Table of Contents
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QuantStudio
USER GUIDE
for use with:
™
QuantStudio
3D Digital PCR Instrument
™
ProFlex
2 × Flat PCR System or Dual Flat Block GeneAmp
System 9700
™
QuantStudio
3D Digital PCR 20K Chip v2
™
QuantStudio
3D Digital PCR Master Mix v2
™
QuantStudio
3D Digital PCR Chip Loader
Catalog Number A29154
Publication Number MAN0007720
Revision E.0
For Research Use Only. Not for use in diagnostic procedures.
™
3D Digital PCR System
™
PCR
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Table of Contents
Related Manuals for Thermo Scientific Applied Biosystems QuantStudio
Summary of Contents for Thermo Scientific Applied Biosystems QuantStudio
- Page 1 ™ QuantStudio 3D Digital PCR System USER GUIDE for use with: ™ QuantStudio 3D Digital PCR Instrument ™ ™ ProFlex 2 × Flat PCR System or Dual Flat Block GeneAmp System 9700 ™ QuantStudio 3D Digital PCR 20K Chip v2 ™...
- Page 2 Manufacturer: Products: Life Technologies Holdings Pte Ltd | QuantStudio ™ 3D Digital PCR Instrument Block 33 | ™ ProFlex 2 × Flat PCR System Marsiling Industrial Estate Road 3 | ™ Dual Flat Block GeneAmp PCR System 9700 #07-06, Singapore 739256 ™...
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Page 3: Table Of Contents
Contents ■ CHAPTER 1 Product information ........8 ™... - Page 4 Contents Determine the optimal dilution when the target is known ......21 Determine the optimal dilution when the target is unknown ..... . 22 Prepare the digital PCR reactions .
- Page 5 Contents ■ CHAPTER 6 Troubleshooting ......... . 54 Troubleshooting chip images using the Chip View .
- Page 6 Contents Replace the instrument fuses ........... . 90 Materials required .
- Page 7 Contents ■ Documentation and support ......... . . 123 Related documentation .
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Page 8: 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. ™ Use the QuantStudio 3D Digital PCR Instrument to perform imaging and preliminary ™... -
Page 9: 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. Instrument system Item Catalog No. Amount ™ QuantStudio 3D Digital PCR System package A29154 1 system with v2 chips and master mix, includes: •... -
Page 10: Required Materials Not Supplied
Chapter 1 Product information Required materials not supplied Instrument system Item Catalog No. Amount ™ QuantStudio 3D Digital PCR Chip Loader 4482592 1 loader ™ QuantStudio 3D Digital PCR Chip Lids v2 and A29247 12 each ™ QuantStudio 3D Digital PCR Sample Loading Blades ™... - Page 11 Chapter 1 Product information Required materials not supplied Item Source Water, DNase-free, sterile-filtered Water, deionized Isopropanol (Required for manual chip loading only) Heated block (capable of maintaining 40±1°C) QuantStudio ™ 3D Digital PCR System User Guide...
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Page 12: Power Line Regulator
Chapter 1 Product information About the instrument Power line Use a 1.5-kVA power line regulator in areas where the supplied power fluctuates in regulator excess of ± 10% of the normal voltage. Power fluctuations can 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 13: Data Collection
Chapter 1 Product information About the software Data collection ™ The QuantStudio 3D Digital PCR Instrument collects raw fluorescence data from the ™ QuantStudio 3D Digital PCR 20K Chip v2 following PCR amplification. The instrument performs multiple image captures of the chip in the following three phases: 1. -
Page 14: About The Chip
Chapter 1 Product information About the chip About the chip ™ The QuantStudio 3D Digital PCR 20K Chip v2 is a 10-mm high-density reaction plate that has 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 15: Chapter 2 Getting Started
Getting Started ™ For system installation instructions, see Appendix A, “Install the QuantStudio Digital PCR System”. QuantStudio ™ 3D Digital PCR System User Guide... -
Page 16: Operational Workflow
Chapter 2 Getting Started Operational workflow Operational workflow ™ The following shows a single experiment workflow on the QuantStudio 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 17: Connect The Quantstudio ™ 3D Digital Pcr Instrument To A Network
Chapter 2 Getting Started Connect the QuantStudio ™ 3D Digital PCR Instrument to a network ™ Connect the QuantStudio 3D Digital PCR Instrument to a network ™ If you choose not to connect the QuantStudio 3D Instrument using the setup wizard during installation, you can connect it to a network at any time afterwards to ™... - Page 18 Chapter 2 Getting Started Choosing a thermal cycler ProFlex PCR System POWER STOP GeneAmp ® PCR System 9700 ENTER ProFlex Instrument GeneAmp Instrument USB port Touchscreen Heated cover LCD display Keypad Power button QuantStudio ™ 3D Digital PCR System User Guide...
