Thermo Scientific PikoReal User Manual
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Thermo Scientific PikoReal User Manual

Real-time pcr system
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Thermo Scientific PikoReal
Real-Time PCR System
User Manual
Rev. 2.0
Plesmanlaan 1d
2333 BZ Leiden
The Netherlands
T. +31 (0)71 568 10 00
T. Belgium: 0800 71640
sharing knowledge
F. +31 (0)71 568 10 10
info@bioke.com
www.bioke.com

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  • Page 1 Thermo Scientific PikoReal Real-Time PCR System User Manual Rev. 2.0 Plesmanlaan 1d 2333 BZ Leiden The Netherlands T. +31 (0)71 568 10 00 T. Belgium: 0800 71640 sharing knowledge F. +31 (0)71 568 10 10 info@bioke.com www.bioke.com...
  • Page 3 Thermo Scientific PikoReal Real-Time PCR System User Manual Rev.2.0, Cat. no. N11471...
  • Page 4 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. Trademarks “ALPS”, “DyNAmo”, “Finnpipette”, “Matrix”, “Maxima”, “Multidrop”, “Piko”, “PikoReal”, “Solaris”, “Versette”, “Verso” and “UTW” are trademarks or registered trademarks of Thermo Fisher Scientific Inc. and its subsidiaries.

  • Page 5: Intended Users

    About This User Manual Intended users About This User Manual Intended users The PikoReal Real-Time PCR System, as a standalone instrument or with Thermo Scientific PikoReal Software, can be used in research laboratories by professional personnel. How to use this This user manual is for the following instruments: 24-well PikoReal Real-Time PCR System (Cat.

  • Page 6: Safety Symbols And Markings

    This is shipping position only! The other hole is operating position, refer to the manual. ▲ 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...

  • Page 7: Warning And Other Markings Used In The Documentation

    ▲ Safety Read the User Manual Operating the PikoReal Real-Time PCR System without first reading the entire User Manual may constitute a instructions risk to your health. Only a person capable of handling electrical equipment should use the PikoReal Real-Time PCR System.
  • Page 8 About This User Manual Safety instructions 6 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 9: Table Of Contents

    How to use this user manual ............. 3 For more information ............... 3 Safety symbols and markings............. 4 Safety symbols and markings used on the PikoReal Real-Time PCR System.................... 4 Warning and other markings used in the documentation ....5 Safety instructions ................
  • Page 10 Safety specifications................. 48 In conformity with the requirements..........48 Chapter 7 Troubleshooting Guide................51 Handling abnormal situations ............51 Power failure ................... 51 Warning and error codes ..............51 8 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...
  • Page 11 List of spare parts and accessories ............ 55 List of consumables ................. 56 List of reagents ................57 List of heat sealers ................57 Appendix A System Log ....................59 Appendix B Certificate of Decontamination..............61 Thermo Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...
  • Page 12 Contents 10 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 13: Introduction To The Pikoreal Real-Time Pcr System

    ® 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 and allelic discrimination.
  • Page 14 Introduction to the PikoReal( Real-Time PCR System Safety instructions 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.

  • Page 15: Introduction To Qpcr

    It also facilitates high-throughput and multiplexing applications. Intended use The PikoReal Real-Time PCR System is a thermal cycler with a fluorescence measuring system available in 24-well and 96-well formats. It is intended for qPCR technologies and related fluorogenic chemistries.
  • Page 16 Caution Operate the instrument only with software and hardware that is specifically designed or selected for it. Thermo Fisher Scientific assumes no liability for the use of third-party software applications. ▲ 14 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 17: Chapter 2 General Description

    General Description Instrument views Chapter 2 General Description This chapter describes the main parts of the PikoReal instrument. Instrument The front view of the PikoReal instrument is shown in Figure 2–2. views User interface Data port Air exhaust Drawer Feet Air intake Figure 2–2.
  • Page 18 General Description Instrument views The rear view of the PikoReal instrument is shown in Figure 2–3. Air exhaust Type label Power connector Ethernet port (RJ45) 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).

  • Page 19: Pikoreal User Interface

    General Description PikoReal user interface PikoReal user The PikoReal user interface (UI) and its functions are shown in Figure 2–4. interface Status indicator: Blue Power button Backlit LCD display Arrow keys for moving on the display Cancel key Enter key...

