Bio-Rad QX100 User Manual

QX100™ Droplet Generator

Instruction Manual

Catalog #186-3002

Preface

Bio-Rad Technical Support

For help and technical advice, please contact the Bio-Rad Technical Support department. In the United
States, the Technical Support department is open Monday–Friday, 5:00 AM–5:00 PM, Pacific time.

Phone: [phone]
Fax: [phone]
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Online technical support and worldwide contact information are available at www.consult.bio-rad.com.

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at any time. This instruction manual is subject to change without
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Although prepared to ensure accuracy, Bio-Rad assumes no liability
for errors, or for any damages resulting from the application or use
of this information.

Pipetman is a trademark of Gilson, Inc. twin.tec is a trademark of
Eppendorf AG.

Notice regarding Bio-Rad thermal cyclers and real-time systems:
Purchase of this product conveys a limited, non-transferable
immunity from suit for the purchaser’s own internal research and
development and for use in human in vitro diagnostics and all
other applied fields under U.S. Patent Number 5,475,610 (Claims
1, 44, 158, 160–163, and 167 only), or corresponding claims in its
non-U.S. counterpart, owned by Applera Corporation. No right
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Bio-Rad’s thermal cyclers and real-time thermal cyclers are covered
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counterparts owned by Eppendorf AG: U.S. Patent Numbers
6,767,512 and 7,074,367.

Copyright © 2012 by Bio-Rad Laboratories, Inc. All rights reserved.

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Table of Contents

QX100™ Droplet Generator 1

1.1 Introduction 1

1.2 QX100 Droplet Generator 2

1.3 Installation and General Operation 3

Droplet Generation 5

2.1 Sample Preparation 5

2.2 Operation of the QX100 Droplet Generator 6

2.3 Preparation for PCR 10

Specifications and Maintenance 13

3.1 Specifications 13

3.2 Maintenance 14

Appendix A Ordering Information 15

Preface

Safety and Regulatory Compliance

This instrument has been tested and found to be in compliance with all applicable requirements of the
following safety and electromagnetic standards:



IEC 61010-1:2001 (2nd ed.), EN61010-1:2001 (2nd ed). Electrical Equipment for Measurement, Control, and
Laboratory Use — Part 1: General requirements



EN 61326-1:2006 (Class A). Electrical equipment for measurement, control, and laboratory use. EMC
requirements, Part 1: General requirements

This equipment generates, uses, and can radiate radiofrequency energy and, if not installed and used in
accordance with the instruction manual, may cause harmful interference to radio communications. Operation
of this equipment in a residential area is likely to cause harmful interference, in which case the user will be
required to correct the interference at his own expense.

The CE mark indicates that the manufacturer ensures the product conforms with the essential
requirements of the applicable EC directives.

The CSA mark indicates that a product, process or service has been tested to a Canadian or
U.S. standard and it meets the requirements of the applicable CSA standard.

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 Waste Electrical and Electronic Equipment Directive symbol indicates that when the
end-user wishes to discard this product, it must be sent to separate collection facilities for
recovery and recycling.

Instrument Safety Warnings

Alteration of this instrument voids the warranty and safety certification 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 use of this instrument for purposes other than those for which it is intended, or by
modifications of the instrument not performed by Bio-Rad Laboratories or an authorized agent. Follow the
safety specifications listed here and throughout this manual. Use only the power cord supplied with the
instrument, using only the plug adaptor that corresponds to the electrical outlets in your region. Use of
unapproved supermixes may harm the instrument and voids the warranty.