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Page 19: The Chips
Prepare the digital PCR reaction and load the chips ■ Guidelines for loading and sealing chips ....... . 19 ■... -
Page 20: Prepare The Dna Samples
Chapter 3 Prepare the digital PCR reaction and load the chips Prepare the DNA samples • Apply the chip lid and add Immersion Fluid immediately after loading each chip to avoid evaporation. • Load and seal chips in batches of up to 24 chips (the maximum number that can be loaded onto one thermal cycler). -
Page 21: Sample Dilution
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 22: 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 optimal dilution copies per genome or RNA of unknown expression level), we recommend that you when the determine the optimal dilution by preparing a dilution series of each sample that includes three to four data points above and below the expected digital range. -
Page 23: Recommended Dna Volume And Concentration
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 DNA volume sample at 10 ng/µL concentration (final concentration in the reaction is ~3.45 ng/μL), with the target sequence present at two copies per diploid genome. -
Page 24: 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 5. Mix well by gently pipetting up and down (or gently vortex on low-medium speed). 6. Transfer 34.8 µL of the dPCR reaction mix to the labeled reaction tube. 7. -
Page 25: 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 The LED on top of the chip loader indicates the instrument status. The light is status light illuminated at all times when the loader is powered on and changes color according to instrument readiness. -
Page 26: Prepare The Syringe Containing The Immersion Fluid
Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader Prepare the 1. Remove the Immersion Fluid syringe, plunger, and tip from the packaging. syringe 2. Before uncapping the syringe, gently pull back the plunger 1-2 mm and release containing the it to break any resistance that may have formed during storage. -
Page 27: 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 Load and seal ™ Before using the QuantStudio 3D Digital PCR Chip Loader, wait until the status light the chips illuminates solid green, indicating that the chip nest has reached operating temperature. - Page 28 Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader Lid nest button Lid nest, with the lid in the correct orientation 6. Briefly vortex and centrifuge the prepared dPCR reaction (from “Prepare the dPCR reaction mix for each sample”...
- Page 29 Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader 7. Ensure that the loading blade is firmly seated on the loader arm. 8. Press the dark grey/black loading button to load the chip. Loading button The status light flashes green during the loading sequence, and displays solid green when finished.
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Page 30: 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 10. Rotate the loader arm so that the chip lid solidly contacts the chip. Firmly press down on the arm for 15 seconds to ensure a tight seal (you can count each flash of the status light, which flashes at 1‑second intervals). -
Page 31: Seal The Chip Case With The Label
Chapter 3 Prepare the digital PCR reaction and load the chips Load the chips using the QuantStudio ™ 3D Digital PCR Chip Loader Proceed to sealing the chip case. Seal the chip 1. Gently pull back the top half of the label on the chip lid. case with the 2. -
Page 32: Chapter 4 Thermal Cycle The Chips
Thermal cycle the chips ■ Materials required ........... . 32 ■... - Page 33 Chapter 4 Thermal cycle the chips Prepare the thermal cycler ™ • Confirm that a QuantStudio 3D Digital PCR 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.
- Page 34 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 later. 08:00 AM 4/25/13 25.0°C GeneAmp® PCR System 9700 Version: 3.12 Name:tc001 User:<<pe>> Create Edit Util...
