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QuantStudio
(for Human Identification)
USER GUIDE
Installation, maintenance, and administration
for use with:
HID Real‑Time PCR Analysis Software v1.3
Publication Number MAN0017162
Revision A.0
For Research, Forensic, or Paternity Use Only. For licensing and limited use restrictions
visit thermofisher.com/HIDlicensing.
™
5 Real-Time PCR Instrument
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Table of Contents
Related Manuals for ThermoFisher Scientific QuantStudio 5 Real-Time PCR
Summary of Contents for ThermoFisher Scientific QuantStudio 5 Real-Time PCR
- Page 1 ™ QuantStudio 5 Real-Time PCR Instrument (for Human Identification) USER GUIDE Installation, maintenance, and administration for use with: HID Real‑Time PCR Analysis Software v1.3 Publication Number MAN0017162 Revision A.0 For Research, Forensic, or Paternity Use Only. For licensing and limited use restrictions visit thermofisher.com/HIDlicensing.
- Page 2 Manufacturer: Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256 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.
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Page 3: Table Of Contents
Contents ■ CHAPTER 1 Product information ........7 Instrument overview . - Page 4 Contents ■ CHAPTER 4 Configure the instrument and manage instrument profiles ............23 Initial start up .
- Page 5 Contents Calibrate dyes for HID‑validated workflows ........41 Workflow: Calibrate dyes for HID‑validated workflows .
- Page 6 Contents ■ APPENDIX C Instrument specification and layout ....61 Configured system dimensions ..........62 Instrument and computer connections .
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Page 7: Chapter 1 Product Information
Product information ■ Instrument overview ..........7 ■... -
Page 8: Installation, Verification, And Calibration
Chapter 1 Product information Installation, verification, and calibration Installation, verification, and calibration Your HID Support Representative will contact you to schedule the installation. During instrument installation, the service representative will perform the initial instrument verification using an RNase P plate and calibrate the instrument for the versions of and JUN dye used by HID-validated workflows. -
Page 9: Instrument Filters And Supported Dyes
Chapter 1 Product information Instrument filters and supported dyes Instrument filters and supported dyes System dyes The instrument uses a de-coupled six-color optical filter set that supports the dyes shown in the following table and figure. For more information about the spectral dye calibration kits available for the instrument, contact your HID Support Representative. -
Page 10: Custom Dyes
Chapter 1 Product information Parts of the instrument Custom dyes The instrument can run assays designed with custom dyes. Custom dyes include: • Dyes that are not supplied by Thermo Fisher Scientific. • Dyes or versions of dyes that are not factory-calibrated on the instrument. ™... -
Page 11: Parts Of The Home Screen
Chapter 1 Product information Parts of the home screen Parts of the home screen Avatar and Instrument name Settings button Eject instrument drawer icon Access templates buttons (not applicable for HID‑validated workflows) Help system icon Connectivity icons Status dial Sign In (or My Profile) button Instrument profile name;... - Page 12 Chapter 1 Product information Parts of the home screen Element of the home screen Function Settings button Touch Settings to configure, calibrate, or learn about the instrument. • – The instrument is connected via a wired configuration. Connectivity icons • –...
