Applied Biosystems QuantStudio 3D Digital PCR User Manual
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Applied Biosystems QuantStudio 3D Digital PCR User Manual

Applied Biosystems QuantStudio 3D Digital PCR User Manual

For use with: quantstudio 3d digital pcr instrument proflex 2x flat pcr system or dual flat block geneamp pcr system 9700 quantstudio 3d digital pcr chip v2 or quantstudio 3d digital pcr chip quantstudio 3d digital pcr master mix v2 or quantstudio 3d digi
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USER GUIDE
QuantStudio
for use with:
™
QuantStudio
3D Digital PCR Instrument
™
ProFlex
2x Flat PCR System or Dual Flat Block GeneAmp
™
QuantStudio
3D Digital PCR Chip v2 or QuantStudio
™
QuantStudio
3D Digital PCR Master Mix v2 or QuantStudio
Master Mix
™
QuantStudio
3D Digital PCR Chip Loader
Catalog Number A29154 and A29157
Publication Number MAN0007720
Revision D.0
For Research Use Only. Not for use in diagnostic procedures.
™
3D Digital PCR System
™
PCR System 9700
™
3D Digital PCR Chip
™
3D Digital PCR

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  • Page 1 USER GUIDE ™ QuantStudio 3D Digital PCR System for use with: ™ QuantStudio 3D Digital PCR Instrument ™ ™ ProFlex 2x Flat PCR System or Dual Flat Block GeneAmp PCR System 9700 ™ ™ QuantStudio 3D Digital PCR Chip v2 or QuantStudio 3D Digital PCR Chip ™...
  • Page 2 The information in this guide is subject to change without notice. DISCLAIMER TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT. Limited Use Label License No.

  • Page 3: Table Of Contents

    Contents About this guide ............8 Revision history .
  • Page 4 Contents ■ CHAPTER 3 Prepare the digital PCR reaction and load the chips ..............20 Guidelines for loading and sealing chips .
  • Page 5 Contents ■ CHAPTER 5 Image and analyze the chips ......44 About imaging and primary analysis ..........44 ™...
  • Page 6 Contents Environmental requirements ........... . 88 Network requirements .
  • Page 7 Contents ■ APPENDIX F Safety ........... . 120 Symbols on this instrument .

  • Page 8: About This Guide

    About this guide CAUTION! ABBREVIATED SAFETY ALERTS. Hazard symbols and hazard types specified in procedures may be abbreviated in this document. For the complete safety information, see the “Safety” appendix in this document. IMPORTANT! Before using this product, read and understand the information in the “Safety”...

  • Page 9: Purpose

    About this guide Purpose Purpose This user guide provides step-by-step instructions for preparing and loading samples onto a QuantStudio ™ 3D Digital PCR Chip v2 and QuantStudio ™ 3D Digital PCR ™ Chip, thermal cycling the prepared consumables using a ProFlex 2x Flat PCR System ™...

  • Page 10: Chapter 1 Product Information

    Product information ™ About the QuantStudio 3D Digital PCR System ™ The QuantStudio 3D Digital PCR System provides quantitative and qualitative detection of target nucleic acid sequences (targets) using post-PCR (endpoint) analysis. Using the QuantStudio ™ 3D Digital PCR Instrument, you perform imaging ™...

  • Page 11: Instruments, Kits, Consumables, And Accessories

    Chapter 1 Product information Instruments, kits, consumables, and accessories Instruments, kits, consumables, and accessories The following tables describe the products covered in this user guide. IMPORTANT! Always prepare the QuantStudio ™ 3D Digital PCR Chip v2 with ™ QuantStudio 3D Digital PCR Master Mix v2. Do not prepare v2 chips with old master mix, or vice versa.
  • Page 12 Chapter 1 Product information Instruments, kits, consumables, and accessories Chips and accessories Product Catalog no. Quantity ™ QuantStudio 3D Digital PCR Chips v2, includes: A26316 1 kit (12 chips) ™ • 12 v2 chips, chip lids, and QuantStudio Digital PCR Sample Loading Blades •...

  • Page 13: Chapter 1 Product Information Materials Required But Not Provided

    Chapter 1 Product information Materials required but not provided Reagents Product Catalog no. Quantity ™ QuantStudio 3D Digital PCR Master Mix v2 (for A26358 1.5 mL use with v2 chips) A26359 5.0 mL ™ QuantStudio 3D Digital PCR Master Mix (for use 4482710 1.5 mL with v1 chips)

  • Page 14: Power Line Regulator

    Chapter 1 Product information About the instrument Power line We recommend the use of a 1.5-kVA power line regulator in areas where the supplied power fluctuates in excess of ± 10% of the normal voltage. Power fluctuations can regulator adversely affect the function of the systems. Note: A power line regulator monitors the input current and adjusts the power supplied to the systems.

