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N11471 ver 2.2 PikoReal Real-Time PCR System User Manual

1. Status indicator Blue po Red O Power button Thermo Backlit LCD display Arrow keys for moving on the display Cancel key Enter key Open Close drawer button OPEN PIKOREAL 96 Real Time PCR System Figure 2 4 PikoReal user interface Status indicator On the top left corner of the instrument user interface is a status indicator light that has the following states Table 2 1 Table 2 1 Status indicator Indicator Status Constant blue Instrument is on but not in use Upper light Blinking blue Instrument is on and in use Lower light Constant red System error For more information see Chapter 7 Troubleshooting Guide Power SU I The PikoReal Real Time PCR System is equipped with an external y y quipp 200 watt power supply A green light on the power supply indicates normal operation The power supply will get warm during normal operation supply will go off The power supply must be unplugged from the power outlet for 5 minutes to reset it Note If the internal circuit breaker trips the green light of the power Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 17 General Description PikoReal Software PikoReal Software Block formats Consumables Note Do not cover the power supply with anything as this will impede the ability of the power supply to efficiently dissipate heat The PikoReal is operated with the PikoReal Softwar
2. 14 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Thermo Fisher Scientific Instrument views Chapter 2 General Description This chapter describes the main parts of the PikoReal instrument The front view of the PikoReal instrument is shown in Figure 2 2 i ii A NES ae Ais en wall aa i EST J b Tete 4 k 2 ial Wc ps rf a oe l ee Gat ee Buc ys Ex Te s ee Loy SS me Poon Sept iii 5 EEEE ae a a Air inta ke Figure 2 2 PikoReal front view Thermo Scientific PikoReal Real Time PCR System User Manual 15 General Description Instrument views The rear view of the PikoReal instrument is shown in Figure 2 3 Air exhaust Type label Power connector T 9 a re i g D A ye Z irs Eae d paired it a Racers 5 ARY i EEA E a Yes a a oe NT A 7 Pree sal i etal E E mea Ei Te Figure 2 3 PikoReal rear view Caution Do not block the air intake or the air exhaust vents Figure 2 2 and Figure 2 3 Be careful not to place for example a piece of paper under the air intake Warning Do not place anything in front of the drawer Items may be knocked over when opening the drawer gt D 16 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific General Description PikoReal user interface Piko Real user The PikoReal user interface UI and its functions are shown in Fi 2 4 interface
3. CHECK THAT THE HEATSINK IS CLEAN CHECK LOGFILES CHECK LOGFILES CHECK LOGFILES CHECK LOGFILES Action text CHECK LOGFILES CONTACT SUPPORT CONTACT SUPPORT ENSURE THAT THE AIRFLOW TO THE FAN IS NOT OBSTRUCTED IF PROBLEM PERSIST CONTACT SUPPORT Thermo Fisher Scientific Thermo Fisher Scientific Cont Code E11 E12 E13 E14 E15 E17 E18 E21 E22 E31 E32 Symbolic name CALIB TABLE SINK TEMP LOW BLOCK TEMP LOW LID TEMP LOW BLOCK TEMP SHIFT LID TEMP SHIFT LID POS FAILURE BLOCK TEMP CHANGE LOG FILE CAMERA FAILURE RT UNIT FAILURE Description This error is set if any calibration values or the calibration derived from them is corrupt This error is set if the sink temperature is below 20 C This error is set if the block temperature is below 20 C This error is set if the lid temperature is below 20 C This error is set if the block temperature changes more than 10 C during a 500 ms interval This error is set if the lid temperature changes more than 20 C during a 500 ms interval This error is set if the lid encounters pressure too early In case of Piko 24 this makes it incompatible with doomed caps This error is set if the block is heated with more than a 6 A current for 5 sec and the change in the block temperature is not bigger than 1 C The log files have been corrupted and the log file memory has been cleared
4. Thermo Scientific PikoReal Real Time PCR System User Manual Rev 2 2 Cat no N11471 Copyright 2013 Copyright Thermo Fisher Scientific Inc First edition published in 2010 All rights reserved All trademarks are the sole property of Thermo Fisher Scientific Inc and its subsidiaries Reproduction of the accompanying user documentation in whole or in part is prohibited License and trademark information This product is covered by the following patents and patents pending EP1973664B1 JP5248503B2 and US20080061429A1 Notice Purchase of this instrument conveys a limited non transferable immunity from suit for the purchaser s own internal research and development and applied fields other than human in vitro diagnostics under Canadian Patent 1 339 653 owned by Applied Biosystems No right is conveyed expressly by implication or by estoppel under any other patent claim Further information on purchasing licenses may be obtained by contacting the Director of Licensing Applied Biosystems 850 Lincoln Centre Drive Foster City California 94404 USA Disclaimer Thermo Fisher Scientific reserves the right to change its products and services at any time to incorporate technological developments This manual is subject to change without prior notice as part of a continuous product development Although this manual has been prepared with every precaution to ensure accuracy Thermo Fisher Scientific assumes no liability for any errors or
5. 47 air 16 24 25 43 exhaust 16 flow 25 intake 16 allelic discrimination 11 application 2 5 11 12 13 14 18 automatic lid 12 B block 5 11 12 16 18 19 20 32 36 41 42 43 47 52 53 61 format 11 12 18 47 wells 41 43 C calibration 21 53 CCD camera 12 clock 34 35 37 communication ports 47 consumables 3 13 18 20 32 56 cycle 33 D data port 26 decontamination 41 42 43 44 45 46 61 Certificate of 45 61 procedure 41 42 43 44 45 46 61 diagnostics 2 34 35 36 37 display 29 33 34 35 36 37 47 disposal of instrument 46 disposal of materials 44 DNA analysis 13 drawer 16 36 44 45 54 dye calibration 21 Thermo Fisher Scientific E emission 48 environmental requirements 24 25 error 17 27 29 46 51 52 53 54 codes 27 51 52 messages 27 46 52 Ethernet connection 12 24 26 30 55 external power supply 2 12 17 18 24 25 26 44 47 51 55 F file 33 53 fluorescence 13 63 intensity 13 fluorogenic 13 folder 30 33 USB 30 G glossary 63 H heat 11 12 18 19 21 25 41 43 56 57 sink 11 12 25 41 43 heated lid 5 12 heating 29 47 51 54 how to clean the block wells 41 43 how to clean the heat sink 41 how to decontaminate the instrument 41 42 43 44 45 46 61 how to ensure startup 29 how to install the PikoReal 23 25 27 49 how to maintain the instrument 41
6. Piko PCR Plates Aluminum Support rack for 384 well plates and 96 well Piko PCR Plates Adhesive Seal Applicator Oty Thermo Scientific PikoReal Real Time PCR System User Manual Contact your local Thermo Fisher Scientific representative for ordering and service information Table 8 7 through Table 8 11 Table 8 7 Instrument catalog number 5 Ordering Information List of consumables List of consumables Code SPLO240 SPLO241 SPLO960 SPLO961 SFRO241 SFRO961 TCS1080 AB 0812 TUCO010 TUCO011 ASF0020 AB 0771 AB 0771 w AB 0866 58 Thermo Scientific PikoReal Real Time PCR System User Manual Table 8 9 Codes for consumables Item Thermo Scientific Piko PCR Plate 24 well clear Thermo Scientific Piko PCR Plate 24 well white Thermo Scientific Piko PCR Plate 96 well clear Thermo Scientific Piko PCR Plate 96 well white Thermo Scientific Piko 24 well PCR Plate Frame white Thermo Scientific Piko 96 well PCR Plate Frame white Thermo Scientific flat 8 cap strips for Piko PCR Plates optically clear Clear Seal Diamond Heat Sealing Film Thermo Scientific Piko UTW individual tubes clear tube clear cap Thermo Scientific Piko UTW individual tubes white tube clear cap Thermo Scientific sealing film Piko PCR Plate size Low Profile Thermo Strip clear 0 2 ml low profile thin walled 8 tube strips Low Profile Thermo Strip white 0 2 ml low profile thin walled 8 tube strips Ultra Cl
7. The PikoReal Real Time PCR System is fast fulfills high level requirements of temperature uniformity over the wells and creates significant savings in reagent plastic material and energy consumption The PikoReal Real Time PCR System uses Thermo Scientific UTW ultra thin wall microwell plates that are 1 4 of the size of conventional microwell plates The plates adhere to industry standards regarding well Thermo Scientific PikoReal Real Time PCR System User Manual 11 Introduction to the PikoReal Real Time PCR System Safety instructions spacing and sample capacity and are compatible with multichannel pipettes reagent dispensers and automated liquid handling systems The PikoReal 24 also utilizes standard low profile 8 well strips and 0 2 ml tubes The optical system comprises a charge coupled device CCD camera optical filters and an individual light emitting diode LED for each of the five channels The channel selection is built on a motorized linear shuttle that moves to five channel positions The PikoReal is controlled by PikoReal Software via an Ethernet connection with up to 5 connections or alternatively as a standalone instrument with USB memory stick loaded protocols The PikoReal Real Time PCR System has the following features e Compact design The PikoReal Real Time PCR System has a compact design giving a minimal footprint for personal bench top use and field applications e Unique thermal system
