Taura Syndrome Virus (TSV) Real Time RT
Contents
1. Liferiver Revision No ZJ0004 Issue Date Jul 16 2012 Taura Syndrome Virus TSV Real Time RT PCR Kit User Manual For In Vitro Diagnostic Use Only YZ y 20 C 25 AR 0200 01 For use with LightCycler1 0 2 0 Instrument ash Shanghai ZJ Bio Tech Co Ltd www liferiver com cn Tel 86 21 34680596 trade liferiver com cn Fax 86 21 34680595 2 floor No 15 Building No 188 Xinjunhuan Road PuJiang Hi tech Park Shanghai China 1 Intended Use TSV real time RT PCR kit is used for the detection of Taura syndrome virus TSV in gill or muscle samples of Shrimp by real time PCR systems 2 Principle of Real Time PCR The principle of the real time detection is based on the fluorogenic 5 nuclease assay During the PCR reaction the DNA polymerase cleaves the probe at the 5 end and separates the reporter dye from the quencher dye only when the probe hybridizes to the target DNA This cleavage results in the fluorescent signal generated by the cleaved reporter dye which is monitored real time by the PCR detection system The PCR cycle at which an increase in the fluorescence signal is detected initially Ct is proportional to the amount of the specific PCR product Monitoring the fluorescence intensities during Real Time allows the detection of the accumulating product without having to re open the reaction tube after the amplification 3 Product Description The single stranded genomic RNA of Taura syndrome virus TSV is 10205 nuc2. and none as Noise Band method then adjust the Noise band just above the maximum level of molecular grade water and adjust the threshold just under the minimum of the positive control 11 Calibration for quantitative detection Input each concentration of standard controls at the end of run and a standard curve will be automatically formed 12 Quality control Negative control positive control internal control and QS curve must be performed correctly otherwise the sample results is invalid Molecular Grade Water Positive Controlqualitative assay 35 Sd y y 13 Data Analysis and Interpretation The following results are possible peepee AOcycles Result Analysis 2 lt 38 Positive and the software displays the quantitative value 38 40 25 35 Re test if it is still 38 40 report as 1 PCR Inhibition no diagnosis can be concluded For further questions or problems please contact our technical support at trade liferiver com cn
3. are available from various manufacturers You may use your own extraction systems or the commercial kit based on the yield For the RNA extraction please comply with the manufacturer s instructions The recommended extraction kit is as follows Nucleic Acid Isolation Kit Cat Number RNA Isolation Kit ME 0010 ME 0012 ZJ Biotech QIAamp Viral RNA Mini extraction Kit 50 52904 QIAGEN 9 2 Internal Control It is necessary to add internal control IC in the reaction mix Internal Control IC allows the user to determine and control the possibility of PCR inhibition Add the internal control IC 1ul rxn and the result will be shown in the 560nm 9 3 Quantitation The kit can be used for quantitative or qualitative real time RT PCR For performance of quantitative real time PCR standard dilution must be prepared first as follows Molecular Grade Water is used for dilution Dilution is not needed for performance of qualitative real time PCR Take positive control 1x10 copies ml as the starting high standard in the first tube Respectively pipette 36ul of Molecular Grade Water into next three tubes Do three dilutions as the following figures Dilution of Standards Aul 4ul Anl Y WY V Y 1X107 1X10 1X10 1X104 copiessmi To generate a standard curve on the real time system all four dilution standards should be used and defined as standards with specification of the corresponding concentrations Attention A Mix thoroughly before n
4. ext transfer B The positive control contains high concentration of the target DNA Therefore be careful during the dilution in order to avoid contamination 9 4 RT PCR Protocol The Master Mix volume for each reaction should be pipetted as follows 13l 1 pl Tul Super Mix Enzyme Mix Internal Control Sul 15l Extraction RNA Master Mix Reaction Plate Tube i PCR Instrument XPCR system without 560nm channel may be treated with 1ul Molecular Grade Water instead of 1ul IC 1 The volumes of Super Mix and Enzyme Mix per reaction multiply with the number of samples which includes the number of controls standards and sample prepared Molecular Grade Water is used as the negative control For reasons of unprecise pipetting always add an extra virtual sample Mix completely then spin down briefly in a centrifuge 2 Pipet 15ul Master Mix with micropipets of sterile filter tips to each of the Real time PCR reaction plate tubes Separately add 5ul RNA sample positive and negative controls to different reaction plate tubes Immediately close the plate tubes to avoid contamination 3 Spin down briefly in order to collect the Master Mix in the bottom of the reaction tubes 4 Perform the following protocol in the instrument 45 C for 10min Icycle Selection of fluorescence channels 95 C for 15min Icycle Target DNA or RNA 95 C for Ssec 60 C for 30sec Fluorescence measured at 60 C 10 Threshold setting Choose Arithmetic as back ground
