85 0kPa 106 0 kPa Altitude below 2000m Storage and Transportation Enviroment Temperature 20 C 55 C with transport package Relative humidity less than 93 Running Noise While the instrument is running the maximum noise does not exceed 65 decibel 3 1 2 Instrument Technical Parameters Thermal Parameters Temperature Accuracy 0 1 C Te...

Page 18: ... Touch Screen with built in 7 0 inches full color touch screen providing more simple operation The instrument can run alone without the control computer The stand alone running saves more space and energy Main Control Computer the recommend configurations of main control computer are listed as below customs are allowed to purchase by themselves CPU 2 4GHz dicaryon Internal Storage 2G Hard Disk 500...

Page 19: ...tly from the computer Independent Temperature Control Gentier instrument adopts independent temperature control technology and high repeatability temperature zone Truly realize the optimization of PCR Power off Protection Gentier instrument possesses instantaneous power off protection function which can protect all configuration settings in case of power off and the interrupted experiment can cont...

Page 20: ...torage Gentier instrument can store over 1000 experiment setting experiment data files Program Setting each Stage can contain 99 steps and the maximum cycle number is 99 User can set the program for low temperature long term preservation after the experiment Report Template Design the unique universal report function is designed by XATL Co LTD for user to customize their own report form more suita...

Page 21: ...ag and well supported by protective foams Figure B 1 Package Details 1 1 Unpacking Steps The unpacking of the Gentier transport package mainly includes 4 steps as shown in figure B 2 The specific operation method is as follow 1st Step cut off the packing belt and unseal the transpot package 2nd Step take out the instrument accessories and remove the protective foam on top of the instrument 3rd Ste...

Page 22: ...present and intact report any missing items to XATL Co LTD Reminding please fill in the relevant content on installation information feedback table after acceptance and send it back to our company for document and warranty Caution please reserve the original packing materials for future use The transport package of Gentier instrument is designed to reduce the instrument damage and ensure its trans...

Page 23: ...y wave electrical equipment 5 For single Gentier instrument running the distance between adjacent objects and the surrounding ventilation openings shall be no less than 30cm 6 For protection against overheating hazards the openings on the Gentier instrument are designed for ventilation Please do not block or cover these ventilation openings while it is running 7 Do not place the Gentier instrument...

Page 24: ...vicinity of the instrument Caution do not put anything on the power cord and keep it away from places where people move around Hold the power plug when you plug the power cord and make sure the power plug is perfectly inserted into the socket do not pull the power cord to pull out the plug Reminding under normal circumstances please use the instrument attached power cord If the original power cord...

Page 25: ...the identifiable Gentier instruments within LAN 1st step please first check the network information of Gentier instrument which is displayed on the network information window of the instrument software as shownin figure B 3a For detiled operation please refer to E 2 4 Gental Settings 2 4 2 Configuration Sub tab Network Information 2nd step please open the Contol Panel Network and Sharing Center Lo...

Page 26: ...e Gentier instrument subnet mask Default gateway the control computer deault gateway should be identical to the Gentier instrument deault gateway 4th step click OK to confirm the control computer network setting 5th step after the control computer network setting user can connect the identifiable Gentier instruments within LAN for detailed operations please refer to D 3 1 Menu Bar Tool T submenu I...

Page 27: ...on before power on the Gentier instrument please ensure The external devices of the Gentier instrument are properly connected The power supply of Gentier instrument is properly connected Caution in case the Gentier instrument fails to pass the self inspection do not slap or shake it please contact the distributor or XATL Co LTD 2 Reagent Preparation 1st Step please follow the operation instruction...

Page 28: ...description in this user manual the instrument and software interface figures presented herein are all based on Gentier 48E instrument model For different Gentier instrument models the software interface will display the corresponding features and instrument model names this user manual will specify the differences of software interfaces or functions 1 Startup Application Software After successful...

Page 29: ...p quick start bar on this interface as shown in figure D 2 Figure D 2 Startup interface of application software 2 Quick Start Bar The quick start bar of application software is as shown in figure D 2 1 At this interface user can login create new experiments open data file set default instrument view instrument information and conduct other operations ...

Page 30: ...e in the drop down menu and then click Login to log in as the current user account as shown in figure D 2 1a Reminding the application software provides two user names by default user and admin Figure D 2 1a Quick start bar Login Register New User Account user can click Switch User and select Add User option in the drop down menu of User Name input box then the application software will automatica...

Page 31: ...riment with the logged in user account name and experiment creation time Reminding the experiment name can consist of numbers letters horizontal lines underlines or Chinese characters but cannot contain special characters Click New Experiment from Existed Experiment and the application software will automatically pop up the choose experiment file window user can choose an pre existed experiment fi...

Page 32: ...e application software again after setting the default instrument the application software will automatically connect the default instrument and display its status User can check the Display at Startup check box to decide whether to open the quick start bar automatically when starting the application software User can click the icon on the upper left corner of quick start bar to close the quick st...