8. performing real time PCR based DNA analyses e PikoReal Real Time PCR System e PikoReal Software see PikoReal Software on page 18 e UTW consumables see Consumables on page 18 e qPCR reagents see Reagents on page 21 Introduction to Quantitative real time PCR qPCR is a method for analyzing DNA by q PCR detecting the amount of PCR product after each PCR cycle by the incorporation of fluorescent dyes into the reaction The amplification and detection of a specific DNA sequence is integrated into a simultaneous process within a single instrument The product accumulation is detected and measured throughout the reaction in real time The detection is based on monitoring fluorescent molecules that are incorporated into the amplified products as a dsDNA binding dye or within labeled target specific primers or probes The quantitation is based on correlation between the measured fluorescence intensity and the amount of DNA formed Collecting quantitative data of a known dilution series of the target DNA can be used to give insight into the PCR reaction kinetics and reaction efficiency The gene quantification analysis method can be absolute copy number concentration or relative to a known reference gene and calibrator sample Examples of qualitative analysis include gene identification and genotyping e g studying DNA sequence variations such as single nucleotide polymorphism The basic difference from end point
9. PikoReal Real PikoReal Time PCR System CD Cat no N12119 The CD also contains the instrument and software user manuals Software For installation instructions refer to the PikoReal Software User Manual Cat no N12076 Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 27 Installation Installing PikoReal Software 28 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Switching on Status indicator Thermo Fisher Scientific Upper light Lower light Chapter 4 Routine Operation The operation of the PikoReal Real Time PCR System is described below Before switching the instrument on check that all the cables are g properly fitted according to the installation instructions Note that when you plug the instrument into the mains it automatically starts If the instrument is plugged in and on standby mode switch the instrument on by pressing the POWER button After startup the instrument lid pre heats automatically After three hours inactivity the lid pre heating is turned off To the left side of the power button on the keypad are two indicator lights with the following indications Constant blue system is on and NOT in use Blinking blue system is on and in use Constant red system has recently experienced an error or warning Refer to Chapter 7 Troubleshooting Guide for more information Thermo Scientific PikoReal Rea
10. nm Emission range 666 740 nm Channel 5 Excitation range 475 500 nm Emission range 520 590 nm Safety This section describes the safety specifications for the PikoReal Real g Time PCR S specifications S In conformity with PikoReal Real Time PCR System bears the following markings the requirements Type 5100 CE mark 90 240 Vac 50 60 Hz EUT 24 VDC 8 33 A PSU 90 240 Vac 50 60 Hz 2 5 A or 4 A PikoReal Real Time PCR System conforms to the following requirements 2006 95 EC Low Voltage Directive 2004 108 EC Electromagnetic Compatibility Directive EMC 2002 96 EC WEEE Directive 50 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Thermo Fisher Scientific Technical Specifications Safety specifications The safety specifications are also met under the following environmental conditions in addition to or in excess of those stated in the operating conditions Altitude Up to 2000 m Temperature 5 C to 40 C Humidity Maximum relative humidity 80 for temperatures up to 31 C decreasing linearly to 50 relative humidity at 40 C Mains supply fluctuations 10 from nominal Installation category ll according to IEC 60664 1 see Note 1 overvoltage category Pollution degree 2 according to IEC 60664 1 see Note 2 Note 1 The installation category overvoltage category defines the level of transient overvoltage which the instrument is designed to withstand safe
11. omissions nor for any damages resulting from the application or use of this information This manual supersedes all previous editions Remark on screenshots and product images Screenshots and product images may differ from your system depending on the product and firmware versions No liability for consequential damages Thermo Fisher Scientific shall not be liable for any damages whatsoever arising out of the use or inability to use this product Power failure The system requires uninterrupted power supply in order to operate correctly Thermo Fisher Scientific has no responsibility whatsoever for system malfunctions arising from power failures Cat No N11471 October 2013 Manufacturer Thermo Fisher Scientific Oy Ratastie2 P O Box 100 FI 01621 FINLAND Intended users Firmware versions How to use this user manual Thermo Fisher Scientific For more information About This User Manual Intended users About This User Manual The Thermo Scientific PikoReal Real Time PCR System as a standalone instrument or with Thermo Scientific PikoReal Software can be used in research laboratories by professional personnel This user manual is applicable to PikoReal firmware version combination Piko 2 2 41 and RT 1 1 12 23 Firmware versions can be checked by selecting TOOLS in main menu and then selecting SYSTEM INFO If you are using instrument with older version of the firmware please refer to older version of th
12. single tubes you must use at least eight tubes that are placed symmetrically with at least one tube in each corner of the block You can use empty tubes to fill the above requirement when analyzing fewer samples Figure 2 7 Piko PCR plates Thermo Fisher Scientific Piko PCR plates strips and tubes utilize UTW ultra thin wall technology and are recommended to be used with PikoReal UTW reaction vessels were used in the optimization of the temperature algorithms of the instrument as well as in the validation of its performance Note For the highest signal to background ratio and elimination of possible well to well cross talk white plates strips and tubes are recommended Thermo Scientific PikoReal Real Time PCR System User Manual 19 General Description Consumables The UTW consumables are half the thickness lt 0 15mm of conventional PCR consumables and thus improve the thermal transfer between block and sample see Figure 2 8 and Figure 2 9 The uniform tube design allows repeatable and consistent results from well to well Figure 2 8 he tube wall thickness of UTW consumables marked as blue is half that of standard consumables marked as red Figure 2 9 he lower portion of the UTW reaction vessels is ultra thin For more information on the consumables refer to Chapter 8 Ordering Information and http www thermoscientific com pikoreal 20 Thermo Scientific PikoReal Real Time PCR System Use
13. soft cloth or tissue paper soaked in a mild detergent solution soap solution or 70 ethanol Wipe up spills immediately Do not use formaldehyde or strong alkalines 4 Clean the block wells with swabs moistened with water 95 ethanol or a 1 100 dilution of bleach in water Warning If you have spilt infectious agents on the block wells decontaminate the instrument Refer to Decontamination procedure on page 46 Inspect the fins of the heat sink on a regular basis Dirty heat sinks have a significantly lower capacity to eject heat Clean the fins if they become dirty or covered in dust Use a cotton swab a brush or compressed air or a vacuum device to remove dust Thermo Scientific PikoReal Real Time PCR System User Manual 45 Maintenance Disposal of materials Disposal of materials Decontamination procedure A Follow laboratory and country specific procedures for biohazardous or radioactive waste disposal Refer to local regulations for the disposal of infectious material Warning The samples can be potentially infectious Dispose of all used disposable UTW vessels strips and tubes syringes disposable tips disposable gloves and so on as biohazardous waste Be cautious and always use gloves If you have spilled infectious agents carry out the decontamination procedure Warning The decontamination procedure should be performed by authorized and trained personnel in a well ventilated room wearing dispos
14. 4351 AB 4352 Plus ROX vial including ROX including Low ROX K 002200 C1 XXXX solaris RNA Spike Control Kit Package size XXXX 100 200 400 1000 x 25uL rxns cDNA Synthesis Kits for qPCR K1641 K1642 Maxima First Strand cDNA Synthesis Kit for RT qPCR AB 1453 A AB 1453 B Verso cDNA Synthesis Kit with Solaris qPCR Master Mixes List of heat Table 8 11 List of heat sealers sealers code Item AB 0384 110 Thermo Scientific ALPS 25 Manual Heat Sealer 110 V AB 0384 220 Thermo Scientific ALPS 25 Manual Heat Sealer 220 V AB 1443 Thermo Scientific ALPS 50 V Microplate Heat Sealer Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 59 Ordering Information List of heat sealers 60 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Appendix A System Log Instrument name number User Date Comments PHOTOCOPIABLE Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 61 System Log 62 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Appendix B Certificate of Decontamination Name Address Tel Fax Instrument Serial no A I confirm that the returned items have not been contaminated by body fluids toxic carcinogenic or radioactive materials or any other hazardous materials B I confirm that the returned items have been decontaminated and can be handled without exposing the per