5. leotides in length excluding the 3 poly A tail and contains two large open reading frames ORFs that are separated by an intergenic region of 207 nucleotides The ORFs are flanked by a 377 nucleotide 5 untranslated region UTR and a 226 nucleotide 3 UTR followed by a poly A tail While the severity of this bout of Taura Syndrome is somewhat atypical the shrimp farmer s experiences in coping with the disease underscore the devastating impact that illness can have on the larval and growout production of marine shrimp and the need for practical tools for disease management TSV real time RT PCR kit contains a specific ready to use system for the detection of TSV by Reverse Transcription Polymerase Chain Reaction RT PCR in the real time PCR system The reaction is done in one step real time RT PCR The first step is a reverse transcription RT during which the TSV RNA is transcribed into cDNA Afterwards a thermostable DNA polymerase is used to amplify the specific gene fragments by means of polymerase chain reaction PCR Fluorescence is emitted and measured by the real time systems optical unit during PCR The detection of amplified TSV cDNA fragment is performed in fluorimeter channel 530nm with the fluorescent quencher BHQ1 In addition the kit contains a system to identify possible PCR inhibition by measuring the 560nm fluorescence of the internal control IC An external positive control 1x10 copies ml contained allows the determinati
6. on of the gene load For further information please refer to section 9 3 Quantitation 4 Kit Contents TSV Super Mix 1 vial 350u1 RT PCR Enzyme Mix 1 vial 28ul Molecular Grade Water 1 vial 400u1 Internal Control 1 vial 30u1 TSV Positive Control 1x10 copies ml 1 vial 30ul Analysis sensitivity 5X 10 copies ml LOQ 1X 10 1 X 10 copies ml Note Analysis sensitivity depends on the sample volume elution volume nucleic acid extraction methods and other factors If you use the RNA extraction kits recommended the analysis sensitivity is the same as it declares However when the sample volume is dozens or even hundreds of times greater than elution volume by some concentrating method it can be much higher 5 Storage e All reagents should be stored at 20 C Storage at 4 C is not recommended e All reagents can be used until the expiration date indicated on the kit label e Repeated thawing and freezing gt 3x should be avoided as this may reduce the sensitivity of the assay e Cool all reagents during the working steps e Super Mix should be stored in the dark 6 Additionally Required Materials and Devices e Biological cabinet e Real time PCR system e Desktop microcentrifuge for eppendorf type tubes RCF max 16 000 x g e Vortex mixer e RNA extraction kit e Real time PCR reaction tubes plates e Cryo container e Pipets 0 5 ul 1000 ul e Sterile filter tips for micro pipets e Sterile microtubes e Disposable gloves powde
7. rless e Biohazard waste container e Refrigerator and freezer e Tube racks 7 N Warnings and Precaution Carefully read this instruction before starting the procedure e For in vitro diagnostic use only e This assay needs to be carried out by skilled personnel e Clinical samples should be regarded as potentially infectious materials and should be prepared in a laminar flow hood e This assay needs to be run according to Good Laboratory Practice e Do not use the kit after its expiration date e Avoid repeated thawing and freezing of the reagents this may reduce the sensitivity of the test e Once the reagents have been thawed vortex and centrifuge briefly the tubes before use e Prepare quickly the Reaction mix on ice or in the cooling block e Set up two separate working areas 1 Isolation of the RNA DNA and 2 Amplification detection of amplification products e Pipets vials and other working materials should not circulate among working units e Use always sterile pipette tips with filters e Wear separate coats and gloves in each area e Do not pipette by mouth Do not eat drink smoke in laboratory e Avoid aerosols 8 Sample Collection Storage and transport e Collected samples in sterile tubes e Specimens can be extracted immediately or frozen at 20 C to 80 C e Transportation of clinical specimens must comply with local regulations for the transport of etiologic agents 9 Procedure 9 1 RNA Extraction RNA extraction kits
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