  • Page 15: Data Collection

    Supported dyes The QuantStudio 3D Digital PCR System features a filter set that is optimized for the ™ ™ ™ ™ Applied Biosystems , ROX , and VIC dyes. About the software ™ The QuantStudio 3D Digital PCR System includes a software suite used to analyze ™...

  • Page 16: About The Chips

    Chapter 1 Product information About the chips About the chips The QuantStudio ™ 3D Digital PCR Chip v2 and QuantStudio ™ 3D Digital PCR Chip are 10-mm high-density reaction plates that each have a single array of 20,000 reaction wells. Hydrophobic coatings on the chip surface enable loading and isolation of independent PCR reactions within the wells.

  • Page 17: Chapter 2 Getting Started

    Getting Started ™ For system installation instructions, see Appendix A, “Install the QuantStudio Digital PCR System“. Operational workflow ™ The following shows a single experiment workflow on the QuantStudio 3D Digital PCR System. The procedures for sample and/or consumable preparation and result analysis can vary depending on the specific experiment that you are performing.

  • Page 18: Connect The Quantstudio ™ 3D Instrument To A Network

    Chapter 2 Getting Started Connect the QuantStudio ™ 3D Instrument to a network Note: Refer to the user documentation for the QuantStudio ™ 3D AnalysisSuite ™ Software for detailed information on data analysis. ™ Connect the QuantStudio 3D Instrument to a network If you choose not to connect the QuantStudio ™...

  • Page 19: Chapter 2 Getting Started Choosing A Thermal Cycler

    Chapter 2 Getting Started Choosing a thermal cycler sample blocks prior to each PCR run. The covers apply pressure to the chips to seat them firmly and precisely on the sample blocks, ensuring efficient heat transfer. ProFlex PCR System POWER STOP GeneAmp ®...

  • Page 20: Guidelines For Loading And Sealing Chips

    Prepare the digital PCR reaction and load the chips ■ Guidelines for loading and sealing chips ....... . 20 ■...

  • Page 21: Prepare The Dna Samples

    Chapter 3 Prepare the digital PCR reaction and load the chips Prepare the DNA samples • Load and seal chips in batches of up to 24 chips (the maximum number that can be loaded onto one thermal cycler). • If you do not intend to load an opened chip immediately, cover the chip using the aluminum plate included in the chip package to prevent contamination.

  • Page 22: Quantitation Methods

    Chapter 3 Prepare the digital PCR reaction and load the chips Prepare the DNA samples Quantitation methods Before performing digital PCR experiments, consider quantifying the amount of gDNA or cDNA in each sample. We recommend the following methods of quantitation: •...

  • Page 23: Determine The Optimal Dilution When The Target Is Unknown

    Chapter 3 Prepare the digital PCR reaction and load the chips Prepare the digital PCR reactions Determine the If the target copy number per genome is unknown (e.g., for a locus of unknown copies per genome or RNA of unknown expression level), we recommend that you optimal dilution determine the optimal dilution by preparing a dilution series of each sample that when the target is...

  • Page 24: Chapter 3 Prepare The Digital Pcr Reaction And Load The Chips Prepare The Digital Pcr Reactions

    Chapter 3 Prepare the digital PCR reaction and load the chips Prepare the digital PCR reactions Recommended The recommended DNA volume in the following reaction is based on a human gDNA sample at 10 ng/μL concentration (final concentration in the reaction is ~3.45 ng/μL), DNA volume and with the target sequence present at two copies per diploid genome.

  • Page 25: Load The Chips Using The Quantstudio ™ 3D Digital Pcr Chip Loader

    Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader 8. Transfer 12 μL of each DNA sample, diluted as appropriate, to the corresponding reaction tube. Mix well by gently pipetting up and down after each transfer (or gently vortex on low-medium speed).

  • Page 26: Chip Loader Status Light

    Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader Chip loader status The LED on top of the chip loader indicates the instrument status. The light is illuminated at all times when the loader is powered on and changes color according to light instrument readiness.

  • Page 27: Prepare The Chip Sealant (V1 Chip Lids Only)

    Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader ™ Prepare the Chip Note: The QuantStudio 3D Digital PCR Chip Lid v2 does not require the use of sealant.

  • Page 28: Load And Seal The Chips

    Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader 4. Carefully depress the plunger until Immersion Fluid flows from the tip of the assembled syringe. Place it on a clean surface and proceed to the next steps. IMPORTANT! Confirm that the tip is locked firmly in place before proceeding.
  • Page 29 Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader 3. Press the sample loading blade lever, then install the QuantStudio ™ 3D Digital PCR Sample Loading Blade into the loader head. IMPORTANT! Press the blade firmly against the loader head to confirm that the blade is properly seated.
  • Page 30 Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader 6. Briefly vortex and centrifuge the prepared dPCR reaction (from “Prepare the dPCR reaction mix“ on page 24), then carefully transfer 14.5 μL of the solution into the sample loading port of the loading blade.
  • Page 31 Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader 8. After loading, hold the Immersion Fluid syringe at an angle over the chip surface without touching the surface, and slowly add several drops of fluid directly onto the chip so that the fluid covers the entire surface.

