INSTALLATION, USE, AND MAINTENANCE

1 For Research Use Only. Not for use in diagnostic 3 and 5 Real-Time PCR SystemsINSTALLATION, USE, AND MAINTENANCEF irmware Number MAN0010407 Revision information in this guide is subject to change without 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 Use Label License No. 474: Real-Time PCR System for Research Use OnlyNotice to Purchaser: The purchase of this instrument conveys to the purchaser the limited, non-transferable right to use the purchased instrument only, under intellectual property rights that are owned and/or controlled by Life Technologies and relate specifically to the instrument.

2 Purchase of the instrument includes the right to use the instrument for internal research and to perform services (including the right to report the results of services for a fee) by the purchaser only, but does not convey rights to use any other products, reagents, assays or methods such as the 5' nuclease assay process. The sale of this instrument is expressly conditioned on the purchaser not reselling, repackaging, or distributing this instrument, or any of its components, and no such rights are conveyed expressly, by implication, or by estoppel. For information on obtaining additional rights, please contact or Out Licensing, Life Technologies, 5791 Van Allen Way, Carlsbad, California Use Label License No.

3 572: Cy and CyDye Notice to Purchaser: Cy and CyDye are registered trademarks of GE entityLife Technologies | Carlsbad, CA 92008 USA | Toll Free in USA is a trademark of GE Healthcare UK Limited. Adobe, Acrobat, and Reader are trademarks of Adobe Systems, Inc. Microsoft, Internet Explorer, and Windows are trademarks of Microsoft Corporation. Apple, Safari, and Macintosh are trademarks of Apple, Inc. Mozilla and Firefox are trademarks of Mozilla Foundation. TaqMan is a registered trademark of Roche Molecular Systems, Inc., used under permission and license. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. 2015 Thermo Fisher Scientific Inc.

4 All rights this 8 Revision 9 CHAPTER 1 Product hardware of the , desktop, and cloud software , templates, experiments, and software connection CHAPTER 2 Start, sign on, and configure the and instrument for on the of the home the instrument without signing a new instrument your instrument profile to your Thermo Fisher Cloud your instrument profile to Thermo Fisher an instrument profile and link to Thermo Fisher instrument 3 and 5 Real-Time PCR Systems installation , Use, and MAINTENANCE Guide 3 CHAPTER 3 Create and run experiments on the for running an and run an experiment from a an experiment from a saved your last experiment an experiment before starting a experiment a plate and unload a plate in the , pause, or stop a well or stop a the graphical view of an the touchscreen during a , view, or manage files and experiment run template (.)

5 Edt) CHAPTER 4 Calibrate and verify instrument and verification the calibration status and set calibration status and set reminders in the calibration status and set reminders in the ROI/Uniformity, Background, and Dye : a calibration calibration images and transfer results to calibration a background plate (optional)..48 Perform instrument verification using RNase P verification description and P Instrument Verification an RNase P RNase P verification 3 and 5 Real-Time PCR Systems installation , Use, and MAINTENANCE GuideCalibrate custom dyes the custom dye to an optimal the custom for a custom melt curve CHAPTER 5 Maintain the or restore the the sample the sample for cleaning the sample the instrument the on or off, store, and sleep on the off the the instrument to ship, move, or the the instrument for CHAPTER 6 Profile and instrument configuration start an administrator all user profiles (Administrator only).

6 71 Manage all instrument profiles (Administrator only)..71 Edit a user SAE mode (Administrator only)..72 Require sign-in (Administrator only)..73 Enable remote instrument monitoring (Administrator only)..73 Update instrument software (Administrator only)..73 Restore factory the up a wired up a wireless a Cloud region (Administrator only)..75 Manage the instrument name (Administrator only)..75 Set the date and the Sign Out Timer (Administrator only)..76 ContentsQuantStudio 3 and 5 Real-Time PCR Systems installation , Use, and MAINTENANCE Guide 5 APPENDIX A Install and connect the instrument to a : Install and connect to a you and install the on and follow the startup the instrument and the computer directly or to a and computer and install the QuantStudio Design and Analysis desktop requirements for the desktop the desktop the network configuration and monitor networked the Ethernet ports that must be guidelines and best APPENDIX B APPENDIX C Parts and , consumables, and ( ) Fast ( )

