Summary of Contents for Thermo Scientific QuantStudio 1
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™ QuantStudio 1 Real-Time PCR System INSTALLATION, USE, AND MAINTENANCE Firmware v1.0.x Publication Number MAN0017853 Revision A.0 For Research Use Only. Not for use in diagnostic procedures.
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Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256 For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition. The information in this guide is subject to change without notice. DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC.
About this guide This guide provides information about installing, using, and maintaining the QuantStudio ™ 1 Real-Time PCR System. For information and instructions on ™ performing experiments on this system, refer to QuantStudio Design and Analysis Desktop Software User Guide (Pub. No. MAN0010408). QuantStudio 1 Real-Time PCR System Installation, Use, and Maintenance Guide ™...
Product information ■ Instrument hardware description ........9 ■...
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Chapter 1 Product information Instrument hardware description Instrument filters and supported dyes System dyes The instrument use a coupled three-color filter set that supports the dyes shown in the following table and figure. For more information about available spectral dye calibration kits, contact Support.
Chapter 1 Product information Instrument hardware description Parts of the instrument Touchscreen – Controls the instrument. USB port – For connection to an external network drive or external data storage device. Instrument drawer – Contains sample plate. The instrument includes three additional USB ports on the back of the instrument. Note: The instrument recognizes only one external storage device at a time for data transfer.
Chapter 1 Product information Instrument hardware description Parts of the home screen Avatar and Instrument name Settings button Help icon Buttons for accessing Experiment Template files (EDT) Drawer status Connectivity icons Status dial Sign In (or My Profile) button Current user name; instrument block type Table 2 Parts of the home screen Element of the Function...
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Chapter 1 Product information Instrument hardware description Element of the Function For more information, see... home screen • When the instrument is in use — Displays the Status dial — sample block temperature, the elapsed run time, and the run status. You can swipe the dial to the left or touch access real-time views of the run.
Chapter 1 Product information Software description Software description Instrument, The instrument and the software (desktop and cloud) include the features described in the following table. desktop, and cloud software Feature Instrument Desktop Cloud features Use as guest (no sign in) —...
Chapter 1 Product information Software description Folders, Term Definition Supported in templates, Folders in Load Location in which you can store templates (EDT Instrument experiments, and Experiment files) on the instrument: projects • My Instrument – Displayed if you are signed in •...
Chapter 1 Product information Supported options for instrument and computer connections Template and experiment Instrument Desktop Cloud components Plate Sample names Define and assign samples, targets or SNP assays, and tasks in the Quick Setup and Advanced Setup panes of the You cannot edit targets/SNP assays Plate tab.
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Chapter 1 Product information Supported options for instrument and computer connections Note: For detailed information about networking your instrument, see the ™ QuantStudio 1 Real-Time PCR System IT Checklist (Pub. No. MAN0018164). Direct configuration option • A computer provided by Thermo Fisher Scientific with the QuantStudio ™...
Chapter 1 Product information Experiment types Experiment types Purpose Description Standard curve experiment Determines absolute 1. The software measures amplification of the target in a standard dilution series and in target quantity in test samples. samples. 2. The software generates a standard curve using data from the standard dilution series. 3.
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Chapter 1 Product information Experiment types Purpose Description Genotyping experiment Detects single Genotyping experiments use preformulated TaqMan ® SNP Genotyping Assays that include nucleotide the following components: polymorphism (SNP) • Two sequence-specific primers for amplification of sequences containing the SNP of variants of a target interest nucleic acid...
Chapter 2 General procedures to operate the instrument Power on the instrument Power on the instrument 1. Touch anywhere on the touchscreen to determine if the instrument is in sleep mode. If the home screen is displayed, the instrument is already powered on. 2.
Chapter 2 General procedures to operate the instrument Load and unload a plate in the QuantStudio 1 Real-Time PCR Instrument ™ ™ Load and unload a plate in the QuantStudio 1 Real-Time PCR Instrument CAUTION! Use flat caps for 0.2-mL tubes. Rounded caps can damage the heated cover.