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Page 35: 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 36: Perform The Pcr
Chapter 4 Thermal cycle the chips Perform the PCR Perform the PCR CAUTION! PHYSICAL INJURY HAZARD. During operation, the sample block can be heated to 100°C. Before performing the following procedure, be sure to wait until the sample block reaches room temperature. IMPORTANT! Thermal cycle prepared chips within 2 hours after loading them. - Page 37 Chapter 4 Thermal cycle the chips Perform the PCR 4. Lay the Thermal Pads over the chips. CAUTION HOT IMPORTANT! Make sure that each thermal pad is centered on the sample block and it completely covers the chips. Do not allow the pads to become dirty. Fluids, debris, and other contaminants that adhere to the pad can transfer to the chips during thermal cycling and fluoresce during imaging.
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Page 38: Unload The Thermal Cycler
Chapter 4 Thermal cycle the chips Unload the thermal cycler When cycling is complete, proceed to 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 39 Chapter 4 Thermal cycle the chips Unload the thermal cycler 4. Remove the Chip Adapters from the sample block and place them on a clean, dry surface. Remove the chips from the adapters and allow them to equilibrate to room temperature. Note: To remove a chip from a adapter, push the chip from beneath and grasp the edges of the case, then remove it.
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Page 40: Chapter 5 Image And Analyze The Chips
Image and analyze the chips ■ About imaging and primary analysis ........40 ■... -
Page 41: About The Instrument Interface
Chapter 5 Image and analyze the chips About the instrument interface About the instrument interface ™ Network status icon—Represents the status of the QuantStudio 3D Digital PCR Instrument network connection: • —Wired (Ethernet) connection selected; connected to network. • —Wired (Ethernet) connection selected; no connection available. •... -
Page 42: 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 imaging below: multiple chips... -
Page 43: Image The Chips
Chapter 5 Image and analyze the chips Chip imaging Note: Whichever destination you select, imaging data is also saved on the instrument, up to a limit of ~600 experiment files, after which the oldest files will be purged from memory and replaced with newer files. Image the IMPORTANT! Before imaging, confirm that the latest firmware is installed on the chips... - Page 44 Chapter 5 Image and analyze the chips Chip imaging 2. Open the chip tray and load the chip face-up into the tray, with the chip ID and fill port toward the front of the instrument. Note: The chip will only fit in the tray in one orientation. 443MPJ Orient the chip barcode toward the front of the instrument.
- Page 45 Chapter 5 Image and analyze the chips Chip imaging Using the prefix example shown above, the resulting file name would be MyPrefix_date_time_chipID.eds. 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.
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Page 46: Primary Analysis
Chapter 5 Image and analyze the chips Primary analysis 7. After chip analysis on the instrument is complete, the results are stored on the instrument. • If you have not removed the chip from the tray, the touchscreen will display the results after analysis (see “About the results screen”... -
Page 47: About The Results Screen
Chapter 5 Image and analyze the chips Primary analysis About the ™ After chip imaging and analysis, the results are stored on the QuantStudio results screen Digital PCR Instrument. • If you have not removed the chip from the tray, the instrument touchscreen will display the results after analysis. -
Page 48: Data Quality Flags
Chapter 5 Image and analyze the chips Primary analysis Data quality Data quality flags generated and displayed by the software are a measure of the flags 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 ™... -
Page 49: Transfer The Results
Chapter 5 Image and analyze the chips Primary analysis ™ Following an image analysis, the QuantStudio 3D Digital PCR Instrument transfers the experiment (.eds) file for the chip to the selected destination and saves a copy of the file locally to the instrument. You can access and/or download the experiment (.eds) files of previous runs from the Run History screen. - Page 50 Chapter 5 Image and analyze the chips Primary analysis 4. In the Run History screen, touch the entry of the experiment that you want to transfer or view. The Run History screen displays the data transfer status next to each file in the instrument memory: •...
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Page 51: Using The Quantstudio ™ 3D Analysissuite ™ Software
Chapter 5 Image and analyze the chips Using the QuantStudio ™ 3D AnalysisSuite ™ Software ™ ™ Using the QuantStudio 3D AnalysisSuite Software ™ After the analyzed imaging data has been transferred to the QuantStudio ™ AnalysisSuite Software, you can log into the software to perform the secondary analysis as described below. - Page 52 Chapter 5 Image and analyze the chips Using the QuantStudio ™ 3D AnalysisSuite ™ Software Access the software from the server desktop 1. Double-click QuantStudio ™ 3D AnalysisSuite ™ on the server desktop. ™ ™ By default, the software opens in the Google Chrome browser.