Page 33: ...ription 1 New Experiment N create a new experiment 2 New Experiment from Existed Experiment user can select a saved experiment file and create a new experiment file with same experiment settings as the selected experiment file 3 New Experiment from PANA Gentier insturment can be connected with PANA nucleic acid workstation and the Gentier application software can establish experiment according to ...

Page 34: ... and manage the experiment report information after the experiment 12 Exit exit and close the application software View V submenu includes three options Options and Functional Description 1 Quick Start open the Quick Start bar For detailed functions refer to D 2 Quick Start Bar 2 Show Toolbar user can decide whether to Show Toolbar on the main interface of application software For detailed functio...

Page 35: ...d instrument which is Ready or Running Tool T submenu include three options Options and Functional Description 1 Instrument Management Click Instrument Management option in Tool submenu and the application software will automatically pop up the instrument management interface which consists of these parts Instrument List Details tab and File Transmission tab as shown in figure D 3 2 User can manag...

Page 36: ...ument List User can double click a certain instruemnt IP address in the Instrument List and the selected IP address will be displayed in the IP Address input box on the right click Test and the application software will test the selected IP address if the test passes the selected instrument can be connected then click OK to add the current instrument If user already know the IP address of a certai...

Page 37: ...ment Information Area display the relevant information of instrument selected in the Instrument List such as Name IP Address Model Serial No and Version No of instrument components etc Computer information Area display the IP address list of the Connected Computer within LAN Reminding the IP address of the Connected Computer should be set according to the default IP address of Gentier instruemnt R...

Page 38: ...Local Directory the Local File list will display all experiment files and data files in this directory c Instrument File display all experiment files and data files saved in the connected instrument Click to download the selected Local File to the connected instrument Click to upload the selected Instrument File to the control computer and save in the Local Directory selected by user Click Refresh...

Page 39: ...n input the salt concentration value in Salt Concentration input box by using the keyboard or keys User can click Calculate and the application software will automatically calculate Fwd Primer Tm value Rev Primer Tm value Avg Tm value and Annealing Temperature 3 Research Report Click Research Report option in Tool submenu and the application software will automatically pop up the research report i...

Page 40: ...he report information selection bar Update Report user can click Update Report to refresh the information in the research report Save Research Report after editing the research report please click Save icon to choose a path for saving the research report and choose a file format from the drop down list after the icon to save the research report as a PDF or html file Print Research Report After edi...

Page 41: ...ure D 3 5a Option submenu Configuration Management interface Default Path tab Interface Introduction and Functional Description Default Path tab the configuration management interface dispalys the Default Path tab by default as shown in figure D 3 5a User can set the default path for saving run parameter template sample parameter template and other experiment files in Default Path tab User can man...

Page 42: ...defined standard temperature templates are displayed in this tab as shown in figure D 3 5b These templates are provided by the application software for temperature program stage settings Figure D 3 6 Configuration Management interface Standard Temperature Template tab User can modify the predefined Standard Temperature Template in this tab change the correnponding stage and step settings For detai...

Page 43: ...leic acid workstation to be connected Finally click test to check whether the PANA instrument can be connected as shown in figure D 3 5c Figure D 3 5c Configuration Management interface PANA tab 2 User click User option in the Option submenu and the application software will automatically pop up the user interface as shown in figure D 3 6a Figure D 3 6a User interface User Management tab ...

Page 44: ...y check relevant Permissions check box in the Permit column Admin user can click Save to save the current general user permission settings b If user login as general user account user can view the general user permissions in this tab 3 Choose Language click Choose Language option in the Option submenu and the application software provide two optional sofware languages Chinese check Chinese option ...

Page 45: ...iment from Existed Experiment user can select an existed experiment file and create a new experiment file with same experiment setting as the selected experiment file Open Data File open a data file for viewing or analyzing Save Experiment the experiment file is saved to the default file path set in configuration management interface Close Experiment close an opened experiment file Export after ex...

Page 46: ... be activated as shown in figure D 4 Figure D 4 Operation area on main interface 1 The experiment file created or opened will be displayed in the experiment file tab at the bottom of operation area and user can select or close any experiment file in this tab Reminding if several experiment files are created or opened at the same time user can click and icon on the right side of the experiment file...

Page 47: ...dditional function icons will be shown in the tool bar on the sample setting interface Choose Sample Parameter Template click this icon in the tool bar and the application software will automatically pop up choose sample parameter template window user can choose a saved sample parameter template andset current experiment based on this template Save Sample Parameter Template click this icon in tool...

Page 48: ...ting The operation area on main interface displays Run Setting tab by default as shown in figure D 5 Figure D 5 Run Setting interface Run Setting The Run Setting interface consists five parts temperature program area stage and step lists experiment and step editing areas 1 Temperature program area user can view the temperature program of the current experiment or edit the temperature program stage...

Page 49: ... is show below the solid blue line The solid blue line between two stages steps represents the temperature ramp or increment or readings of melting step If user decide to read the fluorescence at a certain step icon will be displayed in the corresponding step box Reminding user can hover mouse over the temperature and time of a certain step in the temperature program area and the application softw...