  • Page 32: Fill The Chip Case With Immersion Fluid

    Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader Fill the chip case 1. Hold the chip and lid assembly by its edges at a 45° angle so that air can escape from the fill port as you fill it.

  • Page 33: Seal The Chip Case With The Label (V2 Chip Lids Only)

    Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader ™ Seal the chip case Note: The following procedure only applies to the QuantStudio 3D Digital PCR Chip Lid v2.

  • Page 34: Seal The Chip Case With Chip Sealant (V1 Chip Lids Only)

    Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader ™ Seal the chip case Note: The QuantStudio 3D Digital PCR Chip Lid v2 does not require the use of sealant.
  • Page 35 Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader 3. When the light shuts off (approximately ³15 seconds), remove the chip and place it on a clean, dry, lint-free surface. IMPORTANT! Do not squeeze sealed chips.

  • Page 36: Chapter 4 Thermal Cycle The Chips

    Thermal cycle the chips ■ Materials required ........... . 36 ■...
  • Page 37 Chapter 4 Thermal cycle the chips Prepare the thermal cycler • Confirm that a QuantStudio ™ 3D Tilt Base is installed beneath the thermal cycler. IMPORTANT! The Tilt Base inclines the sample block by 11°, the angle required for the optimal performance of the chips. 11°...
  • Page 38 Chapter 4 Thermal cycle the chips Prepare the thermal cycler – GeneAmp ™ PCR System 9700 – The version number displayed in the main menu must be 3.12 or greater. 08:00 AM 4/25/13 25.0°C GeneAmp® PCR System 9700 3.12 or Version: 3.12 greater Name:tc001 User:<<pe>>...

  • Page 39: Guidelines For Handling Loaded Chips

    Chapter 4 Thermal cycle the chips Guidelines for handling loaded chips Guidelines for handling loaded chips To ensure the proper function of your loaded chips, handle them according to the following guidelines: • Always wear powder-free gloves. IMPORTANT! Oils from your hands can contaminate the chips and interfere with imaging.

  • Page 40: Chapter 4 Thermal Cycle The Chips Perform The Pcr

    Chapter 4 Thermal cycle the chips Perform the PCR 3. Place the chips onto the sample block so that the fill ports on the chips are positioned toward the front of the thermal cycler. The fill port must be elevated during thermal cycling to ensure that any bubbles float to the top of the case.
  • Page 41 Chapter 4 Thermal cycle the chips Perform the PCR 6. Use the thermal cycler to select and start the pre-programmed run for the chips. See the user guide for your thermal cycler for more information on running methods. When cycling is complete, proceed to unload the thermal cycler. QuantStudio ™...

  • Page 42: Unload The Thermal Cycler

    Chapter 4 Thermal cycle the chips Unload the thermal cycler Unload the thermal cycler You can remove the chips from the thermal cycler immediately after the final extension step at 60°C is complete and the temperature of the block is £25°C. Alternatively, the chips can remain on the block for up to 24 hours at 10°C.
  • Page 43 Chapter 4 Thermal cycle the chips Unload the thermal cycler The chip is now ready to be imaged. IMPORTANT! Store chips in a clean, dry, dark location until you are ready to image them. Prolonged exposure to light can diminish the fluorescence of the photosensitive dyes in the chips.

  • Page 44: Chapter 5 Image And Analyze The Chips

    Image and analyze the chips ■ About imaging and primary analysis ........44 ■...

  • Page 45: About The Instrument Interface

    Chapter 5 Image and analyze the chips About the instrument interface About the instrument interface Network status icon – Represents the Settings button – Touch to open the ™ status of the QuantStudio 3D Digital PCR Instrument Settings menu that allows you Instrument network connection: to set the system date and time, the network connection, the data destination,...

  • Page 46: Chip Imaging

    Chapter 5 Image and analyze the chips Chip imaging Chip imaging Materials • Prepared and thermal cycled chips required • Isopropanol • Gloves, powder-free, nitrile • Low-lint polyester wipes, clean-room grade Guidelines for For optimal efficiency when running large numbers (>6) of chips, follow the guidelines below: imaging multiple chips...

  • Page 47: Specify The Data Destination

    Chapter 5 Image and analyze the chips Chip imaging Specify the data Imaging data is always saved on the instrument, but you can also automatically transfer the data from a run to a USB, cloud, or network destination, as described destination below.