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Page 13: Comparison Of Features In Desktop Software And The Instrument
Chapter 1 Product information Comparison of features in desktop software and the instrument Comparison of features in desktop software and the instrument To run experiments using HID assays, the instrument must be integrated with the HID Real-Time PCR Analysis Software v1.3. Actions Desktop software Instrument... -
Page 14: Chapter 2 Install The Instrument
Install the instrument ■ Workflow: Install the instrument ........14 ■... -
Page 15: Unpack And Install The Instrument
Chapter 2 Install the instrument Unpack and install the instrument Unpack and install the instrument 1. Prepare the installation site as described in the QuantStudio 5 Real-Time PCR ™ Instrument Site Preparation Guide (for Human Identification) (Pub. No. MAN0016701). 2. Follow the pre-printed instructions on the instrument box to unpack the instrument, accessories, and reference documentation. -
Page 16: Instrument And Computer Connections
Chapter 2 Install the instrument Instrument and computer connections Instrument and computer connections Figure 1 Instrument back panel USB ports RS232 Port—For service use only WiFi USB port—Not applicable Fuse Cover Ethernet Port—RJ45 port for Power Switch 100/1,000 Mbps Ethernet communication Power Port—100 to 240 VAC with the instrument Figure 2 Instrument‑to‑computer connections (minitower configuration) -
Page 17: Computer-To-Instrument Configuration
Chapter 2 Install the instrument Computer-to-instrument configuration Computer-to-instrument configuration ™ IMPORTANT! For HID use, the QuantStudio 5 Real-Time PCR System has been validated for a direct (computer-to-instrument) configuration. During installation, a Thermo Fisher Scientific service representative can set up only a direct configuration. Direct configuration •... -
Page 18: Chapter 3 General Procedures To Use The Instrument
General procedures to use the instrument ■ Precautions for use ........... 18 ■... -
Page 19: Power On The Instrument
Chapter 3 General procedures to use the instrument Power on the instrument Power on the instrument To power on the instrument from a powered-off state: 1. Touch anywhere on the touchscreen to determine if the instrument is in sleep mode. If the home screen displays, the instrument is already powered on. 2. -
Page 20: Sign In
Chapter 3 General procedures to use the instrument Sign in Sign in Create an instrument profile before signing into the instrument (see “Create a new instrument profile“ on page 28). Note: An instrument profile is a user account specifically for the instrument. It is not related to any other user account for the system or software. -
Page 21: Load And Unload Plate In The Instrument
Chapter 3 General procedures to use the instrument Load and unload plate in the instrument Load and unload plate in the instrument CAUTION! Use optical flat caps for tubes. Rounded caps can damage the heated cover. 1. Load the plate. a. -
Page 22: View Real-Time Data And Plots On The Instrument Touchscreen
Chapter 3 General procedures to use the instrument View real-time data and plots on the instrument touchscreen View real-time data and plots on the instrument touchscreen In the instrument home screen, during an instrument run: 1. Touch or swipe left twice. 2. -
Page 23: Initial Start Up
Configure the instrument and manage instrument profiles ■ Initial start up ............23 ■... -
Page 24: Overview Of Instrument Settings (Administrator)
Chapter 4 Configure the instrument and manage instrument profiles Overview of instrument settings (Administrator) (Administrator) Overview of instrument settings Touch Settings in the home screen to configure the instrument settings as needed. Access to most settings are restricted to administrator instrument profiles. Options Description Instrument Settings... - Page 25 Chapter 4 Configure the instrument and manage instrument profiles Overview of instrument settings (Administrator) Options Description Notifications — Enable home screen notifications of instrument errors. The number of new, unviewed notifications displays over Settings in the home screen. Maintenance and Service Monitoring Enable the Remote Monitoring Service to automatically notify Thermo Fisher Scientific support teams in real time of potential instrument issues.
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Page 26: Overview Of Instrument Settings (Standard Or Guest)
Chapter 4 Configure the instrument and manage instrument profiles Overview of instrument settings (Standard or Guest) (Standard or Guest) Overview of instrument settings Touch Settings in the home screen to configure the instrument settings as needed. Access to most settings are restricted to administrator instrument profiles. Options Description About Instrument... -
Page 27: Manage Instrument Profiles
Chapter 4 Configure the instrument and manage instrument profiles Manage instrument profiles Manage instrument profiles Note: An instrument profile is a user account specifically for the instrument. It is not related to any other user account for the system or software. •... -
Page 28: Create A New Instrument Profile
Chapter 4 Configure the instrument and manage instrument profiles Manage instrument profiles Create a new In the home screen: instrument profile 1. Touch Sign In, then touch Get Started. 2. Touch Name, enter a username, then touch Done. 3. Touch PIN Code, enter a four-digit numerical password, then touch Enter. Note: Touch the Show PIN checkbox to switch PIN display on or off. -
Page 29: Require Instrument Profile Sign-In