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Page 53: Obtain Information From The Help System
Chapter 5 Image and analyze the chips Using the QuantStudio ™ 3D AnalysisSuite ™ Software 3. Sign in to the software as one of the following users. • Administrator—Enter the user name and password (see “Access the software from the server desktop” on page 52). •... -
Page 54: Chapter 6 Troubleshooting
Troubleshooting Troubleshooting chip images using the Chip View The following table summarizes some of the more common problems that can affect chip imaging. In the examples shown below, the conditions triggered a data flag and ™ ™ were diagnosed using the Chip View of the QuantStudio 3D AnalysisSuite Software. - Page 55 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action ™ A bubble was present in the If possible, use the AnalysisSuite loading blade when it was Software to filter the low quality data used to apply the PCR points, or discard the chip and run the reaction to the chip.
- Page 56 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action • The chip leaked during If you use the chip loader to seal the thermal cycling or chips, ensure that you are using at imaging. least 20 lbs of pressure when applying the chip lid.
- Page 57 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action The chip was not completely Add Immersion Fluid as soon as the covered with Immersion loading blade is off of the chip. Fluid immediately after Ensure that the entire chip is covered loading (while still on the with Immersion Fluid, even the edges.
- Page 58 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action Condensation may have IMPORTANT! Condensation may been present on the chip not be visible on the chip. during imaging. • If condensation is not visible – If possible, read the chip again after it has warmed to room temperature.
- Page 59 Chapter 6 Troubleshooting Troubleshooting chip images using the Chip View Observation Possible Cause Action ™ Excess template was loaded In the AnalysisSuite Software, check onto the chip. the copies per reaction and dilute the sample accordingly so that it is within the digital range.
- Page 60 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 was generated by ™...
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Page 61: Appendix A Install The Quantstudio
™ Install the QuantStudio Digital PCR System Time required for installation ™ You can install the QuantStudio 3D Digital PCR System in approximately 1 hour. Note: The time can vary depending on the type of networking solution that you choose. See Appendix D, “Networking” for a complete description of the networking options supported by the system. -
Page 62: 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 63: 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 64 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 65 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 66 Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the QuantStudio 3D Digital PCR Instrument Connection Action Wireless 1. Touch Wireless. 2. In the Available Wireless Network screen, touch the desired wireless hotspot. Note: The signal strength of a wireless hotspot is indicated by the number of bars present in the wireless icon ( ).
- Page 67 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. •...
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Page 68: Install The Proflex ™ 2 × Flat Pcr System
Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the ProFlex 2 × Flat PCR System 15. Open the QuantStudio ™ 3D Digital PCR Chip Loader package and place the loader on the surface where you will load chips. Attach the power cord to the chip loader and connect it to an outlet. -
Page 69: Prepare The Workspace And Instrument
Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the ProFlex 2 × Flat PCR System 3. 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... - Page 70 Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the ProFlex 2 × Flat PCR System 2. Use the screwdriver to remove the four footings from the instrument. 3. Fit the four risers between the base and the footings, then reattach the footings using the screwdriver.
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Page 71: Unpack And Install The Sample Block Module
Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the ProFlex 2 × Flat PCR System Unpack and 1. Open the package containing the sample block module and inspect it for install the damage caused during transportation. sample block If the module is damaged, note the location and appearance of the damage, module... - Page 72 Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the ProFlex 2 × Flat PCR System 2. Connect the power cord, power on the ProFlex ™ PCR System, then wait for it to start (about 45 seconds). Follow the onscreen instructions to complete the installation.
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Page 73: Install The Geneamp ™ Pcr System 9700
Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the GeneAmp PCR System 9700 Note: For information on opening templates and programming the thermal ™ cycler, see the ProFlex PCR System User Guide (Pub. No. MAN0007697). If ™... -
Page 74: Unpack And Install The Dual Flat Block Module
Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the GeneAmp PCR System 9700 3. 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) POWER STOP... -
Page 75: Install The Tilt Base And Chip Adapter
Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the GeneAmp PCR System 9700 Install the Tilt 1. Open the package containing the QuantStudio ™ 3D Digital PCR Tilt Base for Base and Chip ™ GeneAmp PCR System 9700 and install it beneath the thermal cycler. Adapter 11°... - Page 76 Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the GeneAmp PCR System 9700 2. When the thermal cycler displays the main menu, confirm that the version number displayed on the screen is 3.12 or later. If the version number is earlier than 3.12, contact technical support to upgrade the instrument firmware before continuing.