  • Page 20: Pikoreal Software

    ▲ PikoReal The PikoReal is operated with the PikoReal Software application. Up to ten PikoReals can be simultaneously operated from a single computer. Software For more information, refer to the PikoReal Software User Manual (Cat.

  • Page 21: Utw Technology

    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 Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...

  • Page 22: Reagents

    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.

  • Page 23: Dye Calibration

    General Description Dye calibration For more information on the reagents, refer to Chapter 8: “Ordering Information” and http://www.thermoscientific.com/pikoreal. Dye calibration The PikoReal has been precalibrated to use the following fluorophores: ● ● Yakima Yellow® ● ● Texas Red® ● Cy®5 ●...
  • Page 24 General Description Heat sealers 22 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 25: Chapter 3 Installation

    Installation What to do upon delivery Chapter 3 Installation This chapter describes the installation of the PikoReal Real-Time PCR System. What to do upon This section covers the relevant procedures to be carried out on receipt of the instrument. delivery Unpacking the Move the packed instrument to its site of operation.

  • Page 26: Environmental Requirements

    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).

  • Page 27: Air Flow

    Never use a power supply cable other than the Thermo 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.

  • Page 28: Connecting To The Network

    Ethernet 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 System (Figure 3–10). You must use a shielded Ethernet cable network (Cat5e/Cat6e, FTP/STP).

  • Page 29: Operational Check

    Note Partial self tests are performed every time a protocol is started. ▲ Installing The PikoReal Software is on the Thermo Scientific PikoReal Real-Time PCR System CD (Cat. no. N12119). The CD also contains the PikoReal instrument and software user manuals.
  • Page 30 Installation Installing PikoReal Software 28 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 31: Chapter 4 Routine Operation

    Lower light Chapter 7: “Troubleshooting Guide” for more information. 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: Runs a protocol from USB or instrument memory.

  • Page 32: Running A Protocol

    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.
  • Page 33 6. After selecting the view mode (list or graph), start a run by selecting and pressing Enter. START 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.

  • Page 34: Monitoring A Run

    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. 32 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 35: Time Screen

    CYCLE – Displays the current cycle number (within a GOTO ● loop). Functions in the In both the Status and Time status screens, the following actions can be used: screens Thermo Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...

  • Page 36: Tools Menu

    Copies the data of the previous protocol to the memory stick once the protocol is ready. System info Select SYSTEM INFO in the TOOLS menu with the arrow keys and press Enter. 34 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 37: Diagnostics

    Routine Operation Tools menu The System Info screen displays information about the device and software: TYPE – Displays the type of PikoReal instrument. ● S/N – Displays the serial number of the device. ● PIKO – Displays the firmware version of the PIKO module (i.e. the ●...

  • Page 38: Sensors

    LID – Displays the state of the lid (UP/DOWN). ● Display Select DIAGNOSTICS in the TOOLS menu with the arrow keys and press Enter. Select DISPLAY with the arrow keys and press Enter. 36 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 39: Clock

    Routine Operation Tools menu 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.

  • Page 40: Service

    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. Service Note that this function is to be used by authorized Thermo Fisher Scientific service personnel only.

  • Page 41: Run Data To Usb

    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. Thermo Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...

  • Page 42: Shutting Down

    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 button POWER continuously. 40 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 43: Chapter 5 Maintenance

    42 and “Maintaining a system log” on page 46. = depending on the laboratory conditions and the use and configuration of the instrument Instrument care For proper instrument care, follow the instructions below. Thermo Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...

  • Page 44: Cleaning Of The Instrument

    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.

  • Page 45: Cleaning The Block And Wells

    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 Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...

  • Page 46: Disposal Of Materials

    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. 4. Empty the drawer. 44 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 47: Packing For Service

    “Certificate of Decontamination”) both inside the transport package and attached to the outside of the package. Packing for To pack the PikoReal Real-Time PCR System for service, follow the instructions presented below: service Inform about the use of hazardous materials.

  • Page 48: Maintaining A System Log

    Appendix A: “System Log”. Copy the table as many times as necessary, but leave the blank original inside the user manual. Disposal of the If the PikoReal Real-Time PCR System is exposed to potentially infectious chemical samples, toxic or corrosive chemicals or radioactive instrument chemicals, waste management of the complete instrument must be carried out to ensure that there is no risk of contamination.