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PrefacePreface

PPE (Personal Protective Equipment) Training

Proper use of gloves is recommended with use of oils and sample plates. OSHA requirements for PPE are set
forth in the Code of Federal Regulations (CFR) at 29 CFR 1910.132 (General requirements); 29 CFR 1910.138
(Hand protection); 29 CFR 1926.95 (Criteria for standard personal protective equipment). Any gloves with
impaired protective ability should be discarded and replaced. Consider the toxicity of the chemicals and
factors such as duration of exposure, storage, and temperature when deciding to reuse chemically exposed
gloves. Features to aid glove selection for handling of machines, assays, oils, and cleaning solvents:



Butyl gloves are made of a synthetic rubber and protect against peroxide, hydrofluoric acid, strong bases,
alcohols, aldehydes, and ketones



Natural (latex) rubber gloves are comfortable to wear and feature outstanding tensile strength, elasticity, and
temperature resistance



Neoprene gloves are made of synthetic rubber and offer good pliability, finger dexterity, high density, and
tear resistance; they protect against alcohols, organic acids, and alkalis



Nitrile gloves are made of copolymer and provide protection from chlorinated solvents such as trichloroethylene
and tetrachloroethene; they offer protection when working with oils, greases, acids, and caustic substances

QX100 Droplet Generator Instruction Manual | v

QX100 Droplet Generator Instruction Manualvi |

QX100™ Droplet

1

Generator

1.1 Introduction

Th e QX100™ Droplet Digital™ PCR (ddPCR™) system performs digital PCR with
unrivaled accuracy and precision. The system consists of two instruments, the
QX100 droplet generator and the QX100 droplet reader, and their associated
consumables. The QX100 droplet generator partitions samples into 20,000
nanoliter-sized droplets, and after PCR on a thermal cycler, droplets from each
sample are analyzed individually on the QX100 droplet reader. PCR-positive and
PCR-negative droplets are counted to provide absolute quantification of target
DNA in digital form.

The ddPCR system lets you:



Detect rare DNA target copies with unmatched sensitivity



Determine copy number variation with unrivaled accuracy



Measure gene expression levels with precision

Applications and uses include:



Copy number variation



Rare sequence detection



Mutation detection



Gene expression analysis



miRNA analysis



Next-generation sequencing sample quantification

This manual covers use of the QX100 droplet generator and preparation
for PCR. For information on the QX100 droplet reader, please refer to
bulletin 10026321.

QX100 Droplet Generator Instruction Manual | 1

Chapter 1 QX100 Droplet Generator

1.2 QX100 Droplet Generator

The QX100 droplet generator uses microfluidics to combine oil and water (sample) to create the droplets
required for ddPCR analysis. It processes up to eight samples at a time, in under 2 minutes.

Following sample preparation using either the ddPCR supermix or One-Step RT-ddPCR kit for probes,
20 μl each of eight prepared samples (or blanks) and droplet generator oil are transferred to the droplet
generator (DG
generator. There, the samples and oil are combined within the microchannels of the cartridge to create an
emulsion of ~20,000 monodisperse, nanoliter-sized droplets for each of the samples. Following droplet generation,
the droplets are transferred to a standard 96-well PCR plate and amplified to end point using a standard thermal
cycler.

When cycling is complete, the plate is loaded into the QX100 droplet reader. The droplet reader sips each
sample, singulates the droplets, and streams them in single file past a two-color detector. The detector reads
each droplet and determines which contain a target (+) and which do not (–).

The QX100 droplet generator includes the components listed in Table 1.1. Additional requirements for droplet
generation and PCR are listed in Table 1.2. For complete system requirements, refer to the QX100 Droplet
Reader Instruction Manual (bulletin 10026321).

Table 1.1. QX100 droplet generator components. Catalog # refers to replacement items (quantities may be different).

Component Description Catalog #

QX100 droplet generator Instrument used for droplet generation 186-3002

DG8 droplet generator Microfluidic cartridge used to mix sample and oil to 186-3008
cartridges and gaskets (24) generate droplets; gaskets seal the cartridge to
prevent evaporation and apply pressure required
for droplet formation

Droplet generator cartridge Position and hold the droplet generator cartridge 186-3051
holders (2) in the instrument for droplet generation

Power cord Connects QX100 droplet generator to power source Call technical support

™

) cartridge. The loaded cartridge is covered with a gasket and placed in the QX100 droplet

QX100 droplet generator.

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