Page 50: ...id user can enter the hot lid temperature for current experiment in the Hot Lid input box User can also check the Open check box to determine whether to use the hot lid heating function Reminding the hot lid temperature setting the range is 40 0 C 110 0 C 3 Stage list as shown in figure D 5 3 Figure D 5 3 Stage list Stage List Introduction Stage display the number of each stage Stage Type display ...

Page 51: ...ge User can click Delete icon to delete the selected stage User can click Up icon to move up the selected stage User can click Down icon to move down the selected stage Reminding User can also click icon in the dotted box of temperature program area or click Insert Stage icon below any stage box to add a new stage Reminding User can also click Delete Stage below any stage box in the temperature pr...

Page 52: ...ge please click Close to return to the run setting interface The new stage will be added to the temperature program area and stage list Reminding at least one stage should be included in the temperature program 4 Step list as shown in figure D 5 5 Figure D 5 5 Step list Step List Introduction Step display the number of each step Temperature display the target temperature of the current step Time d...

Page 53: ...e selected step as shown in figure D 5 6a Figure D 5 6a Step Setting dialog box Standard step mode Introduction to Step Setting Dialog box Step Mode user can set the step mode for the selected step in the drop down list of Step Mode which including Standard Touchdown Long and Gradient Model Step Mode Gentier 48E Gentier 48S Gentier 48R Standard Touchdown Long Gradient I Standard Step Mode user can...

Page 54: ...ange C per second User can use and keys or manually enter the temperature change rate in the Ramp input box Reminding the ramp setting range is 0 1 C s 8 C s II Touchdown Step Mode the touchdown step mode allows the temperature program to change the annealing step temperature from the initial temperature to the target temperature as the cycling proceeds User could set the corresponding parameters ...

Page 55: ...g Dialog Box Long Step Mode Initial Time the initial value of the elongation time change range Target Time the target value of the elongation time change range Delta Time the time change per cycle Start Cycle the cycle number after which the time change is started Reminding the initial initial and target time setting range is 1s 60min Reminding the delta time setting range is 1s 10min Reminding th...

Page 56: ... of Gentier 48S instrument model Reminding the temperature center setting range is 35 5 C 99 5 C Reminding the temperature offset setting range is 0 5 C 20 0 C Details User can click Details to the specific gradient temperatures of each column and the Gradient distribution as shown in figure D 5 6e Figure D 5 6e Step Setting Dialog Box Gradient Temperature Details ...

Page 57: ... increment in the Increment input box Reminding the temperature increment setting range is 0 1 C 5 0 C VI Continuous Melting continuous melting stage allows the system to read the fluorescence more frequently If the current step is the last step of continuous melting stage user can set the fluorescence reading times per C for the current step in the Step Setting dialog box as shown in figure 5 6g ...

Page 58: ...g area as shown in figure D 6 Figure D 6 Sample Setting interface Sample Setting Operation 1 Sample Setting Area After entering the sample setting interface user shall first choose a sample well in the sample setting area as shown in figure D 6 1 The well distribution in sample setting area corresponds to the sample block well distribution in loading platform There are 48sample wells in total arra...

Page 59: ...nd click corresponding column number to select multiple discontinuous columns of wells Press Ctrl key on computer keyboard and click corresponding row number to select multiple discontinuous rows of wells Click the left mouse button and drag the mouse in sample setting area to select multiple continuous wells Click the left mouse button and drag the mouse on the column number to select multiple co...

Page 60: ...ox to select a data analysis color for all samples with the current sample name b Sample Type user can set the relevant sample type for the selected wells from the Sample Type drop down list The optional sample types and their corresponding colors in sample setting area are Unknown Standard Positive Negative NTC NRC and Control c Dye user can check the relevant dye check box to determine the detec...

Page 61: ...ndard Conc user can select a single standard sample and enter its standard concentration in Standard Conc input box c Conc Unit user can select a single standard sample and set its concentration unit from Conc Unit drop down list The application software provides two default concentration units IU ml and Copies ml d After editing the standard concentration and concentration unit for the selected s...

Page 62: ...eries of diluted standard samples from Dye drop down list User can select the number of standard samples from Replicate drop down list User can select the auto concentration setting direction from Direction drop down list Horizontal from left to right and Vertical from up to down User can click OK and the application software will conform to the auto concentration setting direction calculate and d...

Page 63: ...licate group number setting c The application software can automatically divide multiple replicate groups according to user requirements Please first select all wells of same samples in the sample setting area and click Auto Setting then the auto setting dialog box will pop up automatically as shown in figure D 6 6 Figure D 6 6 Sample Setting interface Auto Setting User can select the number of sa...

Page 64: ...l in the sample setting area and set the unique ID for the selected well in the Unique ID input box click Apply to confirm the unique ID User can also select multiple wells in the sample setting area and let the application software to set the corresponding unique IDs Please enter the starting ID number in the Unique ID input box and click Apply the choose direction dialog box will pop up user cou...

