TATA Motors CHECK ExpressPCR User Manual Download Page 10 | Manualshive

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Your ExpressPCR USB Drive contains software for
Windows, Mac OS X, and Linux operating systems.
Please open the software file matching your chosen
operating system. The latest version of the software
can also be downloaded from our website
www.tatamd.com

WINDOWS

Double-click    on  the
Windows installer and follow
the on-screen instructions
to install your ExpressPCR
software on Windows.

MAC OS X

Double-click  on the disk
image and follow the
on-screen instructions to
install your ExpressPCR
software on your Mac PC.

INSTALLING YOUR
EXPRESSPCR SOFTWARE

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Summary of Contents for CHECK ExpressPCR

Page 1: ...REAL TIME PCR MADE SIMPLE USER GUIDE...

Page 2: ...latform for smart molecular testing labs Novel Full Spectrum Optics deliver 120 optical channels of fluorescence data from every tube for exceptional multiplex PCR High performance Peltier elements co...

Page 3: ...ystem from setting it up on your workbench to configuring the instrument and installing the software TIPS Learn some useful tips when using your instrument EXPERIMENT Learn the basics of setting up an...

Page 4: ...NET CABLE 5 USB DRIVE Please keep the flight case and outer box the ExpressPCR system came in in case you need to protect your ExpressPCR system during storage or shipment in future Lid USB Port SETUP...

Page 5: ...es display LEDs to help you understand what the instrument is doing Here is a summary of these display LEDs Blue Initialising Green Idle Red Lid open Please close the lid Yellow Tubes loaded Blue Runn...

Page 6: ...three connections One in the front and two in back as shown below This is for connecting your ExpressPCR to your LAN or computer This is to connect your ExpressPCR system to the provided power supply...

Page 7: ...lab bench and then connect AC power to the power supply unit Your instrument will now turn on after a few seconds The display LEDs will light up blue and then turn green if a lid is closed or red if...

Page 8: ...8 EXPRESSPCR CONNECTION MODES 1 Direct network connection 3 USB drive connection 2 Local area network connection LAN...

Page 9: ...t hot Please do not touch it The heated lid will be preheated to 105 C if user activity is detected This enables your run to start as soon as possible After 5 minutes of inactivity the heated lid will...

Page 10: ...version of the software can also be downloaded from our website www tatamd com WINDOWS Double click on the Windows installer and follow the on screen instructions to install your ExpressPCR software o...

Page 11: ...ith your ExpressPCR software open and your ExpressPCR system connected to the network please connect to your ExpressPCR instrument from the software Please select Configuration CONFIGURING YOUR EXPRES...

Page 12: ...12 To add your new ExpressPCR System select the Add b utton You will now be presented with a list of available instruments Please select ExpressPCR...

Page 13: ...13 Double click on the instrument you wish to connect to or pr ess Select with the instrument selected The instrument will now be added to the list of Registered Instruments for use in the software...

Page 14: ...arm during operation this is completely normal SPIN YOUR TUBES This should ensure that all contents are at the bottom of the tubes and there are no bubbles present Reaction mixtures which are viscous...

Page 15: ...keep your work space clean including all lab equipment like surfaces pipettes and tube racks This will keep the instrument clean and help maintain good results KEEP YOUR INSTRUMENT CLEAN We recommend...

Page 16: ...ExpressPCR experiments You will learn how to create save open and close experiments You will also learn how to set up an experiment including thermal profile sample information and optical settings F...

Page 17: ...ll be displayed as shown below By default the experiment name will be N ew Experiment with a date and time stamp which can be edited The summary will give you information about the instrument you are...

Page 18: ...Type drop down menu gives you the option to open an experiment normally or as a template that can be used for a new run OPEN AN EXPERIMENT By selecting O pen y ou can open an experiment as shown belo...

Page 19: ...s and analyses to re run a previous experiment generating new data When an experiment file is opened as a template it has the same 1 Temperature profile 2 Optical settings 3 Samples and targets 4 Anal...