15. Fat maup a e E EE EE EE EEE EEEE E EE EA EEEE TE Caution To avoid risk of contaminating the instrument always use high quality plastic consumables such as UTW consumables For more information refer to Chapter 8 Ordering Information Note If less than 16 x 0 2 ml tubes have been loaded and gt 16 TUBES OR PLATE is selected by mistake the lid pressure may cause the tubes to become crushed or deformed Note If you are using single tubes you must use at least eight tubes that are placed symmetrically with at least one tube in each corner of the block You can use empty tubes to fill the 8 tube requirement when analyzing fewer samples ADS 32 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Routine Operation Monitoring a run 8 Enter the sample volume ul per well using the arrow keys e 24 well PikoReal 10 50 ul e 96 well PikoReal 5 20 ul oa sy gaas u ETE a 8 Es in A aa 5 7 3 a 8 F c a g a E wan 2 oz F sn rosa praza P u fezsa u na i n as se aa E an P aa n aa 5 BSUS kosus z sza s ssa 9 Press Enter to confirm the desired volume Note When a run begins the lid inside the instrument will begin moving a blue indicator light will flash and the running protocol will be displayed in semi graphical mode on a Status screen see Monitoring a run on page 33 Monito ri ng a run You can monitor a run in two screens Status screen and Time status scree
16. PCR technique is that in addition to the qualitative result detecting the presence of a PCR product a quantitative result the initial amount of the amplified product can be determined qPCR offers many advantages over traditional end point PCR methods high sensitivity over a broad dynamic range reproducibility low contamination risk and the exclusion of post PCR manipulations for analysis It also facilitates high throughput and multiplexing applications Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 13 Introduction to the PikoReal Real Time PCR System Intended use Intended US Purchase of this instrument conveys a limited non transferable immunity from suit for the purchaser s own internal research and development and applied fields other than human in vitro diagnostics under Canadian Patent 1 339 653 owned by Applied Biosystems The PikoReal Real Time PCR System has not been validated for VD purposes Human or veterinary IVD applications may also require additional licenses not covered by the instrument As the PikoReal is part of an analyzing system for the end user the user is responsible for validation of the whole system to enable production of reliable and safe results If the assay performance is essential to the analysis the test result has to be assured using internal quality controls or an alternative test Use for any other than the above mentioned purposes is excluded
17. PORT and the plate is configured This error is set if the lid is active the CONTACT SUPPORT temperature difference to the target is more than 20 C and the response to a 10 seconds heating is less than 2 C This error is set if the lid pressure CONTACT SUPPORT sensor is broken This error is set if the lid position RETRY IF PROBLEM sensor is unable to detect the home PERSISTS SEE position MANUAL This error is set if the drawer is CONTACT SUPPORT opened but the drawer optical sensor state is not changed in 100 ms Thermo Fisher Scientific PikoReal List of spare parts and accessories Thermo Fisher Scientific Chapter 8 Ordering Information Code TCRO024 TCROO96 Code N11471 N12076 N12119 EA12101M 240 VAN 0180220 1210550 1210520 N08421 N12094 TCROOS6EDEMO TCROO24DEMO TCROOS6VAL TCROO24VAL PRK1963 PRK1383 AB 1391 Item PikoReal Real Time PCR System 24 well PikoReal Real Time PCR System 96 well Table 8 8 Codes for spare parts and accessories Item PikoReal Real Time PCR System User Manual PikoReal Software User Manual PikoReal Software for PikoReal Real Time PCR System CD CMP power supply EA12101M 240 VAN Power cable UK Power cable Euro Power cable USA Japan Power cable China Ethernet cable PikoReal 96 demo kit 1 plate PikoReal 24 demo kit 1 plate PikoReal 96 validation plate PikoReal 24 validation plate Aluminum Support rack for 96 well plates and 24 well
18. This error is set if the camera plate read command fails twice This error is set if the connection to the RT unit fails Troubleshooting Guide Warning and error codes Action text REBOOT INSTRUMENT IF PROBLEM PERSISTS CONTACT SUPPORT WAIT FOR THE INSTRUMENT TO REACH OPERATING TEMP IF PROBLEM PERSISTS CONTACT SUPPORT WAIT FOR THE INSTRUMENT TO REACH OPERATING TEMP IF PROBLEM PERSISTS CONTACT SUPPORT WAIT FOR THE INSTRUMENT TO REACH OPERATING TEMP IF PROBLEM PERSISTS CONTACT SUPPORT REBOOT INSTRUMENT IF PROBLEM PERSISTS CONTACT SUPPORT REBOOT INSTRUMENT IF PROBLEM PERSISTS CONTACT SUPPORT RETRY IF PROBLEM PERSISTS SEE MANUAL CONTACT SUPPORT REBOOT INSTRUMENT IF PROBLEM PERSISTS CONTACT SUPPORT REBOOT INSTRUMENT IF PROBLEM PERSISTS CONTACT SUPPORT REBOOT INSTRUMENT IF PROBLEM PERSISTS CONTACT SUPPORT Thermo Scientific PikoReal Real Time PCR System User Manual 55 Troubleshooting Guide Warning and error codes Code E33 E35 E36 E37 E40 56 Thermo Scientific PikoReal Real Time PCR System User Manual Symbolic name SELF TEST FAILURE LID TEMP CHANGE STRAIN GAUGE FAILURE LID OPTO FAILURE DRAWER FAILURE Cont Description Action text This error is set if the RT self test fails REBOOT The self test is run at every boot and INSTRUMENT IF protocol start and it checks that the PROBLEM PERSISTS camera is found the filter is initialized CONTACT SUP
19. Three Peltier elements and a patented heat sink design provide a fast and even heat distribution and removal e 5 LED optical system Separate LEDs for each channel offer a wide excitation range 475 640 nm and multiplexing for four dyes e Piko format The PikoReal Real Time PCR System sample blocks 24 well and 96 well will only accept microplates with a footprint with the dimensions of a microscope slide the Piko format The 24 well sample block is also compatible with all standard low profile 8 tube strips and single tubes e Automatic lid The heated lid is internally motor controlled and the lid will automatically adjust to the optimal temperature and sealing pressure e External power supply The PikoReal Real Time PCR System uses an external 200 watt power supply an approach commonly used with lap top computers Note Conventional format full sized microplates are not compatible pE with the PikoReal blocks The PikoReal Real Time PCR System is available in two different configurations e PikoReal 24 e Cat no TCR0024 e for use with 24 well Piko PCR plates standard 8 well strips and 0 2 ml tubes 12 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Introduction to the PikoReal Real Time PCR System Introduction to qPCR e PikoReal 96 e Cat no TCRO096 e for use with 96 well Piko PCR plates The following components form the complete technology platform for
20. a variety of Thermo Scientifi ALPS heat sealers to be used with heat sealing films For more information on heat sealer products refer to Chapter 8 Pp Pp Ordering Information or http www thermoscientific com and http www matrixtechcorp com Thermo Scientific PikoReal Real Time PCR System User Manual 21 General Description Heat sealers 22 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific What to do upon delivery Unpacking the Checking delivery Instrument A for completeness Thermo Fisher Scientific and damage Chapter 3 Installation This chapter describes the installation of the PikoReal Real Time PCR System This section covers the relevant procedures to be carried out on receipt of the instrument Move the packed instrument to its site of operation To prevent condensation the instrument should be left in its protective plastic wrapping until the ambient temperature has been reached Note Unpack the PikoReal Real Time PCR System according to the separate instructions included in the package Unpack the PikoReal Real Time PCR System and its accessories carefully so that the arrows on the transport packaging point upwards Place the instrument onto a laboratory bench Caution Do not touch or loosen any screws Doing so may cause misalignment and will void the instrument warranty Retain the original packaging for future transportation or in case yo
21. able gloves protective glasses and clothing Decontamination should be performed in accordance with normal laboratory procedures Any decontamination instructions provided with the reagents used should be followed It is strongly recommended to perform the complete decontamination Sty p p procedure before relocating the instrument from one laboratory to another Example of decontaminants e Ethanol 70 e Virkon solution 1 3 e Glutaraldehyde solution 4 e Chloramine T e Microcide SQ 1 64 e Decon 90 min 4 To decontaminate the instrument 1 Wear disposable gloves to protect yourself 2 Prepare the decontaminant 3 Switch off the power and disconnect the power supply cable 46 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Thermo Fisher Scientific Packing for service Maintenance Packing for service 4 Empty the drawer 5 Disinfect the outside of the instrument or to remove stains using a cloth dampened with 70 ethanol 6 Place the instrument in a large plastic bag Ensure that the drawer door is out 7 Place a cloth soaked in the prepared decontaminant solution into the bag Ensure that the cloth does not come into contact with the instrument 8 Close the bag firmly and leave the instrument in the bag for at least 24 hours 9 Remove the instrument from the bag 10 After decontamination clean the instrument using a mild detergent 11 After performing t