Page 65: ...ick Default to clear all QC failure condition settings Clear Selected Wells user can click icon to clear the relevant property settings for all selected wells 3 3 3 Run Monitoring After finishing the experiment run setting and sample setting user can click Run Monitoring tab to enter the run monitoring interface in order to start running the experiment and monitor the experiment running process as...

Page 66: ...Setting Run Info by default Reminding user can select the functional module displayed on the run monitoring interface from the drop down list on the top right corner of each area Reminding user can click the Full Screen icon on the top right corner of each area to display the current functional module of the area in full screen Reminding user can click Run key in the Run Info functional module to ...

Page 67: ...agram Please click Y axis Coordinate Adjustment icon and the coordinate range setting box will pop up automatically as shown in figure D 7 1a User can select Automatic or Manual option in the coordinate range setting box to set the Y axis coordinate If the Automatic option is selected the application software will automatically adjust the Y axis coordinate according to the detected fluorescence va...

Page 68: ...oring interface Temperature Program function module Parameter introduction same with the parameters introduced in D 3 3 1 Run Setting Temperature program area Function key introduction user can click Export icon to export the temperature program monitoring diagram of the current experiment 3 Sample Setting display the sample well setting of the current running experiment as shown in figure D 7 3 F...

Page 69: ...nce and Sample Info function modules 4 Run Info display the current instrument information and the real time running status such as the Stage Step Cycle and Remaining Time of of the current experiment as shown in figure D 7 4 Figure D 7 4 Run Monitoring interface Run Info function module Function key introduction User can click Run key to run the current experiment User can click Stop key to stop ...

Page 70: ... running experiment as shown in figure D 7 6 Figure D 7 6 Run Monitoring interface Heat Map function module 3 3 4 Analysis After experiment running user can click the Analysis tab to enter the analysis interface According to the experiment settings and requirements user shall first select the suitable data analysis method for the current experiment on this interface ...

Page 71: ...alyzed Analysis Method shown the current anlysis method for the current step stage User can choose the relevant data analysis method and click OK to confirm 3 3 4 1 Abs Quant The absolute quantification experiment is intended to quantify the amount of an interest nucleic acid Samples with unknown initial nucleic acid quantities are amplified as well as a dilution series of gene specific standard s...

Page 72: ...rve Standard Curve Sample Setting Result Table by default as shown in figure D 9 Reminding user can select the functional module displayed on the analysis interface from the drop down list on the top right corner of each area Reminding user can click the Full Screen icon on the top right corner of each area to display the current functional module in full screen Figure D 9 Absolute quantification ...

Page 73: ...ene Color Y axis Coordinate Adjustment user can adjust the Y axis coordinate of the amplification curve diagram Please click Y axis Coordinate Adjustment icon and the coordinate range setting box will pop up automatically as shown in figure D 9 1a User can select Automatic or Manual option in the coordinate range setting box to set the Y axis coordinate If the Automatic option is selected the appl...

Page 74: ...ver the mouse over a certain amplification curve the curve will be highlighted and its corresponding channel and well coordinate will be displayed on the right of cursor II Standard Curve displays the threshold Ct value against the initial nucleic acid quantity of each standard sample as shown in figure D 9 2 For absolute quantification the standard curve is used to assign initial nucleic acid qua...

Page 75: ...plification efficiency of standard curve R 2 display the linear regression coefficient square value of standard curve Y axis intercept display the Y axis intercept of standard curve Function key introduction Load Std Curve click Load Std Curve and the application software will automatically pop up the standard curve window which consists of Import Standard Curve Select Standard Curve and Standard ...

Page 76: ... Curve user can click Clear Std Curve to clear the standard curve displayed on the Standard Curve functional module Save Std Curve user can click Save Std Curve and enter a name in the enter name dialog box for the standard curve file to save click OK to confirm as shown in figure D 9 2b Figure D 9 2b Abs Quant analysis interface Enter Name dialog box Export File user can click Export File to expo...

Page 77: ... Result sub tab is selected by default on the result table functional module which display the sample details and results of the current experiment as shown in figure D 9 4a Figure D 9 4a Result Table functional module Result sub tab User can double click the title of each column to sort all sample results according to the content in this column User can click the title of each column and drag the...

Page 78: ... V Raw Curve display the diagram of raw amplification curve without subtract baseline as shown in figure D 9 5 The parameters and function keys of raw curve functional module are same with those of amplification curve functional module Figure D 9 5 Abs Quant analysis interface Raw Curve functional module VI Raw Fluorescence display the raw fluorescence data map of the current experiment as shown i...

Page 79: ... wells Function key introduction User can slide the Cycle slider at the bottom of raw fluorescence functional module to view the raw fluorescence value of different wells at different cycles Y axis Coordinate Adjustment and Export keys are same with those of amplification curve functional module VII Heat Map display the Ct Concentration Fluorescence heat map and QC diagram of the current experimen...

