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Quantasoft Software Download – 3 Bio-Rad Technical Support Department The Bio-Rad Technical Support Department in the US is open Monday through Friday, 5:00 AM to 5:00 PM, Pacific Standard Time. Phone: , option 2 (US/Canada only) For technical assistance outside the US and Canada, contact your local technical support office or click the Contact Us link at Legal Notices No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or in any information storage or retrieval system, without written permission from Bio-Rad Laboratories. Bio-Rad reserves the right to change its products and services at any time. This user guide is subject to change without notice. Although it is willing to ensure accuracy, Bio-Rad assumes no responsibility for errors or any damage resulting from the application or use of this information. Bio-Rad, ddpcr and Droplet Digital PCR are trademarks of Bio-Rad Laboratories, Inc. in certain jurisdictions. All trademarks used herein are the property of their respective owners. EvaGreen is a trademark of Biotium, Inc. Bio-Rad Laboratories, Inc. is licensed from Biotium, Inc. to sell reagents containing EvaGreen dye for use in real-time PCR, for research purposes only. The QX200 Droplet Digital PCR System, as well as consumables and reagents designed for use with these systems, and/or their use are covered by US and/or pending US and non-U.S. patent claims. patent applications owned or licensed by Bio-Rad Laboratories, Inc. See for details. Purchase of the Product includes a limited, non-transferable right under that intellectual property to use the Product solely for internal research purposes in the field of digital PCR. No rights are granted for diagnostic use. No rights are granted to use the product for commercial applications of any kind, including but not limited to manufacturing, quality control, or commercial services, such as contract services or service fees. License information for such use may be obtained from Bio-Rad Laboratories. The customer/end user is responsible for obtaining any additional intellectual property rights that may be required. Copyright 2019 Bio-Rad Laboratories, Inc. All rights reserved. QX200 Droplet Reader and QuantaSoft Software User Manual i

4 Foreword Safety and Regulatory Compliance This instrument has been tested and found to meet all applicable requirements of the following safety and electromagnetic standards: IEC :2010 (3rd Edition), GA :2010 (3rd Edition). Electrical equipment for measurement, control and laboratory use Part 1: General requirements GA :2013 (Class A). Electrical equipment for measurement, control and laboratory use. EMC Requirements, Part 1: General Requirements UL :2012, Laboratory Equipment, Test and Measurement Equipment and Industrial Process Controls CAN/CSA 22.2 No., Electrical Safety Requirements. Equipment for measurement, control and laboratory use, Part I: General. Requirements This equipment generates, uses and can radiate radio frequency energy and, if not installed and used in accordance with the instructions for use, may cause harmful interference to radio communications. The operation of this equipment is likely to cause harmful interference in a residential area, in which case the user will be required to correct the interference at his own expense. The CE mark indicates that the manufacturer ensures that the product meets the basic requirements of the applicable EN directives. The CSA mark indicates that the product has been tested to Canadian and US standards and meets the requirements of those applicable standards. This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to Part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment. The symbol of the Waste Electrical and Electronic Equipment Directive indicates that when the end user wishes to throw away this product, it must be sent to special collection facilities for recovery and recycling. This instrument is for use by trained personnel only. Do not place the equipment so that it is difficult to use the power plug. ii QX200 Droplet Reader and QuantaSoft Software User Manual

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Quantasoft Software Download

5 Instrument Safety Warnings Modification of this instrument voids warranty and safety certifications and creates a potential safety hazard. This instrument is intended for laboratory use only. Bio-Rad Laboratories is not responsible for any injury or damage caused by the use of this instrument for purposes other than those for which it was intended, or by modifications to the instrument not made by Bio-Rad Laboratories or an authorized agent. Follow the safety specifications listed here and throughout this manual. Only use the power cord supplied with the instrument, and only use an adapter suitable for the electrical outlets in your region. Use of non-approved super mixes may damage the instrument and void the warranty. Preface Training PPE (Personal Protective Equipment) Proper use of gloves is recommended along with the use of oil and sample plates. OSHA’s requirements for PPE are set forth in the Code of Federal Regulations (CFR) at 29 CFR (General Requirements); 29 CFR (Hand Protection); 29 CFR (Criteria for Standard Personal Protective Equipment). All gloves with reduced protective capacity should be discarded and replaced. Consider the toxicity of chemicals and factors such as duration of exposure, storage, and temperature when deciding to reuse chemically exposed gloves. Features that will help you choose gloves for handling machines, tests, oils and cleaning solvents: Butyl gloves are made of synthetic rubber and protect against peroxides, hydrofluoric acid, strong bases, alcohol, aldehydes and ketones Natural rubber gloves (latex ) are comfortable to wear and have outstanding tensile strength, elasticity and temperature resistance. protection against alcohol, organic acids and alkalis. Nitrile gloves are made of copolymers and provide protection against chlorinated solvents such as trichlorethylene and tetrachloroethene; offer protection when working with oils, greases, acids and caustic substances QX200 droplet reader and QuantaSoft software user manual iii