  • Page 48: Image The Chips

    Chapter 5 Image and analyze the chips Chip imaging Image the chips IMPORTANT! Before imaging, confirm that the latest firmware is installed on the ™ ™ QuantStudio 3D Digital PCR Instrument. Imaging and analysis of the QuantStudio 3D Digital PCR Chip v2 requires firmware version 3.0 or later. Note: If you are unsure of the firmware version, see “Check the instrument firmware“...
  • Page 49 Chapter 5 Image and analyze the chips Chip imaging 3. Confirm that the chip is correctly aligned, then close the tray to begin chip detection and imaging. You can monitor the progress of the run in the touchscreen, which counts down the time remaining. IMPORTANT! Do not open the chip tray or remove the USB drive (if present) while the instrument displays the countdown.
  • Page 50 Chapter 5 Image and analyze the chips Chip imaging 5. The instrument is done imaging when the touchscreen displays the Analyzing Chip screen. At this point, you can either wait for the instrument to complete the analysis and display the results, or you can open the chip tray and remove the chip.

  • Page 51: Primary Analysis

    Chapter 5 Image and analyze the chips Primary analysis After a chip has been read: • You can reread imaged chips, but we recommend storing them in the dark if you plan to reread them later. We recommend rereading them within 1 hour after the initial reading, though storing them in the dark may prolong their read life.

  • Page 52: Chapter 5 Image And Analyze The Chips Primary Analysis

    Chapter 5 Image and analyze the chips Primary analysis In the results screen, the instrument displays the following information: Chip ID – Displays the ID number of the Data destination icon – Represents the chip. If the instrument cannot read the selected data destination: chip ID, the touchscreen displays the date •...

  • Page 53: Data Quality Flags

    Chapter 5 Image and analyze the chips Primary analysis Data quality flags Data quality flags generated and displayed by the software are a measure of the overall chip quality, based on well quality thresholds and other data analysis characteristics. Note: For more information on quality assessment in the software, see the user documentation for the QuantStudio ™...

  • Page 54: Transfer The Results

    Chapter 5 Image and analyze the chips Primary analysis Transfer the If you did not transfer data from the instrument to a USB, cloud, or network location at the time of the run (as described in “Specify the data destination“ on page 47), you results can use the Run History screen to copy experiment files to a USB drive for storage or manual transfer.

  • Page 55: Reanalyze Well Volumes

    Chapter 5 Image and analyze the chips Primary analysis The Run History screen displays the data transfer status next to each file in the instrument memory: • Pass – The instrument successfully transferred the file to the selected destination. • In Progress – The instrument is either processing the imaging data for the associated file, or transferring the file to the selected destination.

  • Page 56: Using The Quantstudio ™ 3D Analysissuite ™ Software

    Chapter 5 Image and analyze the chips Using the QuantStudio ™ 3D AnalysisSuite ™ Software 3. From the Main Menu of the touchscreen, touch to open the Settings menu, then touch Maintenance & Service. 4. Touch Modify Volume & Reanalyze. If you have not inserted a USB drive, you will be prompted to do so.

  • Page 57: Access The Software From A Cloud Account

    Chapter 5 Image and analyze the chips Using the QuantStudio ™ 3D AnalysisSuite ™ Software ™ Access the When deployed in cloud configuration, the AnalysisSuite Software is accessed as a web-based application that can be run using any compatible web browser (see software from a “System requirements“...

  • Page 58: Chapter 6 Troubleshooting

    Troubleshooting Troubleshooting chip images using the Chip View The following table summarizes some of the more common problems that can affect imaging of chips. In the examples shown below, the conditions triggered a data flag ™ and were diagnosed using the Chip View of the AnalysisSuite Software.
  • Page 59 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action A bubble was present in the If possible, use the ™ loading blade when it was used to AnalysisSuite Software to filter apply the PCR reaction to the the low quality data points, or chip.
  • Page 60 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action • The chip leaked during If present, remove excess thermal cycling or imaging. Immersion Fluid from the chip lid and run the chip again. • A large bubble was present in the chip (insufficient If possible, use the Immersion Fluid).
  • Page 61 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action Chip was not completely covered Add Immersion Fluid as soon as with Immersion Fluid the loading blade is off of the immediately after loading (while chip. still on the chip loader or heated Ensure that entire chip is covered block)
  • Page 62 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action Condensation may have been IMPORTANT! Condensation present on the chip during may not be visible on the chip. imaging. • If condensation is not visible – If possible, read the chip again after it has warmed to room temperature.
  • Page 63 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action ™ Excess template was loaded onto In AnalysisSuite Software, check the chip. the copies per reaction and dilute the sample accordingly so that it is within the digital range. QuantStudio ™...
  • Page 64 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action Too much sample was left in Ensure that you are loading only loading blade. 14.5 µL of reaction mix into the loading blade. Note: The top image on the left ™...

  • Page 65: Appendix A Install The Quantstudio ™ 3D Digital Pcr System

    ™ Install the QuantStudio 3D Digital PCR System Time required for installation ™ You can install the QuantStudio 3D Digital PCR System in approximately one hour. Note: The time can vary depending on the type of networking solution that you choose.