22. am Table 6 4 Table 6 4 Instrument specifications Instrument specifications Dimensions Size 30 cm W 23 cm D 31 cm H 11 8 W x 9 1 D x 12 2 H Weight 9 2 kg 20 3 Ibs includes power supply and cord Electrical Power supply 200 W 24 V 8 3 A Line voltage 90 240 VAC Input current 2 5 A and 4 0 A Frequency 50 60 Hz Power failure recovery Yes for 24 hours Instrument configuration Block formats 24 well 96 well not interchangeable Display Backlit LCD Communication ports Fthernet USB memory stick only Programming Adjustable ramp rate Yes Touchdown Yes Typical thermal performance Max ramp rate gt 5 C s heating gt 4 5 C s cooling Thermal uniformity 0 3 C at 95 C 0 15 at 60 C 0 2 at 72 C Thermal accuracy 0270 Thermal range 4 C and 99 9 C Typical optical performance Excitation 5 LEDs Excitation range 475 640 nm Detection CCD Detection range 520 740 nm Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 49 Technical Specifications Safety specifications Cont Instrument specifications Measuring time All channels lt 13 s Single channel lt 3 s Filter wavelength range Channel 1 Excitation range 475 500 nm Emission range 520 550 nm Channel 2 Excitation range 515 535 nm Emission range 557 590 nm Channel 3 Excitation range 570 590 nm Emission range 615 650 nm Channel 4 Excitation range 600 640
23. aning of the instrument Instrument Care For proper instrument care follow the instructions below e Always ensure that the electricity supply in the laboratory conforms to that specified on the type label of the instrument e To guarantee the continuous reliability and accuracy of the PikoReal Real Time PCR System avoid interfering with any of the optical system components A misalignment of the light path affects measurements e Prevent any liquid from entering the instrument e Keep the instrument free of dust and other foreign matter e It is recommended that you clean the case of the instrument periodically to maintain its good appearance see Cleaning of the instrument on page 44 e Inthe event of any damage contact your local Thermo Fisher Scientific representative for service from high quality materials you must immediately wipe away spilled saline solutions solvents acids or alkaline solutions from outer surfaces to prevent damage and wipe with deionized distilled water Caution Although the PikoReal Real Time PCR System is constructed entering the measurement chamber Caution Keep the instrument block clean to avoid dust and dirt from Cleaning of the Clean the instrument regularly as stated below instrument 1 Turn the power off and unplug the instrument 2 Wear disposable gloves to protect yourself 3 Clean the instrument outside and the keypad with a soft cloth dampened with water 4 Plas
24. e application Up to five PikoReals can be simultaneously operated from a single computer For more information refer to the Thermo Scientific PikoReal Software User Manual Cat no N12076 The PikoReal Real Time PCR instrument is available in two block formats Figure 2 5 and Figure 2 6 Figure 2 6 96 well 20 ul max volume for PCR PikoReal 24 well and 96 well formats utilize Piko PCR plates which are 1 4th the size of standard PCR plates See Figure 2 7 The plates maintain the industry standard for well volumes and well spacing ensuring the compatibility with standard multi channel pipettes both 8 and 16 channel and liquid handling robots Four 24 well plates are equivalent to a standard ANSI 96 well plate and four 96 well Piko PCR plates are equivalent to a standard ANSI 384 well plate 18 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific UTW technology Thermo Fisher Scientific General Description Consumables Plate frames are available to assemble Piko PCR plates into standard ANSI format plate size see Chapter 8 Ordering Information Both 24 well and 96 well Piko PCR Plates are sealed with adhesive seals or heat sealing films The 24 well Piko PCR Plate can also be sealed with strip caps The 24 well sample block is also compatible with low profile 8 tube strips and single tubes with flat optical caps Not available in US Note If you are using
25. e manual stored in the original installation CD This user manual is for the following instruments 24 well PikoReal Real Time PCR System Cat no TCR0024 and 96 well PikoReal Real Time PCR System Cat no TCR0096 It aims to give you the information you need for e Reviewing safety precautions e Installing the PikoReal Real Time PCR System e Operating the instrument e Adjusting the settings and servicing the instrument e Troubleshooting the instrument This user manual also describes all the features and specifications of the PikoReal Real Time PCR System and provides ordering information for instruments spare parts reagents and consumables Read the manual in its entirety before operating the instrument Keep the user manual for future reference The user manual is an important part of the instrument and should be readily available For PikoReal Software related issues refer to the Thermo Scientific PikoReal Software User Manual Cat no N12076 For the latest information on products and services visit our website http www thermoscientific com pikoreal In our efforts to provide useful and appropriate documentation we would appreciate any comments you may have on this user manual to your local Thermo Fisher Scientific representative Thermo Scientific PikoReal Real Time PCR System User Manual 3 About This User Manual Safety symbols and markings Safety symbols and markings Safety symbols and markin
26. ear Cap Strips Thermo Fisher Scientific Quantity 200 plates 200 plates 200 plates 200 plates 50 frames 50 frames 120 strips 100 seals 960 tubes 960 tubes 400 seals 120 strips 120 strips 120 strips Ordering Information List of reagents List of reagents Table 8 10 shows examples of reagents available for the PikoReal For more information and other available products refer to http www thermoscientific com pikoreal Table 8 10 List of reagents SYBR Green chemistry K0251 K0252 Maxima SYBR Green qPCR Master Mix 2X ROX Solution provided F 415S L DyNAmo Flash SYBR Green gPCR Kit F 416S L DyNAmo ColorFlash SYBR Green qPCR Kit Probe based chemistry K0261 K0262 Maxima Probe qPCR Master Mix 2x ROX Solution provided F 455S L DyNAmo Flash Probe gPCR Kit F 456S L DyNAmo ColorFlash Probe qPCR Kit SNP Genotyping based on hydrolysis probes F 480S L XL DyNAmo SNP Genotyping Master Mix Solaris qPCR Gene Expression Assays human and mouse AX XXXXXX XX OX00 Each pre designed Solaris qPCR Assay consists of a Catalog number is product specific single probe 200 nM and primer pair 800 nM each Please refer to specific to your target gene Each assay is designed to www thermoscientific com solaris to a consensus sequence that covers all known splice select the appropriate assay variants of the target gene The sequence information is provided solaris qPCR Gene Expression Master Mix AB 4350 AB
27. eenia a a 40 R mdatrto US Bran a coenan en ceca eameeseeaaeee 41 SU GN Oy kepi aed 41 MamMiENaANGE sinrin 43 Regular and preventive maintenance ssssessssssseeesssesssesssessseesseese 43 Maintenance check lisEnesrr Tr ea T E G 43 TASEEN CATE ora TG 44 Cleaning ofthe instr tient senian e aT 44 Cleaning the block and wells 2cs ssseveusueshaatonsaveurqaavis tearaetdnaneuadeseens 45 Cenin ihe heat atta ash ccd cicadas E R 45 Disposal of materiako sh steadeeuntassacemniarearaso ee 46 Decontamination Procedu erse a E 46 PACKING Tor SELVICE suseni nanea e E 47 Maintaimnine a Syston lOean EE E tastes deths dans 48 Disposal of th Nstrumen teenin n isan a Spice can eects cae 48 Technical Specifications ccccssecsessseseeeseeseeeseensesnesenees 49 TiS CUTIE ES CE ICAU ONS errietan a ses heneadedaarisovencnacs 49 DANCE SC CUNG ALI OTE sane E T cata aa aerate 50 In conformity with the requirement ceeseeeeeeneeceeseeeeeeeeeees 50 Troubleshooting Guide ccccsssssssssecsssesesessssseeseeseseeseesersesseeass 53 Handling abnormal situations eeeeeesceeeeeeecesceeeeseeceseeeesaeeeeaees 53 Povorin celta ieseat ay asta eta ale ae eset 53 Warning and Error COMES ras Ges scecrcs raea caesar dates 53 8 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Thermo Fisher Scientific Contents Ordering Information ccscseeessessssseseesessesesseseeseesessesee
28. gs used on the PikoReal Real Time PCR System Be BHO These symbols are intended to draw your attention to particularly important information and alert you to the presence of hazards The following symbols and markings appear on the type label and the instrument itself Power on Power off Serial number Catalog number Date of manufacture Consult instructions for use WEEE symbol This product is required to comply with the European Union s Waste Electrical amp Electronic Equipment WEEE Directive 2002 96 EC One label with the following text Figure 2 3 ATTENTION Always insert the plug into the Piko first and then insert the power cord into the wall outlet 4 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Warning and other markings used in the documentation DEERE Safety Instructions Thermo Fisher Scientific About This User Manual Safety instructions The following symbols and markings appear in this user manual Warning Risk of electric shock Warning Biohazard risk Warning Hot surface risk of burns Warning Risk of injury to the user s Caution Risk of damage to the instrument other equipment or loss of performance or function in a specific application Note Marks a hint important information that is useful in the optimum operation of the system or an item of interest Read the User Manual Operating the PikoReal Real Time PCR System without firs