- Page 77 Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the GeneAmp PCR System 9700 b. Press the D/M/Y or Y/M/D soft keys until the format you want for the current date displays in the Date field. c. Use the numeric keys to enter the values into the Day, Month, and Year fields.
- Page 78 Appendix A Install the QuantStudio ™ 3D Digital PCR System ™ Install the GeneAmp PCR System 9700 d. Configure the Security Code screen according to your needs. User Name: hank PIN number: None Protection: Unlocked Press PIN # to create a #. Then you set protection to Locked to prevent methods from being overwritten or deleted.
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Page 79: Appendix B Specifications And Layout
Specifications and Layout ■ Component dimensions and weights ........79 ■... -
Page 80: 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 2 × 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 81: 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 82: 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 83: 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 96): •... -
Page 84: Appendix C Maintenance
Maintenance ■ Cleaning the chip tray and sample block ....... . 84 ■... -
Page 85: Clean The Chip Tray Or Sample Block
Appendix C Maintenance Cleaning the chip tray and sample block Clean the chip tray or sample block CAUTION! PHYSICAL INJURY HAZARD. Do not remove the covers to the ™ QuantStudio 3D Digital PCR Instrument or thermal cycler. There are no components inside the instruments that you can safely service yourself. -
Page 86: 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 ™ Note: The serial number of the QuantStudio 3D Digital PCR Instrument is the the instrument ™... -
Page 87: Set The Date And Time
Appendix C Maintenance Check the instrument firmware Set the date Use this procedure to manually configure the time zone, date, and time settings for and time your instrument. ™ Note: If connected to a network, the QuantStudio 3D Digital PCR Instrument will automatically synchronize the date and time settings via Network Time Protocol (NTP). -
Page 88: 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 earlier than 3.0, update the firmware as follows. Update the ™... -
Page 89: Returning Your Instrument For Service
Appendix C Maintenance Returning your instrument for service 4. In the Maintenance & Service screen, touch Software Update then wait while the instrument scans the USB drive for the firmware update. 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. -
Page 90: 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 91: 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 92: View The Instrument Log
Appendix C Maintenance View the instrument log 3. Touch each crosshair as shown in the sequence of calibration utility screens. 4. At the end of the calibration sequence, touch OK to save the new touchscreen calibration settings and restart the instrument. View the instrument log ™... - Page 93 Appendix C Maintenance View the instrument log b. In the Instrument Log screen, touch Export, then wait for the instrument to export the log to a text file on the drive. 5. When you are finished, touch , then touch to return to the Main Menu.
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Page 94: Appendix D Networking
Networking ■ Networking overview ..........94 ■... -
Page 95: Networking Guidelines And Best Practices
Appendix D Networking Connect the instrument to the network ™ ™ • Automatic data transfer to the QuantStudio 3D AnalysisSuite Software using the Hypertext Transfer Protocol over a Secure Socket Layer (HTTPS), or data ™ export to a local Windows operating system-based or SAMBA file server over the Server Message Block (SMB) protocol. -
Page 96: Network Setup Workflow
Appendix D Networking Connect the instrument to the network Network setup Start workflow If dynamic network configuration via DHCP is not available, or if you are uncertain, collect the required network information. ™ Connect the QuantStudio 3D Digital PCR Instrument to the network and power on the instrument. - Page 97 Appendix D Networking Connect the instrument to the network ™ • Windows operating system domain (if applicable) • WINS server address(es) (if applicable) If connecting your instrument to a wireless network, obtain the following information for the local wireless hotspot: •...
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Page 98: Connect The Quantstudio 3D Digital Pcr 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 3D Digital PCR 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 99 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 Instrument is pre-configured for DHCP operation and automatically joins the network when connected.
- Page 100 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.
- Page 101 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. • Netmask—Enter a subnet mask for the network if applicable. •...
- Page 102 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.