Chapter 4 Configure the instrument and manage instrument profiles Require instrument profile sign-in Require instrument profile sign-in In the home screen: 1. Touch Settings4Manage Users4Sign In Required. 2. Slide the control On. Only signed-in users can access the instrument settings. 3. -
Page 30: Enable Sleep Mode
Chapter 4 Configure the instrument and manage instrument profiles Enable sleep mode Enable sleep mode In the home screen: 1. Touch Settings4Instrument Settings4Sleep Mode. 2. Slide the control On to enable sleep mode. 3. Touch Edit Time, then enter the time length of inactivity before the instrument enters sleep mode. -
Page 31: Restore Factory Defaults
Chapter 4 Configure the instrument and manage instrument profiles Restore factory defaults Restore factory defaults IMPORTANT! Back up the instrument before restoring factory defaults (see “Backup or restore the instrument“ on page 48 ). When you restore an instrument to its factory defaults: ·... -
Page 32: Update Instrument Software
Chapter 4 Configure the instrument and manage instrument profiles Update instrument software Update instrument software IMPORTANT! Update the instrument software only under the specific guidance of your HID Support Representative. In the home screen: 1. Touch Settings4Maintenance and Service4Software Update. 2. -
Page 33: Chapter 5 Calibrate And Verify Instrument Performance
Calibrate and verify instrument performance ■ Calibration and verification schedule ........34 ■... -
Page 34: Calibration And Verification Schedule
Chapter 5 Calibrate and verify instrument performance Calibration and verification schedule Calibration and verification schedule The instrument is factory-calibrated and does not require calibration at installation. To ensure optimal performance, perform calibrations at the recommended frequency. Note: During instrument installation, the Thermo Fisher Scientific service representative will perform the initial instrument verification using an RNase P plate ™... -
Page 35: Calibration Descriptions
Chapter 5 Calibrate and verify instrument performance Calibration descriptions Calibration descriptions Calibration description and purpose Pass Criteria ROI/Uniformity • The software captures images for each optical filter. The image for each filter distinguishes all wells of the plate. • The software uses calibration data to map the increase in fluorescence to the plate wells during subsequent runs and to evaluate well-to-well Each well in the image is distinct. -
Page 36: View Calibration Status And Set Reminders In The Instrument
Chapter 5 Calibrate and verify instrument performance View calibration status and set reminders in the instrument View calibration status and set reminders in the instrument In the home screen: 1. Touch Settings4Maintenance and Service4Calibrations4History and Reminders. 2. In the Calibration Reminders screen, view the status of each calibration type. 3. -
Page 37: Prepare A Calibration Plate
Chapter 5 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations Prepare a Materials required for calibration plate preparation calibration plate • Plate(s) for the calibration you are performing: – ROI/Uniformity plate (one ROI plate needed) – Background calibration plate –... -
Page 38: Perform Calibrations
Chapter 5 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations Perform 1. In the instrument home screen: calibrations Calibration Touch ROI/Uniformity Settings4Maintenance and Service4Calibrations4ROI and Uniformity Background Settings4Maintenance and Service4Calibrations4Custom4Background System Dye Settings4Maintenance and Service4Calibrations4Dye Automatically followed by background calibration. Initiate via this route if performing background calibration only. -
Page 39: View Calibration Images
Chapter 5 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations View calibration You can view the calibration images after the background calibration is complete. images 1. In the Calibration Status screen, touch Details. 2. In the Details screen, touch a calibration type to view its images and plots. Calibration Example results indicating successful calibration Green circles around all wells and bright well centers. -
Page 40: Identify Contamination
Chapter 5 Calibrate and verify instrument performance Perform ROI/uniformity, background, and dye calibrations Identify Signals that exceed the limit of normal fluorescence may indicate fluorescent contaminants on the calibration plate or the sample block. Common contaminants contamination include ink residue from permanent pens, powder from disposable gloves, and dust. To identify and resolve a possible contamination problem: 1. -
Page 41: Calibrate Dyes For Hid-Validated Workflows
Chapter 5 Calibrate and verify instrument performance Calibrate dyes for HID‑validated workflows Calibrate dyes for HID‑validated workflows HID-validated workflows use versions of ABY and JUN dyes that are considered ™ ™ custom dyes for the instrument. These dyes require custom dye calibration. To calibrate any other custom dye, contact your HID Support Representative. -
Page 42: Add Custom Dyes To The Instrument For Hid-Validated Workflows
Chapter 5 Calibrate and verify instrument performance Calibrate dyes for HID‑validated workflows 3. Vortex the plate for 5 seconds, then centrifuge at 750 to 1,000 × g for 2 minutes. 4. Confirm that the liquid in each well is at the bottom of the well and free of bubbles. - Page 43 Chapter 5 Calibrate and verify instrument performance Calibrate dyes for HID‑validated workflows 7. Touch Start. 8. When the run is complete and the screen displays Calibration Complete, touch View Results4Details. 9. Review the plot. Passing calibration results show uniform signals with peaks aligned with the dye wavelength.