Page 20: ...hen starting a run you will be prompted with the window displayed below Make sure the first checkbox is selected and your experiments will be automatically saved To prevent the software from showing t...

Page 21: ...iment is saved you will be prompted to select a location and filename to use After this you can click Save to use the same location overwriting the previous version or Save As to choose a new location...

Page 22: ...nsion and optical data acquisition Typically optical data is acquired at the same temperature that strand extension occurs By default this time is set to 30s However this time can be reduced to a mini...

Page 23: ...as shown below PROGRAMS To add a program to your experiment click A dd i n the P rograms p ane Programs can be deleted by selecting them in the list then clicking D elete The program order can also be...

Page 24: ...ure Profile p ane in the order they are present in the P rograms window as shown below PROGRAM SETTINGS To alter the settings of a particular program you should first select it then refer to the right...

Page 25: ...imen being analysed e g Mouse 5 A molecular target e g x174 detected with a specified fluorescent reporter e g FAM Samples or targets do not need to be defined before starting a run They can be added...

Page 26: ...Assign wells by selecting them and clicking Set Samples can also be unassigned by selecting wells you wish to un assign and clicking Clear ASSIGNING TARGETS TO WELLS Targets can be assigned to wells a...

Page 27: ...t labels and a list of available dyes on the ExpressPCR system can be viewed below Factory Calibrated Dyes SYBR Green I ResoLight FAM VIC HEX Cy5 ROX LC Green SYTO 9 Cy5 5 Instrument Specific Calibrat...

Page 28: ...f you wish to save or open sample and target information setup you can select Save As or Open respectively CSV Editable csv files PSD A proprietary locked file format RDML The Real time PCR Data Marku...

Page 29: ...ATING DYES These dyes for example SYBR Green I Resolight Eva Green are bright reagents and require a shorter integration time SEQUENCE SPECIFIC PROBES These dyes for example FAM VIC and HEX are common...

Page 30: ...using a USB drive select Start Run Then when you are asked to choose an instrument select Start run from USB You will then be prompted to find the location of your USB drive Once selected press Save...

Page 31: ...he heated lid is balanced please make sure that the mount contains at least a strip in rows A and D as shown in blue below or single tubes in wells A1 A8 D1 and D8 These positions can be filled with t...

Page 32: ...s of template or relative expression levels of genes using Absolute Quantification or R elative Quantification GENOTYPING Use TaqMan probes or High Melting Resolution to perform SNP genotyping using A...

Page 33: ...lts with minimal user intervention Manual analysis types enable users to apply traditional analytical methods SELECT ANALYSIS TYPE Once your experiment has completed you can add an analysis type by se...

Page 34: ...urves AUTOMATIC QUANTIFICATION POSITIVE NEGATIVE CALLING The first step in amplification analysis is to determine which targets have produced a positive amplification curve and which amplifications ha...

Page 35: ...t this may be smaller for amplifications with a negative baseline drift PERFORMANCE Performance is a measure related to the observed efficiency of amplification at later cycles This value will tend to...

Page 36: ...e Graph Axes drop down menu All 3 thresholds are used for calling even if they are not currently displayed on the graph SETTINGS The software uses a combination of Quality Q Performance P and Intensit...

Page 37: ...g a run These are often observed during early cycles Filtering out these artefacts can improve the accuracy of amplification analysis Two settings enable you to control the process of filtering out su...

Page 38: ...osables Normalised amplifications are rescaled to a nominal value of 1 relative fluorescent unit with exact endpoint values a function of curve shape QUANTIFIERS If you have assigned standards with di...

Page 39: ...of the A uto Quant pane MULTIPLEXING The ExpressPCR supports multiplexing with a broad variety of dyes FOR BEST RESULTS Ensure using high quality well designed kits such as the Tata MD CHECK RT PCR r...

