QX200TM Droplet Generator
Instruction ManualQX200 Droplet Generator
Instruction Manual

Catalog Number 1864002

Bio-Rad Technical Support Department
The Bio-Rad Technical Support department is open Monday through Friday, 5:00 AM to 5:00 PM, Pacific time.
Phone: 1-800-424-6723, option 2
Email: Support@bio-rad.com (U.S./Canada Only)
For technical assistance outside the U.S. and Canada, contact your local technical support office or click theContact Us link at https://bio-rad.com.

Legal Notices
No part of this publication may be reproduced or transmitted in any form or by any means, electronic ormechanical, including photocopy, recording, or any information storage or retrieval system, without permission
in writing from Bio-Rad Laboratories, Inc.
Bio-Rad reserves the right to modify its products and services at any time. This guide is subject to change
without notice. Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors or omissions, orfor any damage resulting from the application or use of this information.
BIO-RAD, DDPCR, DROPLET DIGITAL, DROPLET DIGITAL PCR, QX200, and QX600 are trademarks of
Bio-Rad Laboratories, Inc. in certain jurisdictions.
EvaGreen is a trademark of Biotium, Inc. Bio-Rad Laboratories, Inc. is licensed by Biotium, Inc. to sell
reagents containing EvaGreen Dye for use in real-time PCR, for research purposes only.
Purchase of Digital PCR and/or Single-Cell NGS Sample Preparation products (the “Products”) from
Bio-Rad Laboratories is subject to Bio-Rad Laboratories, Inc. Standard Terms and Conditions of Sale, which
can be accessed at https://bio-rad.com/en-us/terms-conditions. Unless we expressly state otherwise inadditional Terms and Conditions, no rights are granted for you to distribute or resell the Products. Unless we
expressly state otherwise in additional Terms and Conditions, ​no rights are granted for the development orcommercialization of diagnostic assays for use with the Products without a license from Bio-Rad. It is theuser’s obligation to obtain a commercial license from Bio-Rad for (i) all commercial uses (not just diagnosticuses) and (ii) sale of assays for use on Bio-Rad's dPCR and ddSEQ instruments. The Products and/or theiruse are covered by U.S.​ and foreign patents and/or pending patent applications owned by or under license to
Bio-Rad Laboratories, Inc. See https://bio-rad.com/en-us/trademarks for trademark information.
All trademarks used herein are the property of their respective owner.
Copyright © 2023 by Bio-Rad Laboratories, Inc. All rights reserved.

Revision History

Revision History
Document

Date

Description of Change

QX200 Droplet Generator

July

Instruction Manual

2023

Update the legal statement. Add the Managing
Waste section. In the Order Information section,
replace the word “laptop” with “computer," update
products and catalog numbers, and removereference to QX Manager. Update with other minor
edits.

DIR D094813 (10031907)
Ver G

Instrument Guide | iii

iv QX200 Droplet Generator

Table of Contents
Front Cover
Revision History

Safety and Regulatory Compliance

a
iii

7

Regulatory Compliance7

Safety Warning Labels

9

Safe Use Specifications

10

Personal Protective Equipment

11

Hazards

12

Biohazards

12

Chemical Hazards

13

Explosive or Flammability Hazards

13

Electrical Hazards

13

Surface Decontamination

13

Decommissioning and Disposal

14

Transport

14

Warranty

14

Chapter 1 Introduction to Droplet Digital PCR

15

ddPCR Workflow

16

Finding Out More

16

Chapter 2 About the QX200 Droplet Generator

17

Included Items

18

Instrument Specifications

18

Additional Components

19

Environmental Requirements

22

General Maintenance23

Managing Waste

24

Connecting the QX200 Droplet Generator

25

Status Indicator Lights

25

Instrument Guide | v

Table of Contents

Chapter 3 Droplet Generation

27

Preparing the Sample

27

Operating the QX200 Droplet Generator

28

Inserting the Cartridge into the Cartridge Holder

28

Filling and Preparing the Cartridge for the Run

29

Inserting the Cartridge and Generating Droplets

31

Appendix A Preparing For and Executing PCR

33Aspirating Droplets from the Cartridge

33

Dispensing Droplets into the Plate

34

Sealing the Plate

34

Thermal Cycling and Droplet Reading

36

Appendix B Ordering Information

37

Back Cover45

vi QX200 Droplet Generator

Safety and Regulatory ComplianceThis section cites regulatory requirements for laboratory and electrical equipment, as well as
requirements for working with chemicals and hazardous substances, and also explains safety precautions
and recommendations.
Important: Only trained personnel should use this instrument.