  • Page 49: Chapter 6 Technical Specifications

    ± 0.3°C at 95°C; ± 0.15 at 60°C; ± 0.2 at 72°C Thermal uniformity ± 0.2°C Thermal accuracy Thermal range 4°C and 99.9°C Typical optical performance Excitation 5 LEDs Excitation range 475–640 nm Detection Detection range 520–740 nm Continued Thermo Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...

  • Page 50: Safety Specifications

    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- Time PCR System. specifications In conformity with PikoReal Real-Time PCR System bears the following markings:...
  • Page 51 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 Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...
  • Page 52 Technical Specifications Safety specifications 50 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 53: Chapter 7 Troubleshooting Guide

    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.
  • Page 54 SINK TEMP. This error is set if the sink temperature ENSURE THAT THE is over 85°C. AIRFLOW TO THE FAN IS NOT OBSTRUCTED. IF PROBLEM PERSIST CONTACT SUPPORT Continued 52 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...
  • Page 55 INSTRUMENT. IF PROBLEM PERSISTS CONTACT SUPPORT RT-UNIT FAILURE This error is set if the connection to the REBOOT RT unit fails. INSTRUMENT. IF PROBLEM PERSISTS CONTACT SUPPORT Continued Thermo Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...
  • Page 56 PERSISTS SEE position. MANUAL DRAWER FAILURE This error is set if the drawer is CONTACT SUPPORT opened, but the drawer opto state is not changed in 100 ms. 54 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 57: Chapter 8 Ordering Information

    Code Item accessories N11471 PikoReal Real-Time PCR System User Manual N12076 PikoReal Software User Manual N12119 PikoReal Software for PikoReal Real-Time PCR System CD EA12101M-240-VAN CMP power supply EA12101M-240-VAN 5180220 Power cable (UK) 1210550 Power cable (Euro) 1210520 Power cable (USA/Japan)

  • Page 58: List Of Consumables

    Low Profile Thermo Strip, white 120 strips 0.2 ml low profile thin walled 8 tube strips AB-0866 Ultra Clear Cap Strips 120 strips * Not available in US. 56 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 59: List Of Reagents

    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™...
  • Page 60 Ordering Information List of heat sealers 58 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 61: Appendix A System Log

    System Log Appendix A System Log Instrument name/number: User Date Comments PHOTOCOPIABLE Thermo Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual 59...
  • Page 62 System Log Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...

  • Page 63: Appendix B Certificate Of Decontamination

    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 61...
  • Page 64 Certificate of Decontamination Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...
  • Page 65 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 63...
  • Page 66 Glossary: 64 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...
  • Page 67 2, 34, 35, 36, 37 how to ensure startup, 29 display, 29, 33, 34, 35, 36, 37, 47 how to install the PikoReal, 23, 25, 27, 49 disposal of instrument, 46 how to maintain the instrument, 41 disposal of materials, 44...
  • Page 68 4, 26, 27, 31, 35, 42, 48, 63 product, 13 type label, 4, 27, 42 PIKO, 35 plate, 11, 18, 19, 31, 32, 52, 53, 54, 55, 56 drawer, 16, 36, 44, 45, 54 66 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...
  • Page 69 USB, 12, 26, 29, 30, 31, 34, 39, 40, 47 warranty, 5, 23 user interface, 17, 29, 63 wavelength, 48 UTW, 2, 11, 13, 19, 20, 32, 40, 44, 45, 56, 63 range, 48 Thermo Fisher Scientific Thermo Scientific PikoReal Real-Time PCR System User Manual...
  • Page 70 Notes 68 Thermo Scientific PikoReal Real-Time PCR System User Manual Thermo Fisher Scientific...
  • Page 72 Thermo Fisher Scientific Oy Plesmanlaan 1d 2333 BZ Leiden Ratastie 2, P.O. Box 100 The Netherlands FI-01621 Vantaa T. +31 (0)71 568 10 00 Finland T. Belgium: 0800 71640 sharing knowledge F. +31 (0)71 568 10 10 info@bioke.com www.thermoscientific.com www.bioke.com N11471...

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