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Page 103: Create A Network Destination To Receive Run Data
Appendix D Networking Connect the instrument to the network Note: If your wireless hotspot performs MAC filtering, you can obtain the Media ™ Access Control (MAC) address of the QuantStudio 3D Instrument on the label of the WiFi Adapter that you installed in step 1. Create a The following procedure allows you to create network data destinations to receive network... - Page 104 Appendix D Networking Connect the instrument to the network 4. In the Choose Destination Type screen, touch the desired network destination: • Cloud—Touch to specify a Connect cloud-based platform data ™ ™ destination (for your QuantStudio 3D AnalysisSuite Software projects). •...
- Page 105 Appendix D Networking Connect the instrument to the network – User Name—Enter the user name that the instrument should use when authenticating to the file server. – Password—Enter the password that the instrument should use when authenticating to the file server. 6.
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Page 106: 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 24. ™ The following procedure describes how to load the QuantStudio 3D Digital PCR 20K Chip v2. -
Page 107: 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 108: Load And Seal The Chips Manually
Appendix E Load chips manually Load and seal the chips manually 3. Remove the cap from the syringe, then attach the syringe tip by pushing it into place. IMPORTANT! No twisting or screwing is required to attach the tip. 4. Carefully depress the plunger until Immersion Fluid flows from the tip of the assembled syringe. - Page 109 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 110 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.
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Page 111: 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 112: Seal The Chip Case With The Label
Appendix E Load chips manually Seal the chip case with the label 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 113: 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 114: 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 MISE EN GARDE ! Pour negative environmental impact from disposal of electronic minimiser les conséquences... -
Page 115: 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 116: 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 117: Electrical Safety
Appendix F Safety Instrument safety Electrical safety WARNING! Fuse Installation. Before installing the instrument, verify that the fuses are properly installed and the fuse voltage matches the supply voltage. Replace fuses only with the type and rating specified for the unit. Improper fuses can damage the instrument wiring system and cause a fire. -
Page 118: Cleaning And Decontamination
Appendix F Safety Safety and electromagnetic compatibility (EMC) standards Cleaning and decontamination CAUTION! Cleaning and Decontamination. Use only the cleaning and 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 119: Safety
Appendix F Safety Safety and electromagnetic compatibility (EMC) standards Safety Reference Description EU Directive European Union “Low Voltage Directive” 2006/95/EC CSA C22.2 No. Safety requirements for electrical equipment for measurement, 61010-1 control, and laboratory use – Part 1: General requirements IEC 61010-1 UL 61010-1 IEC/CSA/UL... -
Page 120: Chemical Safety
Appendix F Safety Chemical safety Chemical safety WARNING! GENERAL CHEMICAL HANDLING. To minimize hazards, ensure laboratory personnel read and practice the general safety guidelines for chemical usage, storage, and waste provided below. Consult the relevant SDS for specific precautions and instructions: ·... - Page 121 Appendix F Safety Chemical safety · Limiter l’inhalation des produits chimiques. Ne pas laisser les récipients de produits chimiques ouverts. Ils ne doivent être utilisés qu’avec une ventilation adéquate (par exemple, sorbonne). · Vérifier régulièrement l’absence de fuite ou d’écoulement des produits chimiques. En cas de fuite ou d’écoulement d’un produit, respecter les directives de nettoyage du fabricant recommandées dans la FDS.
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Page 122: 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 123: Documentation And Support
Documentation and support Related documentation The following related documents are available: Publication Document number ™ QuantStudio 3D Digital PCR System Quick Reference MAN0008159 ™ ™ QuantStudio 3D AnalysisSuite Software User Guide MAN0008161 ™ ™ QuantStudio 3D AnalysisSuite Server System Quick Reference 4486248 ™... -
Page 124: Limited Product Warranty
Documentation and support Limited product warranty Limited product warranty Life Technologies Corporation and/or its affiliate(s) warrant their products as set forth in the Life Technologies' General Terms and Conditions of Sale at www.thermofisher.com/us/en/home/global/terms-and-conditions.html. If you have any questions, please contact Life Technologies at www.thermofisher.com/ support. - Page 126 thermofisher.com/support | thermofisher.com/askaquestion thermofisher.com 18 March 2020...
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