  • Page 66: Appendix A Install The Quantstudio Plan The Laboratory Layout

    Appendix A Install the QuantStudio ™ 3D Digital PCR System Plan the laboratory layout Plan the laboratory layout When planning the placement of the QuantStudio ™ 3D Digital PCR System components, follow good laboratory practices for PCR. When preparing samples for dPCR amplification, maintain separate areas and dedicated equipment and supplies for pre-PCR (sample preparation, reaction setup, chip loading and sealing) and PCR/ post-PCR (amplification and chip reading).

  • Page 67: Install The Quantstudio ™ 3D Digital Pcr Instrument

    Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the QuantStudio ™ 3D Digital PCR Instrument ™ Install the QuantStudio 3D Digital PCR Instrument 1. Plan the organization of your laboratory. Identify the locations of all stations in ™...
  • Page 68 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the QuantStudio ™ 3D Digital PCR Instrument c. Inspect the instrument for damage caused during transportation. If the instrument is damaged, note the location and appearance of the damage, then contact customer support or your service representative for assistance.
  • Page 69 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the QuantStudio ™ 3D Digital PCR Instrument 7. Connect the power cord to the instrument, press the power switch to the ON position, then wait for it to start (~30 seconds). The instrument is ready to configure when the touchscreen displays the End User License Agreement.
  • Page 70 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the QuantStudio ™ 3D Digital PCR Instrument 10. In the Choose Connection Type screen, select the appropriate connection: Connection Action Wired Touch LAN, then wait for the instrument to connect to the network.
  • Page 71 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the QuantStudio ™ 3D Digital PCR Instrument 11. In the Network Complete screen, touch OK. 12. In the Configuration screen, touch Edit to change the instrument settings. 13. In the Edit Configuration screen, modify the fields as needed, then touch Save. •...

  • Page 72: Install The Proflex ™ 2X Flat Pcr System

    Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the ProFlex ™ 2x Flat PCR System 14. In the Configuration screen, touch OK to accept the instrument configuration. The QuantStudio ™ 3D Digital PCR Instrument is ready to use when the touchscreen displays the Start Run screen.
  • Page 73 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the ProFlex ™ 2x Flat PCR System c. Remove the Base Module from the package and set it on a clean, level surface, then remove the protective cover. 15.2 cm (6 in) ProFlex PCR System...
  • Page 74 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the ProFlex ™ 2x Flat PCR System b. While holding the riser in place with one hand, insert the thin end of the cable tie through the opening at the base of the foot. When the end is visible on the other side of the foot, draw the cable tie through and connect the ends to form a loop.
  • Page 75 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the ProFlex ™ 2x Flat PCR System e. Using the second cable tie, repeat steps a-d to secure the riser at the other end of the foot. 45° 6. Using scissors, remove the excess material from each cable tie. 7.
  • Page 76 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the ProFlex ™ 2x Flat PCR System 8. Unpack and install the sample block module: a. Open the package containing the sample block module and inspect it for damage caused during transportation. If the module is damaged, note the location and appearance of the damage, then contact customer support for assistance.
  • Page 77 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the ProFlex ™ 2x Flat PCR System 10. Set up the ProFlex ™ PCR System: a. Open the package containing the Chip Adapters and install them. Note: Each Chip Adapter includes a set of four alignment pegs that fit into the holes of a flat sample block.

  • Page 78: Install The Geneamp

    Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the GeneAmp ™ PCR System 9700 11. For optimal results, create a new method from the existing 3D template supplied ™ with the ProFlex PCR System and verify the pre-defined method for thermal cycling the chips: ™...
  • Page 79 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the GeneAmp ™ PCR System 9700 b. Remove the packing crate from the package, and verify that it contains all of the parts listed on the shipping manifest. If you have not received one or more of the parts, contact customer support for replacement (see “Customer and technical support“...
  • Page 80 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the GeneAmp ™ PCR System 9700 d. Push the lever into the Base Module to secure the Dual Flat Block Module. e. Inspect the Dual Flat Block Module for damage caused during transportation.
  • Page 81 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the GeneAmp ™ PCR System 9700 c. Connect the GeneAmp ™ PCR System 9700 power cord, power on the thermal cycler, then wait for it to start (about 30 seconds). The cooling fan powers up and the start-up screens appear.
  • Page 82 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the GeneAmp ™ PCR System 9700 b. Press the 24 Hr (F2) or PM (AM) (F3) soft keys until the format you want for the current time displays in the Time field. c.
  • Page 83 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the GeneAmp ™ PCR System 9700 c. In the User Name field, enter an alphanumeric name up to six characters in length, then press Accept (F1) to accept a name. abcdefghi jklmnopqrj stuvwxyz...
  • Page 84 Appendix A Install the QuantStudio ™ 3D Digital PCR System Install the GeneAmp ™ PCR System 9700 Note: For information on programming the GeneAmp ™ PCR System 9700, see ™ the GeneAmp PCR System 9700 Base Module User Manual (Pub. no. 4303481). ™...