29. he user to prevent unnecessary wear or hazards and are Contact local authorized technical service or your local Thermo Fisher Scientific representative for assistance if necessary described below at the frequency with which they should be applied Table 5 3 Maintenance checklist Item Wipe away spilled saline solutions solvents acids or alkaline solutions from outer surfaces immediately to prevent damage and wipe with deionized distilled water see Cleaning of the instrument on page 44 If any surfaces have been contaminated with biohazardous material disinfect with a mild sterilizing solution See Instrument care on page 44 Clean the case of the instrument periodically See Cleaning of the instrument on page 44 Clean the block wells when necessary See Cleaning the block and wells on page 45 Clean the heat sink when necessary See Cleaning the heat sink on page 45 Decontaminate the instrument when relocating the instrument or sending it for service See Decontamination procedure on page 46 service the instrument regularly See Cleaning of the instrument on page 44 and Maintaining a system log on page 48 Weekly Yearly S When necessary When sending to service vV depending on the laboratory conditions and the use and configuration of the instrument Thermo Scientific PikoReal Real Time PCR System User Manual relocating 43 Maintenance Cle
30. his decontamination procedure enclose a signed and dated Certificate of Decontamination see Appendix B Certificate of Decontamination both inside the transport package and attached to the outside of the package To pack the PikoReal Real Time PCR System for service follow the instructions presented below e Inform about the use of hazardous materials e Remove any UTW vessels tube strips or single tubes before decontamination Decontaminate the instrument e Park the instrument Refer to Park instrument on page 40 e Use the original packaging for shipping e Pack the instrument according to the packing instructions e Enclose a dated and signed Certificate of Decontamination see Appendix B both inside and attached to the outside of the package in which you return your instrument or other items e Enclose the return authorization number RGA given by your local Thermo Fisher Scientific representative e Indicate the fault after you have been in touch with your local Thermo Fisher Scientific representative or the Thermo Fisher Scientific technical service department Thermo Scientific PikoReal Real Time PCR System User Manual 47 Maintenance Maintaining a system log Maintaini ng a A system log which includes a short summary of the use maintenance rocedures error messages and other information about the use of the system log PS2 A nanan system is very useful in properly maintaining the system Refe
31. how to pack for service 23 45 how to switch on 29 how to unpack 23 installation 3 23 25 27 29 49 Thermo Scientific PikoReal Real Time PCR System User Manual 67 category 49 intended use 3 13 intercalator 63 L LED 12 17 29 323 63 function 17 29 lid 5 12 29 32 34 35 36 52 53 54 logfiles 34 38 52 53 maintenance 18 23 25 41 42 46 checklist 41 measurement 42 chamber 42 melt curve 11 melting 11 51 multiplexing 12 13 N network 26 34 37 63 0 operational 27 check 27 optical 12 19 42 47 filter 12 performance 47 system 12 42 ordering information 55 P packing 23 24 45 46 instructions 24 45 list 23 materials 46 park instrument 34 38 45 PCR 3 4 5 11 12 13 16 17 18 19 20 21 23 24 25 26 27 29 31 40 42 45 46 48 55 56 63 cycle 13 method 13 product 13 PIKO 35 plate 11 18 19 31 32 52 53 54 55 56 drawer 16 36 44 45 54 68 Thermo Scientific PikoReal Real Time PCR System User Manual power supply 2 12 17 18 24 25 26 44 47 51 55 protocol 27 29 30 31 32 33 34 38 40 51 52 54 Q qPCR 11 13 20 57 63 reagents 13 20 technology 13 quantification 11 13 ramp rate 47 reagents 11 12 21 RFU 63 RV 3 5 925993 94 97 running a protocol 26 30 S S N 35 sealer 21 57 sensors 35 36 service 5 23 27 34 36 38 41 42 45 51 52 55 shu
32. ing a run Select DIAGNOSTICS in the TOOLS menu with the arrow keys and press Enter Select SENSORS with the arrow keys and press Enter The Sensors screen displays sensor data from the device e BLOCK Displays the current block temperature e LID Displays the current lid temperature e SINK Displays the current sink temperature e DRAWER Displays the state of the drawer OPEN CLOSED e LID Displays the state of the lid UP DOWN Thermo Scientific PikoReal Real Time PCR System User Manual 37 Routine Operation Tools menu Display Clock Select DIAGNOSTICS in the TOOLS menu with the arrow keys and press Enter Select DISPLAY with the arrow keys and press Enter HO DOWN KEYS CL SPLAT The display screen allows you to adjust the contrast of the PikoReal s LCD screen The contrast is lowered or raised by pressing the Up and Down arrow keys The change in contrast will appear immediately Press Enter to accept the new contrast setting Select DIAGNOSTICS in the TOOLS menu with the arrow keys and press Enter Select CLOCK with the arrow keys and press Enter The Clock screen allows viewing of the PikoReal s internal date and time settings Use the PikoReal Software PC software to modify the date and time Note If the PikoReal instrument is unplugged and without power for more than 72 hours you may have to reset the clock 38 Thermo Scientific PikoReal Real Time PCR System U
33. l Time PCR System User Manual 29 Routine Operation Main menu Main menu The PikoReal user interface see Figure 2 4 features four function keys which are used to select different menu options The function fields on the Main menu have the following actions RUN Runs a protocol from USB or instrument memory STAT Shows the Status screen when running TOOLS Accesses global settings or diagnostic routines c The red button with a C is the CANCEL button It will either bring you back to the previous menu or it will cancel your run immediately when you continuously hold down the button Pressing C also clears a message from the display A Selects the highlighted item Running a The protocols can be run using PikoReal Software and Ethernet connection or from a USB memory stick The last protocol which was protoco run using the software can also be rerun from the instrument memory To run a protocol using PikoReal Software refer to the PikoReal User Software Manual Cat No N12076 To run a protocol from USB or from the instrument memory 1 Select RUN in the Main menu and press Enter PROSERSEL A40 Thermo SL 1 EN 1 23 FIKO RT 36 EUH TOOLS 30 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Routine Operation Running a protocol 2 Ifa USB is attached the USB folder will appear and is highlighted as default folder The last performed protocol which was run u
34. ly It depends on the nature of the electricity supply and its overvoltage protection means For example in CAT II which is the category used for instruments in installations supplied from a supply comparable to public mains such as hospital and research laboratories and most industrial laboratories the expected transient overvoltage is 2500 V for a 230 V supply and 1500 V for a 120 V supply 2 The pollution degree describes the amount of conductive pollution present in the operating environment Pollution degree 2 assumes that normally only nonconductive pollution such as dust occurs with the exception of occasional conductivity caused by condensation Thermo Scientific PikoReal Real Time PCR System User Manual 51 Technical Specifications Safety specifications 52 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Handling abnormal situations Power failure Warning and Thermo Fisher Scientific error codes Chapter 7 Troubleshooting Guide Note Do not use the instrument if it appears to malfunction If there is an abnormal situation during operation such as fluids spilling inside the instrument 1 Switch off the instrument Figure 2 4 on page 17 2 Unplug the instrument immediately from the power supply Figure 3 10 on page 26 3 Carry out appropriate corrective measures However do not disassemble the instrument 4 Ifthe corrective measures taken do not help co
35. n Status screen Upon initiation of a run initialization tests are carried out and the Status screen is displayed The current temperature step in the protocol is represented by a flashing line graph view or highlighted list view and the protocol and host folder are displayed on the top of the screen RED DEF ULT ea assa os a a pi 3 ss E iss ies aa a Bees B sersatis eS Teereseszeazceeecsessraconsseanesguce n TER A poem e m HPFE EE xy 4 ex S pereg E 8 f s tea o Note If you press the C key during the run the Main menu screen is displayed with a STAT option Selecting STAT returns the display to the Status screen Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 33 Routine Operation Monitoring a run Time screen Functions in the screens PAUSE NEXT TIME STOP To enter the Time screen select TIME and press Enter The digitals in the middle of the screen display the time hours minutes and seconds remaining until the completion of the running protocol The file name and host folders are displayed on the top of the screen The following status parameters are displayed e FILE Displays the path and filename of the current protocol e STEP Displays the step number temperature and time of the currently running temperature step e CYCLE Displays the current cycle number within a GOTO loop In both the Status and Time status scree