Chapter 2 General procedures to operate the instrument Transfer, view, or manage files and results Transfer, view, or manage files and results Transfer EDS files 1. In the home screen, when a run ends, touch Transfer File. from the 2. Select the data destination for the EDS file. instrument home screen 3.
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Chapter 2 General procedures to operate the instrument Transfer, view, or manage files and results 6. Delete or copy the files. • Touch Delete Files, then confirm deletion. • Touch Copy Files, select a file destination, then touch Paste Files. 7.
Chapter 3 Configure the instrument and manage instrument profiles Installation and instrument verification 5. Create an administrator profile (see “Create an administrator instrument profile during initial start-up“ on page 27). 6. Select one of the following options. • Link the instrument profile to the Thermo Fisher Cloud (see “Link an existing instrument profile with the Thermo Fisher Cloud“...
Chapter 3 Configure the instrument and manage instrument profiles Create an administrator instrument profile during initial start-up Create an administrator instrument profile during initial start-up During initial start-up, the user is automatically prompted to create an administrator instrument profile. See “Initial start-up“ on page 25. •...
Chapter 3 Configure the instrument and manage instrument profiles Overview of Settings Overview of Settings Touch Settings in the home screen to configure settings as needed. Access to many settings are restricted to administrator instrument profiles. Touch for step-by-step instructions on configuring settings. Options Description Instrument Settings...
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Chapter 3 Configure the instrument and manage instrument profiles Overview of Settings Options Description Date/Time Set time zone and date and time formats. Network Connection Set wired or wireless network connection for the instrument. Restore Factory Defaults Restore the instrument to the factory settings. IMPORTANT! Back up the instrument before restoring factory defaults (see “Backup or restore the instrument“...
Chapter 3 Configure the instrument and manage instrument profiles Manage instrument settings Options Description • Backup the instrument Backup / Restore • Restore an instrument backup Ship Prep Mode Place the instrument in a safe state for moving or long term storage. Run History —...
Chapter 3 Configure the instrument and manage instrument profiles Manage instrument settings Manage the 1. In the home screen, touch Settings4Instrument Settings4Instrument Name. instrument name (Administrator 2. Touch the Instrument Name field, enter an instrument name, then touch Done. only) 3.
Chapter 3 Configure the instrument and manage instrument profiles Manage instrument settings Select a Cloud During the initial startup, you will be automatically prompted to select a Cloud region. Return to the selection through Settings, if necessary. region (Administrator 1. In the home screen, touch Settings4Instrument Settings4Cloud Region.
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Chapter 3 Configure the instrument and manage instrument profiles Manage instrument settings Set up a wired connection 1. In the home screen, touch Settings4Instrument Settings4Network Connection4 Wired. 2. In the Network Configuration screen, touch a radio button to connect to a network either by DHCP or by a Static IP address.
Chapter 3 Configure the instrument and manage instrument profiles Learn about the instrument Restore factory IMPORTANT! Back up the instrument before restoring factory defaults (see “Backup defaults or restore the instrument“ on page 70). 1. In the home screen, touch Settings4Instrument Settings4Restore Factory Defaults.
Chapter 3 Configure the instrument and manage instrument profiles Manage home screen notifications View and export 1. In the home screen, touch Settings4About Instrument4License Agreement to view the license agreement. the License Agreement 2. Touch Export to export the license agreement. 3.
Chapter 3 Configure the instrument and manage instrument profiles Manage Users Enable remote 1. In the home screen, touch Settings4Maintenance and Service4Monitoring. instrument 2. Configure the instrument monitoring settings. monitoring (Administrator Option Description only) Remote Slide the control On to enable the Remote Monitoring Service. Monitoring Enabling the Remote Monitoring Service allows the instrument Service...