Page 40: ...t Genotyping Genotypes of samples are determined by the ratio of endpoint fluorescence between two TaqMan probes Thresholds for the fluorescence ratios are generated automatically as shown below A uto...

Page 41: ...of D ifference Normalized a nd M elt g raphs CLUSTERING The difference curves will then be converted into a clustering graph showing clusters of different genotypes GENOTYPES The software will automat...

Page 42: ...42 MELTING AUTOMATIC TM CALLING Add an Automatic Tm Calling analyses to identify and characterise melting peaks You can see the results below Tm values will be presented in the table...

Page 43: ...ines how big a peak should be before it is called Increasing this value will increase specificity of peak detection Decreasing this value will increase the sensitivity of peak detection PEAKS AND MELT...

Page 44: ...analysis To fuse multiple experiments together hold down cmd on a Mac or Ctrl on a PC and select the files you wish to fuse from the open dialog window as shown below Select Open and then from the nex...

Page 45: ...ltiple file locations you must select the first experiment and then select the from the top left of the open file dialogue window as shown below Now hold cmd Ctrl and select the next experiment Select...

Page 46: ...xpressPCR software you can export the results in a variety of ways from raw data to user defined custom reports This section will take you through the steps you need in order to do this From panes sho...

Page 47: ...Export button shown on the previous page Data can be exported in the following formats RDML EXPORT The software is able to export Cq values and amplification curves from Auto Quantification and melt c...

Page 48: ...eparated Variable CSV or Portable Document Format PDF PNG This is a bitmap image SVG A Scalable Vector Graphic is an XML vector based graphic that can be used where a high resolution scalable graph is...

Page 49: ...under the Experiment tab This provides you with the ability to choose which parts of the data to include in a report For example items such as thermal profiles sample information and various analysis...

Page 50: ...MAINTENANCE This section will help you take care of your ExpressPCR It covers the following areas 1 CLEANING 2 DISPOSABLES 3 ENVIRONMENTAL CONDITIONS 4 DISASSEMBLY 50...

Page 51: ...ated background subtraction processes mean that low levels of fluorescence contamination in the wells of your instrument will not affect system performance Dirty wells however can result in lower fluo...

Page 52: ...ust be sent with the instrument and we can not accept electronic versions of the form Failure to comply with these guidelines will result in a charge for decontamination A Physical dimensions should b...

Page 53: ...e placed on a surface that is flat dry and not subject to draughts Do not install your ExpressPCR instrument directly in the flow of air from an air conditioner or fan Do not install your ExpressPCR i...

Page 54: ...ill void all warranties ENVIRONMENTAL OPERATING CONDITIONS DISASSEMBLY ENVIRONMENTAL STORING TRANSPORTING PACKING CONDITIONS Humidity MAX 80 at 32 C MIN 30 at 15 to 32 C Humidity 10 to 95 No condensat...

Page 55: ...red on overnight All experiments can be used as a template Click Open and then using the file type selection in the file dialog to select the Template option then select the file to open as a template...

Page 56: ...based Auto Quant fits a model of a PCR amplification to the fluorescence data observed This model fit then enables the estimation of a number of important parameters including Cq values Correct backg...

Page 57: ...xpressPCR will let you know when something is wrong by displaying an error Most errors are reported as messages in the Status Bar in the ExpressPCR software Some errors are reported by the instrument...

Page 58: ...you may need to contact technical support with the following actions described below Saturation Warning Run Prepare Error followed by one of the following messages a No tubes loaded b Instrument has...

Page 59: ...rt code Please contact Technical Support May be reported at the start of a run Please check that your network is properly configured and is operating at 100Mb s or more Please check that your network...

Page 60: ...re Logs to File HARDWARE ERRORS For Hardware faults go to Configuration ExpressPCR and select Retrieve Instrument Report Files Once exported please make sure you send the error file the serial number...

Page 61: ...61 NOTES All trademarks are the property of their respective owners Design and specifications are subject to change without notice...

Page 62: ...www tatamd com Version 001 EN...

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