Page 80: ...ndition set on the Sample Setting interface then the relevant sample well will be displayed as N A on QC diagram Abs Quant Analysis Setting User can click the Analysis Setting icon in the Tool Bar and the application software will automatically pop up the analysis setting window which is composed of Amplification Plot and Gene and Sample two tabs User can set corresponding parameters for the curre...

Page 81: ...art Cycle and End Cycle for All Selected Rows on top of the Baseline list User can click Restore on the top right corner of Baseline list to restore the Start Cycle and End Cycle of the automatic baseline setting b Reference Dye If user had set the reference dye in the Sample Setting tab according to the experiment requirements user can check the analysis mode check box of Reference Dye e to analy...

Page 82: ...ng dye a User can check a certain check box in the Remove column and click OK to remove the experiment data of the selected target gene and its marking dye b Click Cancel to cancel opertaion and return to the absolute quantification analysis interface Sample display all the sample name of sample setting a User can check a certain check box in the Remove column and click OK to remove the experiment...

Page 83: ...ace consists of eight functional modules Amplification Curve Bar Chart Sample Setting Result Table Standard Curve Raw Curve Raw Fluorescence and Heat Map This interface is divided into four areas and the application software displays four functional modules Amplification Curve Bar Chart Sample Setting Result Table by default as shown in figure D 11 Figure D 11 Relative quantification analysis inte...

Page 84: ...axis shows the Relative Quantity ratio of the compared gene and sample Reminding the application software set the relative quantity ratio of the reference sample to 1 by default Function key introduction The introduction of Y axis Coordinate Adjustment and Export keys are same with those keys introduced in D 3 3 4 1 Abs Quant Amplification Curve Display Setting user can click Display Setting icon ...

Page 85: ...e and reference gene if user select Gene Expression option the Bar Chart functional module will display the relative quantity ratio of target gene sample and reference gene sample d Sort User can use and keys to set the display sort order of Bar Chart functional module including Sample Dye or Gene Rel Quant Analysis Setting After entering the relative quantification analysis interface the applicat...

Page 86: ...t experiment b User can check a certain check box in Remove column and click OK to remove the experiment data of corresponding dye labeled genes from the Analysis interface c User can click a certain Efficiency column use and keys to set the amplification efficiency of the corresponding dye labeled gene Reminding if a standard curve has obtained for the current experiment the application software ...

Page 87: ...including specific and non specific PCR products which means that the presence of primer dimers and other non specific products can affect the quality of real time PCR data Melting curve show that the melting degree of dsDNA varies with the rising temperature Different dsDNA has different melting temperature Tm the temperature at which 50 of the DNA has dissociated from double stramded to single s...

Page 88: ... same with those introduced in D 3 3 4 1 Abs Quant I Melting Curve display the fluorescence intensity against the temperature as shown in figure D 13 1 Figure D 13 1 Melting Curve analysis interface Melting Curve functional module Parameter introduction X axis represents the temperature value Y axis represents the Relative Fluorescence Unit RFU Function key introduction User can select the melting...

Page 89: ...ected in the experiment Figure D 13 2 Melting Curve analysis interface Melting Peak functional module Parameter introduction X axis represents the temperature value Y axis represents the first negative derivative of the fluorescence intensity against the corresponding temperature User can select the melting peak display mode from the drop down list on the bottom left of Melting Peak functional mod...

Page 90: ...ysis setting window I Melt Curve tab display the parameter range of each peak area as shown in figure D 13 3 Figure D 13 3 Melting Curve Analysis Setting interface Melt Curve tab Dye display the settings of Dye and its marked Gene of the current experiment as shown in figure D 13 3 Peak Area display the melting peak area appearing with temperature rise User can use and keys to set the temperature ...

Page 91: ...veral times within one degree of temperature change to accurately detect the difference of melting temperature Therefore high resolution melting curve is often used for single nucleotide polymorphism SNP analysis mutation scanning methylation research and genotyping etc The high resolution melting analysis interface consists of seven functional modules Melting Curve Normalized Melting Curve Differ...

Page 92: ... automatically determine normalized area of melting curve The two vertical sliders on the left are the Pre melting Range threshold lines which are used to specify the pre melting temperature range while two vertical sliders on the right are the Post melting Range threshold lines which are used to specify the post melting temperature range the single line at the bottom is the Pos Neg Threshold line...

Page 93: ...tails please refer to D 3 3 4 4 High Resolution Melting High Resolution Melting Analysis Setting Figure D 14 2 HRM analysis interface Normalized Melting Curve functional module III Difference Plot display the curve after subtracting the baseline group curve or after normalization and optionally or after temperature shift The appearance of the curve on Difference Plot functional module depends on t...

Page 94: ...elting Analysis Setting User can click the Analysis Setting icon in Tool Bar and the application software will automatically pop up the high resolution melting analysis setting window which consists of Dye and Gene Sample and High Resolution Melting three tabs User can set the relevant parameters for current analytical method in the high resolution melting analysis setting window I High Resolution...