Chapter 3 Configure the instrument and manage instrument profiles Manage Users Require 1. In the home screen, touch Settings4Manage Users4Sign In Required. instrument profile 2. Slide the control On. sign-in Only signed-in users are allowed to access the instrument for any task, including (Administrator access to Settings.
Chapter 3 Configure the instrument and manage instrument profiles Link an instrument profile with the Thermo Fisher Cloud 3. Edit the profile. • To delete the profile, touch Delete profile4Delete. • To reset the PIN, touch Reset PIN4Reset. – The user will be directed to enter a new PIN at the next sign in. •...
Chapter 4 Create and run experiments on the instrument Run an experiment Run an experiment Create and run an 1. In the home screen, touch Open Template. experiment from a 2. (Optional) Touch a category in the left column. template 3.
Chapter 4 Create and run experiments on the instrument Edit an experiment before starting a run 7. (Optional) Define plate wells with sample names and view Well ID, Targets, or Dyes (see “Define, assign, and view well details“). 8. Load a plate into the instrument (see “Load and unload a plate in the QuantStudio 1 Real-Time PCR Instrument“...
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Chapter 4 Create and run experiments on the instrument Edit an experiment before starting a run b. Enter the name for the EDS file, then touch Done. • Enter a plate barcode. a. Touch the Plate Barcode field. b. Enter or scan the plate barcode, then touch Done. •...
Chapter 4 Create and run experiments on the instrument Edit an experiment before starting a run Edit the run Access a template (EDT file). For more information, see the following sections. method • “Create and run an experiment from a template“ on page 40. •...
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Chapter 4 Create and run experiments on the instrument Edit an experiment before starting a run • In the Method screen, touch Edit4Manage Steps. Option Procedure 1. Touch Add/Remove steps4Add steps. 2. Touch on the left or right border of a step to add a step before or after the step, respectively.
Chapter 4 Create and run experiments on the instrument Edit an experiment before starting a run Configure ramp rates and pause settings • In the Method screen, touch Edit4Manage Steps4Advanced Options. Option Procedure 1. Touch Ramp Rates. 2. Touch the ramp rates fields. Edit Ramp Rates 3.
Chapter 4 Create and run experiments on the instrument View, pause, or stop a run Option Procedure Define and assign samples 1. Touch in the well table view 2. Touch Edit to edit sample names for individual wells. 3. Touch a sample name field, enter a new name, then touch Done.
Chapter 4 Create and run experiments on the instrument View, pause, or stop a run Adjust the display 1. In the instrument home screen, during an instrument run, touch or swipe left twice to view real-time data and plots. of real-time plots on the instrument 2.
Chapter 4 Create and run experiments on the instrument Transfer EDS files from the instrument home screen Transfer EDS files from the instrument home screen 1. In the home screen, when a run ends, touch Transfer File. 2. Select the data destination for the EDS file. 3.
Chapter 5 Calibrate and verify instrument performance Calibration descriptions Calibration Recommended frequency • Every two years (recommended) Background • Background calibration can also be performed, as needed: – To check for contamination (depends on usage and laboratory conditions). – To obtain the most accurate data for the removal of background fluorescence.
Chapter 5 Calibrate and verify instrument performance View the calibration status and set reminders Calibration description and purpose Pass Criteria • The software extracts a spectral profile for each dye standard, then Dye spectra peak within the same produces a set of spectral profiles plotted as fluorescence vs filter. filter as their group.
Chapter 5 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations 4. In the Calibrations History tab: • View the history of each calibration type. • (Optional) Click to download the calibration history report. Perform ROI/uniformity, background, and dye calibrations Workflow: Perform an ROI/uniformity calibration Calibration...
Chapter 5 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations Thaw, vortex, and centrifuge a calibration plate 1. Remove the calibration plate from the freezer, then thaw the plate in its packaging. Keep plates protected from light until you perform the calibration. •...
Chapter 5 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations 5. When the run is complete and the screen displays Calibration Complete, touch View Results to check the calibration status. Calibration status Action Passed Touch Next to proceed to the next required calibration. Failed See “Troubleshoot calibration failure“...