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Page 44: Perform Instrument Verification Using Rnase P Plates
Chapter 5 Calibrate and verify instrument performance Perform instrument verification using RNase P plates Perform instrument verification using RNase P plates During instrument installation, your HID Support Representative will perform instrument verification. However, perform instrument verification: • After performing instrument calibrations. •... -
Page 45: Rnase P Instrument Verification Plate
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). -
Page 46: Prepare An Rnase P Plate
Chapter 5 Calibrate and verify instrument performance Perform instrument verification using RNase P plates Prepare an Materials required for RNase P plate preparation RNase P plate • RNase P instrument verification plate • Centrifuge with plate adapter; buckets cleaned before use •... -
Page 47: Perform Rnase P Verification
Chapter 5 Calibrate and verify instrument performance Perform instrument verification using RNase P plates Perform RNase P 1. In the home screen, touch Settings4Maintenance and Service4RNase P Verification. verification 2. Load the plate into the instrument. IMPORTANT! The instrument should be used by trained operators who have been warned of the moving parts hazard. -
Page 48: Chapter 6 Maintain The Instrument
Maintain the instrument ■ Backup or restore the instrument ........48 ■... -
Page 49: Decontaminate The Sample Block
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. - Page 50 Chapter 6 Maintain the instrument Decontaminate the sample block 3. Rinse the contaminated wells with deionized water (see page 51). 4. Close the drawer and test the sample block for contamination: a. Push the instrument drawer back in to the instrument. b.
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Page 51: Detailed Procedures For Cleaning The Sample Block
Chapter 6 Maintain the instrument Decontaminate the sample block Detailed IMPORTANT! Use these cleaning procedures only in conjunction with the "Clean the procedures for sample block" procedures. cleaning the sample block Rinse the sample block with deionized water 1. Pipet a small volume of deionized water into each contaminated well. 2. -
Page 52: Replace The Instrument Fuses
Chapter 6 Maintain the instrument Replace the instrument fuses Replace the instrument fuses CAUTION! FIRE HAZARD. For continued protection against the risk of fire, replace fuses only with listed and certified fuses of the same type and rating as those currently in the instrument. Materials required •... -
Page 53: Store, Move, Or Ship The Instrument
Chapter 6 Maintain the instrument Store, move, or ship the instrument Store, move, or ship the instrument Prepare the In the home screen: instrument to 1. Touch Settings4Maintenance and Service4Ship Prep Mode4Next. store, move, or ship 2. Touch to eject the instrument drawer. 3. -
Page 54: Return The Instrument For Service
Chapter 6 Maintain the instrument Store, move, or ship the instrument Return the The service process requires 2 to 3 weeks. instrument for Before returning the instrument for service: service 1. Back up the instrument (see “Backup or restore the instrument“ on page 48 ). 2. -
Page 55: Appendix A Troubleshooting
Troubleshooting Instrument troubleshooting Observation Possible cause Recommended action Insufficient disk space message Insufficient disk space to save a 1. In the home screen, touch run. Settings4Run History4Manage. 2. Delete or transfer experiments from the instrument. The touchscreen is black The instrument is in sleep Touch anywhere on the instrument mode. -
Page 56: Troubleshoot Calibration Failure
Appendix A Troubleshooting Troubleshoot calibration failure Troubleshoot calibration failure Observation Possible cause Recommended action Calibration failed The plate was improperly Ensure the following: prepared. • The correct plate was used for the calibration performed. • The plate was properly thawed. •... -
Page 57: Troubleshoot Verification Failure
Appendix A Troubleshooting Troubleshoot verification failure 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. • The plate was properly thawed. •... -
Page 58: Appendix B Parts And Materials
Parts and materials ■ Kits, consumables, accessories, and reagents ......58 ■ Consumables (96-well, 0.2-mL format) . -
Page 59: Consumables (96-Well, 0.2-Ml Format)
Appendix B Parts and materials Consumables (96‑well, 0.2‑mL format) Consumables (96‑well, 0.2‑mL format) Consumable Amount Cat. No. MicroAmp ™ Optical 8-Cap Strips 300 strips 4323032 MicroAmp ™ Optical 8-Tube Strip, 0.2 mL 125 strips 4316567 MicroAmp ™ Optical Tube without Cap, 0.2 mL 2,000 tubes N8010933 20 plates... -