Page 95: ...nge user can use and keys to set the pre melting temperature range of the normalization area of the melting curve b Post Melt Range user can use and keys to set the post melting temperature range of the normalization area of the melting curve Sensitivity used to set the discrimination sensitivity of melting curve Reminding by default the application software will automatically set the correspondin...

Page 96: ...oup gene for the Difference Plot functional module II Gene and Sample tab the introduction of relevant parameters and function keys is same with those introduced in D 3 3 4 1 Abs Quant Abs Quant Analysis Setting 3 3 4 5 Genotyping The Genotyping analysis adopts two sequence specific probes labeld with different dyes to identify the wild type and mutantion alleles respectively After running the exp...

Page 97: ...otyping analysis interface Interface Introduction and Parameter Description I Scatter Plot display the end point fluorescence distribution of two dyes as shown in figure 16 1 Figure D 16 1 Genotyping analysis interface Scatter Plot functional module ...

Page 98: ...ay the sample details of and result data of the current experiment as shown in figure 16 2 Figure D 16 2 Genotyping analysis interface Result Table functional module User can double click the title of each column to sort all sample results according to the content in this column User can click the title of each column and drag the column to the left or right to adjust the sequence of sample result...

Page 99: ...he genotyping analysis setting window I Genotyping tab user can set Analysis Mode Reference Dye Baseline and Gene Group Parameter in Genotyping tab as shown in figure D 17 Figure D 17 Genotyping Analysis Setting interface Genotyping tab Analysis Mode same with the introduction of D 3 3 4 1 Abs Quant Abs Quant Analysis Setting Amplification Curve tab Gene Group Parameter a Gene display the detectiv...

Page 100: ...Fluorescence The end point fluorescence analysis displays the final detection result based on the fluorescence intensities measured at the end point of amplification plateau phase The end point fluorescence analysis interface consists of seven functional modules Amplification Curve End Point Fluorescence Scatter Plot Sample Setting Result Table Raw Curve Raw Fluorescence and Heat Map The end point...

Page 101: ...fication plateau phase as shown in figure 18 1 Figure D 18 1 End Point Fluorescence analysis interface End Point Fluorescence Scatter Plot Parameter introduction X axis represents the sample well index of the current experiment samples Y axis represents the End Point Fluorescence EPF intensity Each point represents a sample different icons represent the negative or positive interpretation results ...

Page 102: ...rescence analysis setting window I End Point Fluorescence tab as shown in figure D 19 Figure D 19 End Point Fluorescence Analysis Setting interface End Point Fluorescence tab Analysis Mode same with the introduction of D 3 3 4 5 Genotyping Genotyping Analysis Setting Genotyping tab Analytical Method same with the introduction of D 3 3 4 5 Genotyping Genotyping Analysis Setting Genotyping tab II Ge...

Page 103: ...m will automatically conduct self inspection the touch sceen will light up and display instrument software boot screen After the self inspection the instrument software will enter the main interface which is consisted of status bar operation area and main function keys as shown in figure E 1 1 2 3 Figure E 1 Instrument software main interface Interface Introduction Parameter Descriptions 1 Status ...

Page 104: ...op Lid Open the top lid is open Error the instrument hardware or software error has occured cannot execute any operation System Time display the current system date and time 2 Operation Area includes Experiment File Run Setting Run Monitoring General Setting four tabs for more operation details please refer to E 2 Instument Software Operation Area 3 Main Function Keys Run Experiment start running ...

Page 105: ...ng General Setting four tabs User could perform relevant operations and set the corresponding contents according to the specific experimental requirements Experiment File display experiment files and provide the relevant experiment file operations Run Setting provide the experiment temperature and fluorescence setting operations Run Monitoring provide the real time running state of the experiment ...

Page 106: ...scriptions 1 Experiment File Displaying Area display the pre existed experiment files or file folders within the instrument system as shown in figure E 2 1 Figure E 2 1 Experiment File tab Experiment file display area User can press the icon of a certain experiment file or file folder in the experiment file display area to open it ...

Page 107: ... as shown in figure E 2 3 Figure E 2 3 Experiment File tab Experimental file action bar New create a new experiment file or file folder this key is inactivated when the instrument system is under Running status Press the icon there are three options in the drop down list New Folder create a new experiment file folder New Experiment create a new experiment file New Experiment from Selected Experime...

Page 108: ...SB device Import Experiment import the selected experiment file or file folder from the USB device to the instrument system Reminding If there are more than one USB devices connected to the current instrument after selecting the Export Experiment or the Import Experiment option the instrument software will automatically pop up USB device list for user to choose the proper USB device 2 2 Run Settin...

Page 109: ...rument software provides three tube type opetions for user including Clear White and Frosted User can press icon to select 2 Reaction Volume user can press or icons to set the reaction volume Reminding the reaction volume setting range is 0µL 100µL 3 Hot Lid user could press the check box of Hot Lid to decide whether to utilize the hot lid heating function and press or icons to edit the hot lid te...