Chapter 5 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations Calibration Example results indicating successful calibration Uniformity Signals from each well following a uniform trend. Background Few, if any, signals with abnormally high fluorescence. Signals from each well following a uniform trend, and each dye peaks at the correct filter.
Chapter 5 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations Observation Possible cause Recommended action High fluorescence signal in Signals that exceed the limit of See “Identify contamination“ on page 56. individual wells normal fluorescence may indicate fluorescent contaminants on the plate or the sample block.
Chapter 5 Calibrate and verify instrument performance Perform instrument verification using RNase P plates IMPORTANT! Wear powder-free gloves while creating the background plate. 1. Remove a reaction plate from its box and place it on a clean, dry surface. 2. Aliquot 50 µL of deionized water to each well of the reaction plate. 3.
Chapter 5 Calibrate and verify instrument performance Perform instrument verification using RNase P plates RNase P The RNase P plate contains the reagents necessary for the detection and quantitation of genomic copies of the human RNase P gene (a single-copy gene encoding the instrument RNase moiety of the RNase P enzyme).
Chapter 5 Calibrate and verify instrument performance Perform instrument verification using RNase P plates Thaw, vortex, and centrifuge an RNase P plate IMPORTANT! Expose the RNase P plate to room temperature for no more than 45 minutes, inclusive of thawing and preparation time. After thawing, the RNase P plate cannot be refrozen.
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Chapter 5 Calibrate and verify instrument performance Perform instrument verification using RNase P plates 5. In the RNase P Verification Status screen, touch one of the following options: • Accept Results — Save the results to the instrument. • Reject Results — Delete the RNase P verification results. •...
Chapter 5 Calibrate and verify instrument performance Perform instrument verification using RNase P plates Troubleshoot verification failure Observation Possible cause Recommended action Verification failed The plate was improperly Ensure the following: prepared. • The correct plate was used for the verification performed.
Chapter 5 Calibrate and verify instrument performance Calibrate custom dyes Calibrate custom dyes Custom dyes The instrument can run assays designed with custom dyes. Custom dyes include: overview • Dyes that are not manufactured by Thermo Fisher Scientific. • Dyes or formulations of dyes that are not system dyes for the instrument. •...
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Chapter 5 Calibrate and verify instrument performance Calibrate custom dyes Prepare a custom dye dilution plate IMPORTANT! Wear powder-free gloves throughout the procedure. 1. Prepare a 2- or 3-fold dilution series of the custom dye. 2. Dispense aliquots of each dilution into the center of a reaction plate, then seal the plate.
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Chapter 5 Calibrate and verify instrument performance Calibrate custom dyes Run the dilution plate as an experiment 1. Load the plate into the instrument. 2. Set up a genotyping experiment on the instrument. • Load an experiment created in the desktop software. a.
Chapter 5 Calibrate and verify instrument performance Calibrate custom dyes Calibrate the Create a custom dye calibration plate custom dye IMPORTANT! Wear powder-free gloves while creating the dye plate. Create a full plate of the custom dye diluted to the optimal concentration: 1.
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Chapter 5 Calibrate and verify instrument performance Calibrate custom dyes 3. Enter the dye information: Field/option Action Custom Dye Enter a name for the custom dye. Name IMPORTANT! · Do not use a system dye name for a custom dye name. ·...
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Chapter 5 Calibrate and verify instrument performance Calibrate custom dyes 9. Review the plot. Passing calibration results show uniform signals with peaks that are aligned with the dye wavelength. Filter wavelength (nm) Peak filter Excitation Emission x1-m1 470 ± 15 520 ±...
Chapter 5 Calibrate and verify instrument performance Calibrate for a custom melt curve experiment Calibrate for a custom melt curve experiment Note: A custom melt calibration calibrates a custom dye and a melt calibration at the same time. Before running the custom melt calibration complete the following tasks: •...