36. n event of technical problems Press C to clear the warning or error message Table 7 5 Warnings Symbolic name POWER FAILURE BLOCK TEMP HIGH LID TEMP HIGH SINK TEMP HIGH PROTOCOL STOPPED CAMERA FAILURE PROTOCOL PAUSED CYCLES ADDED STEP SKIPPED LID PRESSURE FAIL Table 7 6 Errors Symbolic name POWER FAILURE BLOCK TEMP LID TEMP SINK TEMP Description This warning is set if the power was lost during protocol execution for less than 24 h and the protocol was recovered This warning is set if the block temperature is over 112 C This warning is set if the lid temperature is over 115 C This warning is set if the sink temperature is over 75 C This warning is set if the protocol is stopped before the end of the protocol This warning is set if the first camera plate read command fails This warning is set if the protocol is paused during the protocol run This warning is set if extra cycles are added to a protocol loop This warning is set if the protocol step is skipped NEXT This warning is set if protocol is paused drawer opened and protocol resumed Description This error is set if the power was lost during protocol execution for over 24 h This error is set if the block temperature is over 115 C This error is set if the lid temperature is over 125 C This error is set if the sink temperature is over 85 C Action text CHECK LOGFILES
37. nd press Enter TYPE PIKO RT 96 S N PRO09609011740 PIKO 2 2 39 RT 1 1 12 23 The System Info screen displays information about the device and software e TYPE Displays the type of PikoReal instrument e S N Displays the serial number of the device e PIKO Displays the firmware version of the PIKO module i e the thermal cycler module e RT Displays the firmware version of the RT module i e the real time module Diagnostics Select DIAGNOSTICS in the TOOLS menu with the arrow keys and press Enter The Diagnostics screen displays data about the four following settings e LID see Lid on page 37 e SENSORS see Sensors on page 37 e DISPLAY see Display on page 38 e CLOCK see Clock on page 38 36 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Thermo Fisher Scientific Routine Operation Tools menu Lid Select DIAGNOSTICS in the TOOLS menu with the arrow keys and Sensors press Enter Select LID with the arrow keys and press Enter when PET EEE LE KETS SIEN 22a 1 z ss 3 sa AA ss ss 3 The Lid screen displays the offset settings for ZERO LOW MED MEDIUM and HIGH lid pressure Users may be asked to read these values to the service personnel as part of a troubleshooting procedure The user can drive the LID UP and DOWN by pressing Enter when the offset is selected Note that this is not possible dur
38. ns the following actions can be used SEO DEFAULT woe i SH z a n Pika ont Pauses the run at the present temperature step or at the next step if ramping When paused this option becomes RESUME Skips to the next protocol step Toggles to the Status screen Stops the protocol You can also return to the Main menu while the instrument is running by pressing the C key on the keypad 34 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Thermo Fisher Scientific Tools menu Routine Operation Tools menu Select TOOLS in the Main menu and press Enter The TOOLS menu provides six options which are accessed using the arrow keys and then by pressing Enter SYSTEM INFO Displays system info DIAGNOSTICS Allows users to check lid parameters sensor parameters display settings and clock settings NETWORK Allows users to view network address values for networking PikoReal SERVICE Used by authorized service personnel only LOGFILES Displays protocol and instrument log files PARK INSTRUMENT Prepares the instrument for transportation RUN DATA TO USB Appears when a USB memory stick is inserted Copies the data of the previous protocol to the memory stick once the protocol is ready Thermo Scientific PikoReal Real Time PCR System User Manual 35 Routine Operation Tools menu System info Select SYSTEM INFO in the TOOLS menu with the arrow keys a
39. ntact authorized technical service or your local Thermo Fisher Scientific representative In case of less than a 24 hour power failure the instrument continues the interrupted run from the same protocol step it was performing at the time of the interruption If the protocol was in the melting curve phase see the PikoReal Software User Manual the instrument continues the run from the start of the melting curve protocol The instrument gives a warning code dependent of the length of the power failure W1 or El see Table 7 5 Warnings inform about possible unwanted events occurring during the protocol execution Table 7 5 The protocol is not stopped but the event might have some effect on the results Errors inform about a failure occurring during the protocol execution Table 7 6 All errors except E1 cause the protocol to stop and all heating units to be turned off Thermo Scientific PikoReal Real Time PCR System User Manual 53 Troubleshooting Guide Warning and error codes Code W1 W8 wg W10 W27 W28 W29 W30 W31 W35 Code E1 E3 E4 E5 Continued 54 Thermo Scientific PikoReal Real Time PCR System User Manual When an error is detected the current operation is aborted After an error it is best to restart from the beginning after the problem has been fixed When an error occurs the error code and the suggested actions are presented You can restore the data of the last run i
40. omponents in place This is indicated on the back panel of those instruments 40 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Routine Operation Shutting down Run data to USB Select RUN DATA TO USB in the TOOLS menu with the arrow keys and press Enter Note that he USB memory stick has to be inserted MEMORY Answer the prompt using the arrow keys and press Enter This option enables copying the backup data of the last performed protocol to the memory stick once the protocol is ready This option is disabled while the protocol is active devices are compatible with the instrument Note Thermo Fisher Scientific does not guarantee that all USB memory Shutting down To shut down the PikoReal Real Time PCR System 1 Remove any UTW vessels tube strips or single tubes from the instrument 2 Answer the prompt using the arrow keys and press off the instrument after use by holding down the POWER button continuously Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 41 Routine Operation Shutting down 42 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Regular and preventive Chapter 5 Maintenance maintenance Maintenance checklist Thermo Fisher Scientific This chapter contains an outline of the points mentioned in the checklist below Table 5 3 Routine and service procedures must be performed by t
41. r Manual Thermo Fisher Scientific Reagents Dye calibration Dispensers Heat sealers Thermo Fisher Scientific General Description Reagents Thermo Scientific offers a comprehensive selection of qPCR reagents to be used with the PikoReal Real Time PCR System These include for example universal reagents for SYBR Green and probe chemistries SNP Genotyping as well as Solaris pre designed qPCR assays for gene expression analysis For more information on the reagents refer to Chapter 8 Ordering Information and http www thermoscientific com pikoreal The PikoReal has been precalibrated to use the following fluorophores e FAM e HEX e Yakima Yellow e ROX e Texas Red e Cy 5 The PikoReal Real Time PCR System is also compatible with SYBR Green I and similar DNA binding dyes If you wish to calibrate other dyes into the system refer to Appendix A Color Calibration in the PikoReal Software User Manual Cat no N12076 Thermo Fisher Scientific provides a variety of dispensers compatible with Piko PCR plates Thermo Scientific Finnpipette and Thermo Scientific Matrix multichannel pipettes adjustable electronic Matrix pipettes as well as Thermo Scientific Multidrop Combi reagent dispensers and Thermo Scientific Versette automatic liquid handlers For more information on Thermo products refer to http www thermoscientific com Thermo Fisher Scientific provides
42. r to Appendix A System Log Copy the table as many times as necessary but leave the blank original inside the user manual D isposal of the Ifthe PikoReal Real Time PCR System is exposed to potentially t t infectious chemical samples toxic or corrosive chemicals or radioactive Instrumen chemicals waste management of the complete instrument must be carried out to ensure that there is no risk of contamination a Warning Decontaminate the instrument before disposal Refer to Decontamination procedure on page 46 Follow laboratory and country specific procedures for biohazardous or radioactive waste disposal Dispose of the instrument according to the legislation stipulated by the local authorities concerning take back of electronic equipment and waste The proposals for the procedures vary by country Pollution degree 2 see Safety specifications on page 50 Method of disposal Electronic waste Contaminated waste Infectious waste Regarding the original packaging and packing materials use the recycling operators familiar to you For more information contact your local Thermo Fisher Scientific representative 48 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Chapter 6 Technical Specifications Instrument Thermo Fisher Scientific reserves the right to change any specifications g without prior notice as part of our continuous product development specifications progr