  • Page 85: Appendix B Specifications And Layout

    Specifications and Layout ■ Component dimensions and weights ........85 ■...

  • Page 86: Appendix B Specifications And Layout Quantstudio ™ 3D Digital Pcr Instrument Layout And Connections

    Appendix B Specifications and Layout QuantStudio ™ 3D Digital PCR Instrument layout and connections ™ QuantStudio 3D Digital PCR Instrument layout and connections ™ ™ The QuantStudio 3D Digital PCR Instrument and the ProFlex 2x Flat PCR System ™ (or Dual Flat Block GeneAmp PCR System 9700) can be placed on separate benches or collocated as shown in the following figure.

  • Page 87: Electrical Specifications

    Appendix B Specifications and Layout Electrical specifications Electrical specifications WARNING! For safety, the power outlet used for powering the instrument must be accessible at all times. In case of emergency, you must be able to immediately disconnect the main power supply to all the equipment. Allow adequate space between the wall and the equipment so that the power cords can be disconnected in case of emergency.

  • Page 88: Environmental Requirements

    Appendix B Specifications and Layout Environmental requirements Environmental requirements Ensure that the installation room is maintained under correct environmental conditions. Condition Acceptable Range Installation site Indoor use only Humidity Recommended range: 30% to 60% (noncondensing) Temperature Recommended range: 18°C to 22°C Thermal output During operation the net thermal output, based on the actual current ™...

  • Page 89: Network Requirements

    Appendix B Specifications and Layout Network requirements Network requirements ™ The QuantStudio 3D Digital PCR Instrument supports IPv4 TCP/IP communication and provides two methods for integrating the device into a local area network (LAN, also see “Materials required“ on page 101): •...

  • Page 90: Appendix C Maintenance

    Maintenance ■ Cleaning the chip tray and sample block ....... . 90 ■...

  • Page 91: Appendix C Maintenance Cleaning The Chip Tray And Sample Block

    Appendix C Maintenance Cleaning the chip tray and sample block Clean the chip tray CAUTION! PHYSICAL INJURY HAZARD. Do not remove the covers to the or sample block ™ QuantStudio 3D Instrument or thermal cycler. There are no components inside the instruments that you can safely service yourself. If you suspect a problem, contact technical support (see “Customer and technical support“...

  • Page 92: Configure The Instrument Settings

    Appendix C Maintenance Configure the instrument settings Configure the instrument settings After you install the QuantStudio ™ 3D Digital PCR Instrument, you can configure the instrument settings for your region as explained below. (Optional) Set the ™ Note: The serial number of the QuantStudio 3D Instrument is the default ™...

  • Page 93: Set The Date And Time

    Appendix C Maintenance Check the instrument firmware Set the date and Use this procedure to manually configure the time zone, date, and time settings for your instrument. time ™ Note: If connected to a network, the QuantStudio 3D Instrument will automatically synchronize the date and time settings via Network Time Protocol (NTP).

  • Page 94: Update The Instrument Firmware

    Appendix C Maintenance Check the instrument firmware 3. In the Maintenance & Service screen, touch Software Update. The firmware version is displayed on the screen after Embedded SW Ver:. 4. If the version is <3.0, update the firmware as follows. ™...

  • Page 95: Returning Your Instrument For Service

    Appendix C Maintenance Returning your instrument for service 5. In the Software Upgrade screen, touch OK to proceed with the update. IMPORTANT! Do not remove the USB drive from the instrument until after the update is complete. 6. After the upgrade is complete and the instrument restarts, re-calibrate the touchscreen (if prompted), then re-check the firmware version to confirm the success of the update.

  • Page 96: Replace The Instrument Fuses

    Appendix C Maintenance Replace the instrument fuses 5. Pack the instrument in the provided packaging, without any accessories or power cords. Include a hard copy of the Certificate of Instrument Decontamination in the box. Note: Repairs for instruments without the Certificate of Instrument Decontamination are delayed.

  • Page 97: Calibrate The Touchscreen

    Appendix C Maintenance Calibrate the touchscreen 3. Remove each fuse from its fuse holder and inspect it for damage. Carbon typically coats the inside of failed fuses. 4. Replace each failed fuse with a 1.6A, Time-Lag T, 250VAC, 5 × 20-mm Fuse. Note: The voltage and amperage ratings are on the fuse holder.

  • Page 98: View The Instrument Log

    Appendix C Maintenance View the instrument log View the instrument log ™ You can use the QuantStudio 3D Digital PCR Instrument touchscreen to view and export a log that summarizes the past 6 months of instrument activity. For each event, the log provides a description of the activity and the date/time when it occurred.