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Chapter 5 Calibrate and verify instrument performance Calibrate for a custom melt curve experiment 8. Review the plot. Passing calibration results show uniform signals with peaks that are aligned with the dye wavelength. Figure 3 Example dye calibration plot Note: The peaks for your dye may align with a different filter set. 9.
Chapter 6 Maintain the instrument Decontaminate the sample block Decontaminate the sample block Perform this procedure to eliminate fluorescent contaminants from the instrument sample block. Contamination is generally evident in failed background calibrations where one or more wells consistently exhibit abnormally high signals. CAUTION! PHYSICAL INJURY HAZARD.
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Chapter 6 Maintain the instrument Decontaminate the sample block 3. Rinse the contaminated wells with deionized water (see “Detailed procedures for cleaning the sample block“ on page 73). 4. Close the drawer and test the sample block for contamination. a. Push the instrument drawer back in to the instrument. b.
Chapter 6 Maintain the instrument Replace the instrument fuses Detailed IMPORTANT! Use these cleaning procedures only in conjunction with the complete procedures for decontamination procedure (see “Decontaminate the sample block“ on page 71). cleaning the sample block • Rinse the sample block with deionized water. a.
Chapter 6 Maintain the instrument Prepare the instrument to store, move, or ship Replace the fuses 1. Power off and unplug the instrument, then allow it to cool for 15 minutes. 2. Using a flat-head screwdriver, unscrew and remove the fuse holder. 3.
Chapter 6 Maintain the instrument Prepare the instrument to store, move, or ship Move the CAUTION! PHYSICAL INJURY HAZARD. Do not attempt to lift the instrument instrument or any other heavy objects unless you have received related training. Incorrect lifting can cause painful and sometimes permanent back injury.
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Chapter 6 Maintain the instrument Prepare the instrument to store, move, or ship 5. Pack the instrument in the provided packaging and follow the instructions in the table below. Prepare Include Exclude Any accessories, including: • Instrument 1. Transfer any data files from the •...
Appendix A Install and connect the instrument to a network Before you begin Before you begin This section provides instructions for customer installation of the computer and the instrument. For installation by a field service engineer (FSE), contact Support to order a service call.
Appendix A Install and connect the instrument to a network Unpack and install the instrument Figure 5 Instrument‑to‑computer connections (minitower configuration) Detachable power supply cord compatible with local power supply receptacle. Connection between the computer and the instrument. Connection between the computer and the monitor, keyboard, and mouse. (optional) handheld barcode scanner.
Appendix A Install and connect the instrument to a network Power on and follow the startup wizard 5. Connect your instrument as required by your network configuration (see “Supported options for instrument and computer connections“ on page 16 and “Instrument and computer connections“ on page 78). •...
Appendix A Install and connect the instrument to a network Networking 5. Select Internet Protocol (TCP/IP)4Properties. 6. Set the Internet Protocol (TCP/IP) Properties for either DHCP or Static IP communication: Network Action configuration DHCP 1. Select Obtain an IP address automatically. 2.
Appendix A Install and connect the instrument to a network Networking Note: For detailed information about networking your instrument, see the ™ QuantStudio 1 Real-Time PCR System IT Checklist (Pub. No. MAN0018164). Direct configuration option • A computer provided by Thermo Fisher Scientific with the QuantStudio ™...
Appendix A Install and connect the instrument to a network Networking Ethernet port The Ethernet port of the instrument supports: overview • Static IP network service with subnet mask, primary and secondary data network service (DNS), and default gateway settings, or dynamic host configuration protocol (DHCP) network service.
Troubleshooting Observation Possible cause Recommended action Inconsistent communication The instrument is configured Ensure only one connectivity option is plugged both wired and wireless between instrument and into the instrument (either an Ethernet cable or a wireless adapter, but not both). computer or instrument and network connection.
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Appendix B Troubleshooting Networking Observation Possible cause Recommended action Forgot PIN for instrument If there is not another administrator profile on profile the instrument, you must restore factory defaults (see “Restore factory defaults“ on page 34). High fluorescence signal The reaction volume is not Ensure that reaction volumes in the plate are correct.