43. rmo Scientific power supply cable designed for your region 1 Plug the power supply into the back of the PikoReal Real Time PCR System Figure 3 10 Caution To prevent risk of shock or damage to the instrument always connect the power supply first to the instrument before plugging it into the power outlet Thermo Scientific PikoReal Real Time PCR System User Manual 25 Installation Warnings and cautions 2 Insert the power cord into the power supply 3 Insert the power cord into the power outlet The system will power up automatically Power connector ernet port RJ45 Figure 3 10 Connecting the power supply cable and the Ethernet cable Connecting to the Connect the Ethernet cable to the back of the PikoReal Real Time PCR network System Figure 3 10 You must use a shielded Ethernet cable Cat5e Cat6e FTP STP For more information refer to the PikoReal Software User Manual Cat no N12076 Connecting tothe The data port see Figure 2 2 on page 15 is to be used with USB data port memory devices only For instructions on how to use a USB memory device refer to Running a protocol on page 30 and Run data to USB on page 41 Wa rings and This instrument is designed to be safe for use When correctly installed c auti ons operated and maintained it will present no hazard to the user The following recommendations are given for added user safety Electrical Ensure that the power supply cable s
44. saeseeseeanees 57 DP Tats tet ah setae a E AA 57 List of spare parts and ACCESSON ICS nerc iei N 57 Litol consumable anar E T 58 DISHOl PEACE nis sinets unani a a E 59 List of heat sealers c cccccceccceccoecccecccecccecccsccecccesccsccscesceuscenecs 59 System Lofn cut teishivenndden aantaen ius santtont duitvanndeaddacvetsnnianicasmeantaunte 61 Certificate of Decontamination ccccsccssecsseecsseseseesseecesesesesseeens 63 Thermo Scientific PikoReal Real Time PCR System User Manual 9 Contents 10 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Thermo Fisher Scientific Chapter 1 Introduction to the PikoReal Real Time PCR System The PikoReal Real Time PCR System Figure 1 1 is a gene quantification and genotyping platform in 24 and 96 well block formats Using PikoReal Software the system is applicable to absolute quantification relative quantification melt curve analysis high resolution melt analysis and allelic discrimination The PikoReal Real Time PCR System is designed to a minimal footprint making the system ideal for personal bench top use and field applications for example _ Figure 1 1 PikoReal 96 Real Time PCR System The combination of several innovative technologies applied in design including optics unique heat sink design block design plate size and the usage of special plasticware create many advantages over conventional qPCR systems
45. ser Manual Thermo Fisher Scientific Thermo Fisher Scientific Network Service Logfiles Routine Operation Tools menu Select NETWORK in the TOOLS menu with the arrow keys and press Enter The Network screen allows the user to view the IP address the subnet mask MASK the gateway GW the Domain Name Server DNS and the MAC address MAC It is not possible to edit the MAC address Note It is not possible to change the MASK GW or DNS values without help from authorized technical service Use the PikoReal Software PC software to change the IP address of the instrument if necessary Note that this function is to be used by authorized Thermo Fisher Scientific service personnel only Select LOGFILES in the TOOLS menu with the arrow keys and press Enter The Logfiles screen allows the user to view protocol and instrument related log files e PROTOCOL LOGS Displays the log files of the last 10 executed protocols e INSTRUMENT LOG Displays the instrument log files Thermo Scientific PikoReal Real Time PCR System User Manual 39 Routine Operation Tools menu Park instrument With the park instrument option the user can prepare the device for transportation Select PARK INSTRUMENT in the TOOLS menu with the arrow keys and press Enter Follow the instructions on the screen FARR IHG Ho TRUREMT o Note In older models of the instrument a locking screw is used to securely lock optic c
46. sing the software is stored in the Recent folder and also in the Shared folder S OF E RECENT W 3 Select a folder and press Enter The protocols stored in that folder will be displayed 4 Select the protocol and press Enter The protocol will be displayed in semi graphical mode LEFT EIGHT Note Protocol files on the USB memory stick can have a name that is up to eight characters long Note Thermo Fisher Scientific does not guarantee that all USB memory devices are compatible with the instrument E 5 The protocol can be viewed in list mode or graph mode and browsed using the Left Right or the Up Down arrow keys correspondingly Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 31 Routine Operation Running a protocol 6 After selecting the view mode list or graph start a run by selecting START and pressing Enter With a 24 well PikoReal Real Time PCR System the users will be presented with consumable and volume options With a 96 well PikoReal Real Time PCR System the users will only be presented with volume options 7 Select the consumable that is the vessel type for a 24 well PikoReal Real Time PCR System Select either e lt 16 TUBES if using 8 16 individual 0 2 ml tubes or e gt 16 TUBES OR PLATE if using a 24 well Piko PCR Plate LOM SUPA H pea a mai Pati p Reaeeen u HHEH Gres RuN MaRy F n E paeuessseed monad peat cma Ged
47. sonnel to health hazards Materials used in the unit Chemicals Biological Radioactive Specific information about contaminants Decontamination procedure Date and place Signature Name block capitals The signature of a Radiation Safety Officer is also required when the unit has been used with radioactive materials This unit is certified by the undersigned to be free of radioactive contamination Date and place Signature Name block capitals PHOTOCOPIABLE Please include decontaminating solution used Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 63 Certificate of Decontamination 64 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Glossary CCD Charge coupled device intercalator In biochemistry intercalator is a type of molecule that binds to DNA and inserts itself into the DNA structure LED Light emitting diode MAC Short for Media Access Control address a hardware address that uniquely identifies each node of a network PCR Polymerase chain reaction qPCR Quantitative real time PCR RFU Relative fluorescence unit UI User interface UTW Ultra thin wall Thermo Fisher Scientific Thermo Scientific PikoReal Real Time PCR System User Manual 65 Glossary 66 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Index A accessories 23 24 55 58 accuracy 2 42
48. sture or large temperature fluctuations The instrument will perform optimally and exhibit the highest reliability within the recommended environmental ranges Table 3 2 Although the instrument is rated to operate reliably within the absolute environmental ranges avoid the extremes to best preserve the long term performance and life span of the instrument Table 3 2 Operating conditions Environmental condition Absolute ranges Recommended ranges Ambient temperature 5 30 C 15 25 C Ambient relative humidity below 80 below 50 Altitude below 2000 m below 1000 m Make sure that e The working area is flat dry clean and vibration proof and leaves additional room for cables covers etc e There is sufficiently room behind the instrument to enable disconnecting the device e The ambient air is clean and free of corrosive vapors smoke and dust e The ambient temperature range is between 5 C and 30 C e The humidity is low so that condensation does not occur relative humidity is between 10 and 80 Caution Do not operate the instrument in an environment where potentially damaging liquids or gases are present 24 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Air flow Installation steps A Connecting the power supply cable Thermo Fisher Scientific A A Installation Installation steps Note To ensure that your PikoReal Real Time PCR System will provide
49. t reading the entire User Manual may constitute a risk to your health Only a person capable of handling electrical equipment should use the PikoReal Real Time PCR System NOT FOR CHILDREN Do Not Attempt to Repair the System Do not remove the cover of the system Do not try to repair or replace broken components you put yourself at risk for electrical shock Removing the cover or replacing removing components will void the warranty Contact customer service or your local distributor if your system is not functioning properly Do Not Touch the Sample Block Certain components including the sample block and heated lid will become excessively hot Touching these components may cause burns Do Not Tamper with Electronics Coming into contact with the electronics even when the system is off or unplugged may cause an electrical shock or harm Do Not Use Flammable Hazardous or Radioactive Liquids with the PikoReal Real Time PCR System Thermo Scientific PikoReal Real Time PCR System User Manual 5 About This User Manual Safety instructions 6 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Thermo Fisher Scientific Contents lncended Br Koc cc ener ne ee en Re nC Rete ee en RE 3 PIRWA VElSIOUS aeaa a a a T miewnde 3 Howto ise this ser Manualer E E A 3 For more TOLOIMa tO M44 tesc8 uedun eetoucastsotaadiusnenesgenuadsduteluteecesdeaonagauaiel 3 Safety symbols and mar kines ci siceshs i icaaiaea