  • Page 99: Appendix D Networking

    Networking ■ Networking overview ..........99 ■...

  • Page 100: Appendix D Networking Connect The Instrument To The Network

    Appendix D Networking Connect the instrument to the network The QuantStudio ™ 3D Extended Arm WiFi Adapter sold for use with the instrument can be installed to an internal USB port behind the rear panel to enable wireless network connectivity. See the product documentation accompanying the adaptor for the network requirements, specifications, and product details.

  • Page 101: Materials Required

    Appendix D Networking Connect the instrument to the network Materials Connection Materials required Wired CAT6 Ethernet cable of sufficient length with RJ45 connectors (for a 1000Mbit/s network connection or a CAT5 for a 100Mbit/s connection) ™ Wireless QuantStudio 3D Extended Arm WiFi Adapter (Catalog no. A28598) Required network Before beginning the installation, collect from a network administrator your network policy for obtaining IP addresses (DHCP or static IP).

  • Page 102: Connect The Quantstudio ™ 3D Instrument To A Network

    Appendix D Networking Connect the instrument to the network Connect the 1. Prepare the physical connection to the network: ™ QuantStudio Connection Action Instrument to a Wired ™ 1. Power on the QuantStudio 3D Instrument. network 2. Connect one end of a standard category-6 Ethernet cable to the RJ-45 port on the back panel of the instrument and the other end to an open network port.
  • Page 103 Appendix D Networking Connect the instrument to the network 3. Choose the appropriate option: If connecting your instrument to a… Action Wired network that supports DHCP Network setup is complete. ™ Note: The QuantStudio 3D Digital PCR Instrument is pre-configured for DHCP operation and automatically joins the network when connected.
  • Page 104 Appendix D Networking Connect the instrument to the network d. If your selected wireless hotspot is secure, enter the required authentication information (user name/password), then touch OK. If connecting your instrument to a network that supports DHCP, network setup is complete. Otherwise, go to the next step to configure the TCP/IP settings for the instrument.
  • Page 105 Appendix D Networking Connect the instrument to the network c. If you elected to assign a static IP to the instrument, touch the following fields and enter the: • IP Address – Enter the static IP address for the instrument. •...
  • Page 106 Appendix D Networking Connect the instrument to the network e. Touch , then configure the Windows Internet Naming Service (WINS) settings: • Windows Domain – Enter the domain name of the WINS server. • WINS Server – Enter the IP addresses for the primary (top) and secondary (bottom) WINS servers.

  • Page 107: Create A Network Destination To Receive Run Data

    Appendix D Networking Connect the instrument to the network 7. In the Network Complete screen, touch OK, then touch to return to the Main Menu. After the instrument has successfully connected to the network, the Network Setup screen displays the details of the network connection. Note: If your wireless hotspot performs MAC filtering, you can obtain the ™...
  • Page 108 Appendix D Networking Connect the instrument to the network 3. In the Edit Destinations screen, touch Add to add a data destination. Note: To edit an existing destination, touch the name of the destination. 4. In the Choose Destination Type screen, touch the desired network destination: •...
  • Page 109 Appendix D Networking Connect the instrument to the network • LAN data destination fields: – Target Name – Enter a name to identify the LAN data destination. Note: The target name appears within the Destination Selection and Export screens. – Server – Enter the path of the file server using the following syntax, where smb: and path are optional: –...

  • Page 110: Appendix E Load Chips Manually

    Load chips manually For instructions on loading chips using the QuantStudio ™ 3D Digital PCR Chip Loader, see “Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader “ on page 25. ™ The following procedure describes how to load the QuantStudio 3D Digital PCR ™...

  • Page 111: Appendix E Load Chips Manually Materials Required

    Appendix E Load chips manually Materials required • Load chips in alphanumeric order (according to the chip ID printed on the lid) to avoid data entry errors. • Apply the chip lid and add Immersion Fluid immediately after loading each chip to avoid evaporation.

  • Page 112: Prepare The Chip Sealant (V1 Chip Lids Only)

    Appendix E Load chips manually Prepare the Chip Sealant (v1 chip lids only) Prepare the Chip Sealant (v1 chip lids only) ™ Note: The QuantStudio 3D Digital PCR Chip Lid v2 does not require the use of sealant. If you are using this lid, skip these steps. 1.

  • Page 113: Load And Seal The Chips Manually

    Appendix E Load chips manually Load and seal the chips manually 4. Carefully depress the plunger until Immersion Fluid flows from the tip of the assembled syringe. Place it on a clean surface and proceed to the next steps. IMPORTANT! Confirm that the tip is locked firmly in place before proceeding. IMPORTANT! Open only one syringe at a time.
  • Page 114 Appendix E Load chips manually Load and seal the chips manually 3. Open the chip package, gently grasp the chip by its sides, then place it face-up on the heated block, preheated to 40°C. IMPORTANT! Allow the chip to sit on the heated block for at least 5 seconds before loading it.
  • Page 115 Appendix E Load chips manually Load and seal the chips manually c. While holding the loading blade at a 70-80° angle relative to the heated block so that the port faces up, place the edge of the blade at the end of the chip.