Page 110: ...ther to read the fluorescence at the current temperature step Edit press icon in Edit column to edit the corresponding step Up move up the selected step Add add a new step Delete delete the selected step Down move down the selected step Temperature Program Setting Operation Step 1 Add stage User can press Add in the stage setting box and the instrument software will automatically pop up a stage ty...

Page 111: ...stage will be automatically displayed in the stage setting box and user can select any stage to delete or change its sequence User can select a certain stage and press its cycle number in the corresponding Cycle column the cycle edit box will pop up as shown in figure E 3 2 Figure E 3 2 Cycle edit box User could set the cycle number in the cycle edit box press OK to confirm the cycle setting or pr...

Page 112: ... up the step edit window as shown in figure E 3 3 Figure E 3 3 Temperature Setting sub tab Step Edit window Standard step mode Four Step Mode options are provided by the instrument software Standard Touchdown Gradient and Long User can select a certain step mode option by pressing the icon in front of it and the icon will turn blue 1 The Standard step mode option is selected by default User can pr...

Page 113: ... selected the step edit window will be shown as figure E 3 4 Figure E 3 4 Temperature Setting sub tab Step Edit window Touchdown step mode The touchdown step mode allows the temperature program to change the annealing step temperature from the initial temperature to the target temperature as the cycling proceeds User can press the input boxes of Initial Temp Target Temp Delta Temp and Start Cycle ...

Page 114: ...nge C per cycle Start Cycle the cycle number after which the temperature change is started Reminding the initial and target temperature setting range is 35 0 C 100 0 C Reminding the delta temperature setting range is 0 1 C 5 0 C Reminding the star cycle range is 1 max cycle number of the current stage Reminding the other parameter settings are same with the standard step mode 3 If the Long step mo...

Page 115: ...e elongation step temperature holding time from the initial time to the target time as the cycling proceeds User can press the input boxes of Initial Time Target Time Delta Time and Start Cycle to edit the corresponding parameters for the current long step as shown in figure E 3 5a Figure E 3 5a Step Edit window Long step parameter setting ...

Page 116: ...are same with the standard step mode 4 If the Gradient step mode option is selected the step edit window will be shown as figure E 3 6 Figure E 3 6 Temperature Setting sub tab Step Edit window Gradient step mode The gradient step mode allows the Gentier sample to adopt different temperatures After setting the temperature center value and the temperature offset value for the current gradient step t...

Page 117: ...the other parameter settings are same with the standard step mode Reminding the Gentier 48S instrument model cannot support gradient PCR step mode 5 If the current step is the last step of a melting stage the step setting window of this step is as shown in figure E 3 7 Figure E 3 7 Step Edit window Melting step mode The melting stage allows the instrument system to read fluorescence signals after ...

Page 118: ...melting stage the step setting window of this step is as shown in figure E 3 8 Figure E 3 8 Step Edit window Continuous Melting step mode Continuous melting stage allows the instrument system to read fluorescence more frequently user can press the input boxes of Readings to set the fluorescence reading times per C for the current continuous melting step as shown in figure E 3 8a Readings the fluor...

Page 119: ...ce is as shown in figure E 3 9 Figure E 3 9 Run Setting Interface Fluorescence Setting sub tab User can set the fluorescence channel and dyes for the current experiment in the Fluorescence Setting sub tab User can check the corresponding check box in the Channel column to set the fluorescence channel for the current experiment 1 4 channels for Gentier 48E 48S and 1 2 channels for Gentier 48R ...

Page 120: ... running the current experiment the system will enter the run monitoring interface which is consisted of three parts run status bar run monitoring option bar and run monitoring diagram as shown in figure E 4 1 3 2 Figure E 4 System software Run Monitoring interface 1 Run Status Bar displays the real time running status of the the current experiment includes Remaining Time Stage Cycle and Step 2 Ru...

Page 121: ...curve Melting curve or fluorescence Heat Map of the current experiment as shown in figure E 4 1 a The run monitoring diagram will display the real time Amlificaiton curve of the current experiment by default as shown in figure E 4 1 Figure E 4 1 Run Monitoring Diagram Real time Amplification Curve X axis represents the cycle number Y axis represents the Relative Fluorescence Unit RFU User can pres...

Page 122: ...Unit RFU User can press any dye under the Fluorescence option in the run monitoring option bar and the run monitoring diagram will only display the corresponding real time melting curve c User can press key below the run monitoring diagram to monitor the fluorescence Heat Map of the current experiment as shown in figure E 4 3 Figure E 4 3 Run Monitoring Diagram Heat Map ...

Page 123: ... bar run monitoring diagram will display the temperature program of the current experiment as shown in figure E 4 4 Figure E 4 4 Run Monitoring Diagram Temperature program 2 4 Result Anlysis After the experiment user can click the Result Analysis tab to analysis the current experiment result The result analysis interface displays the fluorescence heat map of the current experiment by default User ...