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7 Table of Contents Chapter 1. QX200 Droplet Digital PCR System Introduction to System Components Digital Droplet PCR Workflow System Setup and General Operating Instructions…4 Chapter 2. Using the QX200 Droplet Reader…5 Chapter 3. Using Setup Software QuantaSoft by Well Editor Using the Experiment Editor Using Advanced Options Run Analysis Viewing Channel Data Viewing Scatterplot Viewing Concentration Data Viewing Copy Number Data Viewing Ratio Data Viewing Event Simulation Mode Chapter 4 Specifications and Maintenance Specifications Maintenance Dropletmo Reader General Maintenance Procedures Replacement Regarding Error Codes …26 Appendix A. Ordering Information…27 QX200 QX200 Droplet Reader System Maintenance Log and QuantaSoft Software User’s Guide v

9 1 QX200 Digital PCR System 1.1 Introduction The QX200 Droplet Digital PCR System (ddpcr) performs accurate and precise digital PCR. The system consists of two instruments, the QX200 Droplet Generator and QX200 Droplet Reader, and associated consumables. The QX200 droplet generator divides samples into ~20,000 nanoliter droplets and, after thermal PCR cycles, droplets from each sample are analyzed individually on a QX200 droplet reader. PCR-positive and PCR-negative droplets are counted to ensure total quantification of the target DNA in digital form. Alternatively, the amplified products can be removed from the droplets after PCR for further applications, such as sequencing or cloning. The ddpcr system allows you to: Detect rare copies of a DNA target with unmatched sensitivity Determine copy number variation with unparalleled accuracy. Precise measurement of gene expression levels. Applications and uses include: Copy number variation Rare sequence detection Gene expression analysis Next generation sequencing (NGS) library quantification Viral load determination Single cell gene expression analysis Total quantification Rare mutation detection NGS silencing analysis Sample preparation Detection GMO GMO Genome editing detection For instructions for use of the droplet generator QX200, please refer to the User Guide for the droplet generator QX200 (bulletin ). For information on the QX200 AutoDG Digital PCR System and the Automated Droplet Generator, see the Automated Droplet Generator User’s Guide ( bulletin ). QX200 Droplet Reader and QuantaSoft Software Manual 1

10 Chapter 1 QX200 Digital PCR System 1.2 System Components The system consists of two instruments and associated software, consumables, and reagents (Table 1.1): The QX200 Droplet Generator uses proprietary reagents and microfluidics to divide samples into 0 droplets ~20 liter-0 reader QX200 droplet after PCR amplification of the nucleic acid target in the droplet, this instrument analyzes each droplet individually using a two-color detection system (set to FAM and VIC, HEX or detect EvaGreen); PCR-positive and PCR-negative droplets are counted to ensure total quantification of the target DNA in digital form using QuantaSoft software. Additional materials required to perform ddpcr are listed in Table 1.2. Table 1.1. Components of the QX200 Digital Droplet PCR System. The items are supplied with the QX200 ddpcr system (part number). Catalog number refers to replacement items (quantities may vary). Component Description Catalog # Droplet Generator QX200 QX200 Droplet Generator Instrument used to generate droplets Cartridges and Seals Droplet Generator DG8 (24) Microfluidic cartridge used to mix sample and oil to generate droplets; seals seal the ink to prevent evaporation and apply the pressure needed to create DG8 cartridge holder droplets

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