  • Page 116: Fill The Chip Case With Immersion Fluid

    Appendix E Load chips manually Fill the chip case with Immersion Fluid 5. Seal the chip: a. Remove the red protective film from the chip lid, then carefully place it onto the prepared chip so that the window in the lid aligns with the chip. IMPORTANT! Before applying the chip lid, make certain that it is correctly oriented to the chip assembly.

  • Page 117: Seal The Chip Case With The Label (V2 Chip Lids Only)

    Appendix E Load chips manually Seal the chip case with the label (v2 chip lids only) Figure 6 QuantStudio ™ 3D Digital PCR Chip Lid 3. Carefully dispense Immersion Fluid into the port until the chip case contains an air bubble slightly larger than the fill port (<2–3 mm in diameter). Rotate the chip slightly to expose any hidden bubble.

  • Page 118: Seal The Chip Case With Sealant Using The Uv Stylus (V1 Chip Lids Only)

    Appendix E Load chips manually Seal the chip case with sealant using the UV Stylus (v1 chip lids only) 4. Inspect the sealed chip for potential problems: • Leaks – Confirm that no fluid is leaking from the fill port or from the seal between the chip and lid.
  • Page 119 Appendix E Load chips manually Seal the chip case with sealant using the UV Stylus (v1 chip lids only) 2. Power on the UV Stylus in the UV Stylus Stand by twisting the cap near the power button. Note: The UV Stylus can remain on until all chips are loaded. To maximize battery life, make sure to power off the UV Stylus after the last chip has been sealed.

  • Page 120: Appendix F Safety

    Safety WARNING! GENERAL SAFETY. Using this product in a manner not specified in the user documentation may result in personal injury or damage to the instrument or device. Ensure that anyone using this product has received instructions in general safety practices for laboratories and the safety information provided in this document.

  • Page 121: Conformity Symbols

    Appendix F Safety Symbols on this instrument Symbol English Français Do not dispose of this product in Ne pas éliminer ce produit avec les unsorted municipal waste déchets usuels non soumis au tri sélectif. CAUTION! To minimize CAUTION! Pour minimiser negative environmental impact from disposal of les conséquences négatives...

  • Page 122: Safety Alerts On This Instrument

    Appendix F Safety Safety alerts on this instrument Safety alerts on this instrument Additional text may be used with one of the symbols described above when more specific information is needed to avoid exposure to a hazard. See the following table for safety alerts found on the instrument.

  • Page 123: Safety Information For Instruments Not Manufactured By Thermo Fisher Scientific

    Appendix F Safety Safety information for instruments not manufactured by Thermo Fisher Scientific Safety information for instruments not manufactured by Thermo Fisher Scientific Some of the accessories provided as part of the instrument system are not designed or built by Thermo Fisher Scientific. Consult the manufacturer's documentation for the information needed for the safe use of these products.

  • Page 124: Cleaning And Decontamination

    Appendix F Safety Safety and electromagnetic compatibility (EMC) standards Cleaning and CAUTION! Cleaning and Decontamination. Use only the cleaning and decontamination decontamination methods specified in the manufacturer's user documentation. It is the responsibility of the operator (or other responsible person) to ensure the following requirements are met: ·...

  • Page 125: Appendix F Safety Chemical Safety

    Appendix F Safety Chemical safety Reference Description Limits and Methods of Measurement of AS/NZS 2064 Electromagnetic Disturbance Characteristics of Industrial, Scientific, and Medical (ISM) Radiofrequency Equipment ICES-001, Issue 3 Industrial, Scientific and Medical (ISM) Radio Frequency Generators Environmental Reference Description design Directive 2002/96/EC European Union “WEEE Directive”...

  • Page 126: Biological Hazard Safety

    Appendix F Safety Biological hazard safety Biological hazard safety WARNING! Potential Biohazard. Depending on the samples used on this instrument, the surface may be considered a biohazard. Use appropriate decontamination methods when working with biohazards. WARNING! BIOHAZARD. Biological samples such as tissues, body fluids, infectious agents, and blood of humans and other animals have the potential to transmit infectious diseases.

  • Page 127: Documentation And Support

    Documentation and support Customer and technical support Visit thermofisher.com/techresources for the latest in services and support, including: • Worldwide contact telephone numbers • Product support, including: – Product FAQs – Software, patches, and updates • Order and web support • Product documentation, including: –...
  • Page 128 For support visit thermofisher.com/techresources or email techsupport@lifetech.com thermofisher.com/lifescience 23 July 2015...

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