Page 124: ... map User can press any well on the fluorescence heat map to check the amplification result of this sample as shown in figure E 5 2 Figure E 5 Run Monitoring Diagram Amplification result The amplification result interface displays the Amplification Curve Well and Ct valure information ...

Page 125: ... Configuration and Service three sub tabs 2 5 1 Instrument Sub tab The General Setting tab displays the Instrument sub tab by default as shown in figure E 6 1 Figure E 6 1 Instument software General Setting tab Instrument sub tab Introduction to Instrument sub tab Instrument Serial Number display the factory serial number of the current Gentier instrument Instrument Model display the current Genti...

Page 126: ...nspection information Alarm Information user can press Details to view the detailed alarm information occurred during the self inspection and experiment running Operation Log user can press Details to view all the operations have been executed on the current Gentier instrument Version User can press Details to view the system version information of the current Gentier instrument User can press Upg...

Page 127: ...current Gentier instrument User can press Edit and the instrument software will pop up the network information window as shown in figure E 6 2a Figure E 6 2a Configuration sub tab Network Information window In the IP Setting box user can view all the network IP addresses or press Edit to modify the corresponding parameter User can press Default to recover the default network IP settings of the cur...

Page 128: ...te time setting window User can press and icons to set the displayed year User can press and icons to set the displayed month User can set the displayed date on the calendar User can press and icons to set the displayed time including Hour Minute and Second In the Date Format setting box user can set the displayed date format in the Format drop down list user can also press 24 hour or 12 hour opti...

Page 129: ...ar all experiment files DebugLog user could connect an USB drive to the Gentier instrument and press press Get DebugLog to download all the log file of the current Gentier instrument this will help our professional engineer to get the relative information in case the instrument require maintenance Build No user could press Details to view the build number of the current instrument Debug Mode press...

Page 130: ...and volatile liquid it s exposure may irritate eyes skin and respiratory tract and may lead to central nervous system hypofunction and liver damage Please wear appropriate protective goggles clothing and gloves when using ethanol to clean High Temp the sample block and hot lid may produce high temperature during running do not clean the sample block until it reaches the room temperature Biohazard ...

Page 131: ...reen as malfunctions of the electronics or may occur Caution do not use abrasive detergent or rough material as they may scratch the touch screen 1 3 Clean Sample Block 1st step switch off the instrument and unplug the power cord 2nd step open the top lid and clean the sample block surface with a piece of damp soft cloth and if needed please rinse the cloth with mild commercial detergent 3rd step ...

Page 132: ...o less than the requirement of instrument 2 3 Maintain Instrument Cleanliness Contamination of sample block or optical parts can interfere with thermal cycling and data collection Avoid contaminating the Gentier instrument Always clean the outside surface of consumables before placing them in the sample block Clean the sample block periodically to prevent the buildup of dirt biohazardous materials...

Page 133: ...e screen after starting up the Genesy thermal cycler please check the fuse tube Caution improper fuse tube may lead to circuit system damage even fire 3 Transportation or Return to Factory 3 1 Instrument Disinfection In case the Gentier instrument will be moved to another lab or needed to return to the after sale service department for maintenance please first disinfection the instrument and fill ...

Page 134: ...designed to reduce the instrument damage and ensure its transportation safety Adopt other packaging materials will broke the warranty and XATL Co LTD will not be responsible for damages as consequences of improper packaging that incurred during the transportation back to maintenance department Reminding the transportation of Gentier instrument can adopt general transport with awnings The specific ...

Page 135: ...121 Gentier Real Time PCR System a b c d f e Figure F 4 The packing steps of Gentier instrument ...

Page 136: ...again or renew the power cord Inappropriate power voltage Adjust the scope of power voltage into a normal range Fuse tube damaged Replace the fuse tube Others Contact us 2 Boot screen display error message The activation of system failed Please contact us and consult the maintenance engineer Power voltage too low Ensure there is no other appliance or circuit in the same electric circuit 3 System c...

Page 137: ...hese failures by yourself please directly contact with our company Caution in case any of following situation occurs please immediately cut off the power supply and contract us We will arrange qualified maintenance personnel for processing Any liquid has entered into the instrument Abnormal sound or smell appears inside the instrument Instrument is soaked with water or rain Any housing damage caus...

Page 138: ...end the instrument back to the maintenance department assigned by our company User shall be responsible for the transportation fees and we will send back the well maintained instrument to the user for free 3 For post warranty service we will charge for the maintenance fee according to specific situation 4 The life span of Gentier instrument is about 5 years for any maintenance of the instrument th...

Page 139: ...ice within 7 days for the customs located in China 3 Contact Information Company Name Xi an TianLong Science and Technology Co LTD Company Address No 389 Zhuhong Road Xi an Shaanxi China Postcode 710018 Company Tel 400 606 1686 86 29 82218051 Company Fax 86 29 82216680 Email Address XATL medtl com Website Address www medtl com EU Representative Share Info Consultant Service LLC Repräsentanzbüro Ad...

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Tianlong Gentier 48E, User Manual

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