50. tacieioeac aa 4 Safety symbols and markings used on the PikoReal Real Time PCR S SU ergo ceetencted decael sar ba E EN 4 Warning and other markings used in the documentation 5 Safe INSEL ICU ONG sxcds tera N A ead nconceatee 5 Introduction to the PikoReal Real Time PCR System 000 11 Introduccion tog PC Resne a wae nnea Geteaqneaoesnes 13 WA TSH U anena a tied null soaceliedianbe 14 General DESCHIPUOM suinn ia aa 15 listr neaE VC Wono A saaeaceastescs anne 15 PikoReaFiser DET aCe sarnane n T N 17 Saus d ALO eeann aetenicuietee taneeatitueieetecoeaee 17 POWER supp oeann E AN 17 PikoReal Sofi Wa C eenn a 18 Dioc k IOMa e aA 18 Conama DIGS cei tes haves AAA 18 UIW a reel ob ere alegre meee ne rere ore Cre ee eer nt rere teeter ee 19 IRS ASE E NE E E A tethers sch A E E T 21 Deca Oee reer tere rC NTT terere A rer sen err 21 IIS DENSEES eil sand eau as papal aaa aausiaaam 21 FL CAG Sea Es ice sic duusaaasiw a Aa a teontaecseeteaaee 21 PS TANAUIOM sos ascdsscsiseesncccneszteuncincsastariuceorushevistededstush aa 23 What todo pOm elven sererai e A saree veel 23 Unpacking the 1S crue Mt siisii iei a a 23 Checking delivery for completeness and damage cesseceeeees 23 Environmental requirements vxcp2iz5ei2iehsdaisshsbenscpdedacxan staves iohecanectens 24 AION serna tp desta boned a aR 25 Fasta lla Onse Doner E A E ETE 25 Connecting the power supply cable sssesseeeseessseessressressressesses 25 Connecting
51. tdown 40 sink 11 25 36 41 43 52 53 spare parts 3 55 specifications 3 46 47 48 49 safety 46 48 49 startup 29 Status screen 29 32 33 34 step 33 34 51 52 switching on 29 symbols 4 system info 34 35 system log 41 46 T Tools menu 34 35 36 37 38 39 transport 23 24 39 45 lock 39 package 24 45 troubleshooting 3 17 29 36 51 tubes 12 19 31 32 40 44 45 56 type 4 26 27 31 35 42 48 63 type label 4 27 42 Thermo Fisher Scientific U uniformity 11 47 USB 12 26 29 30 31 34 39 40 47 user interface 17 29 63 UTW 2 11 13 19 20 32 40 44 45 56 63 Thermo Fisher Scientific W warning codes 26 51 52 warranty 5 23 wavelength 48 range 48 Thermo Scientific PikoReal Real Time PCR System User Manual 69 Notes 70 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Thermo Fisher Scientific Oy Ratastie 2 P 0 Box 100 Fl 01621 Vantaa Finland www thermoscientific com N11471
52. tic covers and surfaces can also be cleaned with a mild laboratory detergent mild bleach or diluted alcohol solution Warning If you have spilt infectious agents on the instrument decontaminate the instrument Refer to Decontamination procedure on page 46 44 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific D gt b gt gt D Cleaning the block and wells Cleaning the heat Thermo Fisher Scientific sink Maintenance Cleaning of the instrument Caution Painted surfaces can be cleaned with most laboratory detergents Dilute the cleaning agent as recommended by the manufacturer Do not expose painted surfaces to concentrated acids or alcohols for prolonged periods of time as damage may occur Caution Do not use any solutions containing oxidative chemicals such as strong hypochlorites and peroxides or strong bases on any of the anodized aluminum surfaces as this may cause permanent damage to the finish Caution Abrasive cleaning agents are not recommended because they are likely to damage the paint finish Caution Never use acetone as it will damage the covers Caution Do not autoclave any part of this instrument To clean the block and wells Figure 2 2 Figure 2 5 and Figure 2 6 follow the instructions below 1 Turn the power off and unplug the instrument 2 Wear disposable gloves to protect yourself 3 Clean the block surface at least once a week using a
53. to Te TS bY OUR zsrsr ni e sees eats 26 Connecting tothedata POR Gs sse acauseaciee rennet enemteeeet 26 SW AT TNIIISS AIC CAULIONSys2ds sateen eet base ERR 26 E e Altatasat os maitakiate eases ae ee a ee eee 26 Operational Neck orare a re mre nah te ee res ree 27 Installing PikoReal Software niissrriaiericsi ieira toeo 27 Thermo Scientific PikoReal Real Time PCR System User Manual 7 Contents Routine Operation ccscssssssssssessssesseeesssessesesaesesseseseesesessesesaesesaeees 29 Sse Wiel care s ener eee arene ery Peer eM ey errata ES 29 Sats IRI CACO I 5 Sos ese ao bains atest sous varies Seabuns oleteel A teeeiesaeseenee 29 DY Medd TPIS TAU ok ots sac naa wares tia cee E ashe anew eenicean eae 30 RGN A POOO lesane O E ds tetncte tars 30 IVLOMACOT UNS Avi 255 issicis sashes istaig aaa tae asa aat mio ceaseseeaea saat 33 SUS Se 0 RE ON ODIO NOE Meet Pe EES Een Ree aE ere 33 TIE GCL E s3icer vei vssa satiate ae E 34 Pimctions A CHS SCLECIS ais cestainne id R 34 Tool i TAL oases See Moats A ETT A T 35 Sy SECM TUM Ora an teen seeaeud TO R 36 BE NOSES aeos E A 36 E EEIE A EEN EE E A EE E AE EE NE TEE 37 O caeeatatin conse E aaa dp oneuenaat ie enacrs 37 Display soars Saati siil nc Seen vecutharte E yee soast seats an ceaubeaetanees 38 CGC EE sea sete gatas AO IE A TAEA N LE E TA 38 IN COW Ot krcnireninkea e a a A ctaex tus ectesute 39 SIVI tacts Sess aaa tive uae estan T SAS 39 o l E E E E A E E E A A E E 39 Park TVS CULV C nt
54. u need to return the PikoReal Real Time PCR System for maintenance The packaging is designed to ensure safe transport and minimize transit damage Use of insufficient packaging materials may invalidate the warranty Retain all instrument related documentation provided by the manufacturer for future use If you relocate your instrument or ship it for service refer to Packin b r P 8 for service on page 47 Check the enclosed packing list against the order Check that the delivery includes the following items e PikoReal Real Time PCR System e PikoReal Software for PikoReal Real Time PCR System CD e Power supply Thermo Scientific PikoReal Real Time PCR System User Manual 23 Installation What to do upon delivery Environmental requirements A e Power cord e Ethernet cable e Unpacking packing instructions Note that a personal computer is not provided by Thermo Fisher Scientific A PC is required for full use of the PikoReal functionalities For recommended PC requirements refer to the PikoReal Software User Manual Cat no N12076 Visually inspect the transport package the instrument and the accessories for any possible damage If any parts are missing or damaged contact your local Thermo Fisher Scientific representative or Thermo Fisher Scientific Oy When setting up your PikoReal Real Time PCR System avoid locations with excessive dust vibrations strong magnetic fields direct sunlight draft excessive moi
55. upplied with the unit is always used If a correct type of mains cable is not provided use only cables certified by the local authorities 26 Thermo Scientific PikoReal Real Time PCR System User Manual Thermo Fisher Scientific Installation Operational check e power plug should only be inserted into a socket outlet with a The p plug should only b ted int ket outlet with protective ground contact Never use an extension cable without a protective ground wire Always ensure that the electricity supply in the laboratory conforms to that specified on the type label of the instrument Warning Only authorized technical service personnel are allowed to open the instrument i Warning Do not touch switches or electrical outlets with wet hands Switch the instrument off before disconnecting it from the mains supply Operational Before you put the instrument into use perform the following check operational check 1 Plug the instrument into the mains The instrument automatically proceeds to perform the self tests The self tests are performed each time the instrument is turned on 2 After approximately 30 seconds a beep signal indicates the test completion 3 The operational check has passed if no error messages appear In case of errors refer to Warning and error codes on page 53 Note Partial self tests are performed every time a protocol is started Insta i ng The PikoReal Software is on the Thermo Scientific
56. years of top level performance and will have the fewest problems adhere to the given environmental requirements Airflow is paramount to high speed performance and high reliability Maintain good heat sink cooling capability by ensuring a cool source of incoming air and an unobstructed exhaust of air To ensure obstruction free intake of air e Do not set the instrument on a hot surface or on laboratory bench paper e Do not slide any paper or other material under the instrument as this may hamper the airflow or be sucked into the instrument To ensure obstruction free exhaust of air e Always keep at least 10 cm of distance between the exhaust vents and any large solid objects or walls e Do not have other instruments exhaust directly at the PikoReal Real Time PCR System Clean the fins of the heat sink and the instrument regularly see Cleaning the heat sink on page 45 This section describes the installation steps that have to be carried out before operating the instrument Caution If the instrument was stored or transported in a cold environment allow it to reach room temperature before plugging it in Leave the instrument to sit for at least three hours before installing and switching it on to prevent condensation causing a short circuit To connect the power supply cable Warning Never operate your instrument from a power outlet that has no ground connection Never use a power supply cable other than the The

N11471 ver 2.2 PikoReal Real-Time PCR System User Manual

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