7 3 and 5 Systems materials and APPENDIX D Instrument specification and system 3 and 5 Real-Time PCR Systems installation , Use, and MAINTENANCE Guide APPENDIX E on this alerts on this of safety labels on the information for instruments not manufactured by Thermo Fisher and and electromagnetic compatibility (EMC) hazard Documentation and information from the Help and technical product 3 and 5 Real-Time PCR Systems installation , Use, and MAINTENANCE Guide 7 About this guideRevision 2015 Updates describes new features in , including: Updated workflow to create an instrumentprofile Streamlined workflow for connectivity to theThermo Fisher Cloud Improved display of VeriFlex Zones Plate insert reminder before starting run Support for 96-well Fast ( mL) 2015 Updates describes new features in , including: Experiment runs: monitor real-time data, editcycle number and lock screen during a run, viewend plot, and support for 384-well plates File management: access Network folders,navigate folder structures and save templateson instrument, and perform batch actions forfile management Instrument configuration.

8 Support for Security,Audit, and e-Signature (SAE), smart monitoring,and choice of server regionIncludes information on software featurecomparison, definitions of terms, parts of method,network connection options, experiment types,desktop software 2015 New document. Describes installation , operation,and MAINTENANCE of the QuantStudio 3 and 5 Real-Time PCR 3 and 5 Real-Time PCR Systems installation , Use, and MAINTENANCE GuidePurposeThis guide provides information about installing, using, and maintaining theQuantStudio 3 and 5 Real-Time PCR : For information and instructions on performing experiments on these systems,refer to the QuantStudio Design and Analysis desktop Software User Guide (Pub.)

9 About this guidePurposeQuantStudio 3 and 5 Real-Time PCR Systems installation , Use, and MAINTENANCE Guide 9 Product information Instrument hardware Software Network connection Experiment hardware descriptionThe QuantStudio 3 and 5 Real-Time PCR Systems use fluorescent-based polymerasechain reaction (PCR) reagents to perform: Quantitative detection of target nucleic acid sequences (targets). Qualitative detection of targets (endpoint analysis). Qualitative analysis of the PCR product (post-PCR melt curve analysis).The following fixed-block configurations are available:QuantStudio 3 Real-Time PCR SystemQuantStudio 5 Real-Time PCR System 96-Well VeriFlex Block(4 Color) 96-Well VeriFlex Block(4 Color) 96-Well VeriFlex Block(6 Color De coupled) 384-Well Block (5 Color) 96 Well VeriFlex Block(6 Color De coupled)The instrument can be run directly from the touchscreen to create and startexperiments.

10 To design experiments or to analyze data, the instrument can beintegrated with QuantStudio Design and Analysis Software (desktop or cloud).An optional barcode scanner and optional wireless adapter can be 3 and 5 Real-Time PCR Systems installation , Use, and MAINTENANCE GuideInstrument filters and supported dyesSystem dyesThe QuantStudio 3 and 5 Systems use a coupled four-color, coupled five-color, or de-coupled six-color filter set that supports the dyes shown in the following table andfigure. For more information about the spectral dye calibration kits available for theQuantStudio 3 and 5 Systems, contact wavelength(nm)[1]Pre-calibrateddyesExamp le customdyesExcitationEmissionx1-m1 Blue470 15520 15 FAM and SYBR GreenSYT09x2-m2 Green520 10558 12 VIC HEX , TET , andJOE [2]x3-m3 Yellow550 10587 10 ABY , NED , andTAMRA Cy 3x4-m4 Orange580 10623 14 JUN and ROX Texas Red x5-m5 Red640 10682 14Cy 5 andMUSTANGPURPLE LIZ x6-m6 Deep-Red662 10711 12 None[3]Cy [1]The central wavelengths are the optimized wavelengths.