Appendix C Instrument specification and layout Configured system dimensions Configured system dimensions Allow space for the configured instrument. A typical setup with a co-located minitower computer is shown below. Note: Dimensions are rounded to the nearest whole or half unit. 15 cm (6 in.) 27 cm (10.5 in.) 30 cm (12 in.)
Appendix C Instrument specification and layout Electrical requirements Instrument During instrument installation and maintenance, it is necessary to access the back of the instrument. If the back of the instrument faces a wall, ensure that there is sufficient clearances clearance on the bench to rotate the instrument for access. IMPORTANT! For safety, the power outlet for the instrument must be accessible.
Appendix C Instrument specification and layout Environmental requirements Environmental requirements Table 3 Environmental requirements Condition Acceptable range Installation site Indoor use only Electromagnetic Do not use this device in close proximity to sources of strong interference electromagnetic radiation (for example, unshielded intentional RF sources).
Appendix C Instrument specification and layout Network requirements Network requirements The instrument: • Is factory-configured for IPv4 TCP/IP communication and includes an Ethernet adapter (100/1,000 Mbps) with an RJ45-type connector for integrating the device into a local area network (LAN). •...
Appendix E Safety Symbols on this instrument Symbols on this instrument Symbols may be found on the instrument to warn against potential hazards or convey important safety information. In this document, the hazard symbol is used along with one of the following user attention words: •...
Appendix E 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 minimiser les conséquences...
Appendix E 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.
Appendix E Safety Safety information for instruments not manufactured by Thermo Fisher Scientific Location of safety labels on the instrument Moving parts Physical injury hazard 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.
Appendix E Safety Safety and electromagnetic compatibility (EMC) standards Physical injury CAUTION! Moving Parts. Moving parts can crush, pinch and cut. Keep hands clear of moving parts while operating the instrument. Disconnect power before servicing. WARNING! Do not attempt to lift or move the instrument without the assistance of others.
Appendix E Safety Safety and electromagnetic compatibility (EMC) standards Safety compliance Reference Description EU Directive European Union “Low Voltage Directive” 2014/35/EU Safety requirements for electrical equipment for measurement, IEC 61010-1 control, and laboratory use – Part 1: General requirements EN 61010-1 UL 61010-1 CSA C22.2 No.
Appendix E Safety Chemical safety Environmental Reference Description design Directive 2012/19/EU European Union “WEEE Directive” – Waste electrical and electronic equipment Directive 2011/65/EU European Union “RoHS Directive” – Restriction of hazardous substances in electrical and electronic equipment Directive 2006/66/EC European Union “Battery Directive” Chemical safety WARNING! GENERAL CHEMICAL HANDLING.
Appendix E Safety Biological hazard safety Biological hazard safety 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. Conduct all work in properly equipped facilities with the appropriate safety equipment (for example, physical containment devices).
Documentation and support Related documentation Document Publication number QuantStudio 1 Real-Time PCR System Installation, Use, and ™ MAN0017853 Maintenance Guide QuantStudio Design and Analysis Desktop Software Command- ™ MAN0010409 Line Application Guide QuantStudio Design and Analysis Desktop Software User Guide ™...
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. QuantStudio 1 Real-Time PCR System Installation, Use, and Maintenance Guide ™...
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Index fluorescence high fuses, replace 74 maintenance 70 melt curve experiments 18 melt curves, add to method 43 method genotyping experiments 18 add melt curves 43 guest profile add stages 43 disable 37 add steps 43 limits 26 data collection points 43 edit 43 parts of 43 pause 45...
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Index Replace with index term stop run 47 require sign in 37 support, customer and technical 102 restore instrument 70 supported dyes 10 RNase P verification symbols, safety 94 pass criteria 58 system dyes 10 plate description 58 run 59 RNase P verification, plate, prepare 59 template properties.
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