Page 60: Accessories
Appendix B Parts and materials Accessories Accessories Item Amount Cat. No. MicroAmp ™ 96-Well Tray/Retainer Set 10 trays 4381850 MicroAmp ™ Multi Removal Tool 1 tool 4313950 MicroAmp ™ Cap Installing Tool (handle style) 1 tool 4330015 ™ MicroAmp Optical Adhesive Film 25 films 4360954 100 films... -
Page 61: Appendix C Instrument Specification And Layout
Instrument specification and layout ■ Configured system dimensions ......... 62 ■... -
Page 62: Configured System Dimensions
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.) -
Page 63: Instrument And Computer Connections
Appendix C Instrument specification and layout Instrument and computer connections Instrument and computer connections Figure 4 Instrument back panel USB ports RS232 Port—For service use only WiFi USB port—Not applicable Fuse Cover Ethernet Port—RJ45 port for Power Switch 100/1,000 Mbps Ethernet communication Power Port—100 to 240 VAC with the instrument Figure 5 Instrument‑to‑computer connections (minitower configuration) -
Page 64: Instrument Clearances
Appendix C Instrument specification and layout Instrument clearances Instrument clearances 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 clearance on the bench to rotate the instrument for access. IMPORTANT! For safety, the power outlet for the instrument must be accessible. -
Page 65: Environmental Requirements
Appendix C Instrument specification and layout Environmental requirements Environmental requirements Table 2 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). -
Page 66: Appendix D Safety
Safety ■ Symbols on this instrument ..........67 ■... -
Page 67: Symbols On This Instrument
Appendix D 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: •... -
Page 68: Conformity Symbols
Appendix D Safety Symbols on this instrument Symbol English Français Earth (ground) terminal Borne de (mise à la) terre Protective conductor terminal (main Borne de conducteur de protection ground) (mise à la terre principale) Terminal that can receive or supply Borne pouvant recevoir ou envoyer alternating current or voltage une tension ou un courant de type... -
Page 69: Safety Alerts On This Instrument
Appendix D 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 70: Safety Information For Instruments Not Manufactured By Thermo Fisher Scientific
Appendix D 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 71: Physical Injury
Appendix D Safety Instrument safety Physical injury CAUTION! Moving and Lifting Injury. The instrument is to be moved and positioned only by the personnel or vendor specified in the applicable site preparation guide. Improper lifting can cause painful and permanent back injury. -
Page 72: Electrical
Appendix D Safety Safety and electromagnetic compatibility (EMC) standards Electrical 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 73: Safety Compliance
Appendix D 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. -
Page 74: Environmental Design
Appendix D 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. -
Page 75: Biological Hazard Safety
Appendix D 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 76: Documentation And Support
Documentation and support Related documentation Document Pub. No. QuantStudio 5 Real-Time PCR Instrument Site Preparation Guide (for Human Identification) ™ MAN0016701 QuantStudio 5 Real-Time PCR Instrument User Guide (for Human Identification) ™ MAN0017162 HID Real‑Time PCR Analysis Software v1.3 User Guide MAN0009819 Obtain information from the Help system The instrument has a Help system that describes how to use each feature of the... -
Page 77: Index
Index accessories 60 date and time 30 administrator instrument profile 27 disk space message documentation, related 76 dye calibration description 35 background calibration plate, prepare 37, 41 create plate 40 run 38 description 35 when to perform 34 plate, prepare 37, 41 dyes run 38 custom 10... - Page 78 Index enable for remote monitoring 31 related documentation 76 heated cover idle temperature 30 Replace with index term move 53 require sign in 29 name 29 restore instrument 48 overview 7 RNase P verification parts of 10 pass criteria 45 power off 19 plate description 45 power on 19...
- Page 79 Index warranty 76 zoom 22 well details, view on instrument touchscreen 22 workflow, custom dye calibration, HID 41 QuantStudio 5 Real-Time PCR Instrument User Guide (for Human Identification) | MAN0017162 A.0 ™...
- Page 80 thermofisher.com/support | thermofisher.com/askaquestion thermofisher.com 15 June 2017...
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