Regulatory Compliance
The instrument has been tested and found to be in compliance with all applicable requirements of thefollowing safety and electromagnetic standards:n

IEC 61010-1:2010 (3rd:2016, EN61010-1:2010 (3rd ed.). Electrical equipment for measurement,
control, and laboratory use - Part 1: General requirementsn

IEC 61326-1:2012 (Class A), EN 61326-1:2013 (Class A). Electrical equipment for measurement,
control, and laboratory use. EMC requirements, Part 1: General requirementsn

IEC 61010-2-081:2015, 3.0 edition, UL 61010-2-081:2015, CAN/CSA C22.2 No. 61010-2-081:19.
Safety requirements for electrical equipment for measurement, control, and laboratory use.
Part 2-081: Particular requirements for automatic and semi-automatic laboratory equipment foranalysis and other purposes (includes Amendment 1)n

CAN/CSA 22.2 No 61010-1-04, Safety requirements for electrical, equipment for measurement,
control, and laboratory use, Part 1: General requirementsn

CAN/CSA C22.2 No. 61010-2-101:2019 IEC 61010-2-101: 2018 (3rd ed.)nRestriction of hazardous substances (ROHS) directive (European Union)nRegistration, evaluation, authorization and restriction of chemicals (REACH). European Chemicals
Agency (ECHA) June 1, 2007n

Waste electrical and electronic equipment (WEEE) directive

This equipment has been tested and found to comply with the limits for a Class A digital device pursuant
to Part 15 of FCC rules. These limits are designed to provide reasonable protection against harmfulinterference when the equipment is operated in a commercial environment.

Instrument Guide | 7

Safety and Regulatory Compliance

Table 1. Regulatory symbols

SymbolDefinition
The CE symbol indicates that the manufacturer ensures the product conforms withthe essential requirements of the applicable EN directives.
The CSA symbol indicates that a project has been tested to Canadian and U.S.
standards, and it 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 toprovide reasonable protection against harmful interference when the equipment is
operated in a commercial environment.
The Waste Electrical and Electronic Equipment (WEEE) Directive symbol indicatesthat when the end-user wishes to discard this product, it must be sent to separate
collection facilities for recovery and recycling.

8 QX200 Droplet Generator

Safety Warning Labels

Safety Warning Labels
Warning labels alert you about sources of injury or harm. Table 2 defines each safety warning label.
Table 2. Meaning of safety warning labels

Icon

Meaning
Warning about risk of harm to body or equipment
Operating the systerm before reading this manual can constitute a personal injury
hazard. For safe use, do not operate this instrument in any manner unspecified in thismanual. Only qualified laboratory personnel trained in the safe use of electricalequipment should operate this instrument. Always handle all components of the systemwith care and with clean, dry hands.
Warning about handling biohazardous materials
When handling biohazardous samples, adhere to the recommended precautions andguidelines and comply with any local guidelines specific to your laboratory and location.
Warning about risk of electric shock
In order to prevent electric shock, use caution when plugging and unplugging the
instrument. Always turn off and unplug the instrument when performing maintenanceprocedures.

Instrument Guide | 9

Safety and Regulatory Compliance

Safe Use Specifications
For safe operation of the instrument, Bio-Rad™ strongly recommends that you comply with instructions
listed in this section.
This instrument is intended for laboratory use only. Bio-Rad 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
to the instrument not performed by Bio-Rad or an authorized agent.
nThis instrument is for use only by trained personnel.

n

Use only the power cord, power switch, and USB port supplied with the instrument, and the plug
adapter corresponding to the electrical outlets in your region.

n

Position the instrument on a solid, stable surface, with adequate room at the back and on each side
so that users can easily reach the power cord and USB port.

nThis equipment generates, uses, and can radiate radio frequency energy and, if not installed andused in accordance with the provided instructional documentation, may cause harmful interference toradio communications. Operation of the systems in a residential area is likely to cause harmfulinterference, in which case users will be required to correct the interference at their own expense.

Note: Bio-Rad recommends maintaining a backup power source in case of power outages. A
universal power supply (UPS) can protect from brown outs and power surges, while a regular backup
generator does not.

10 QX200 Droplet Generator

Personal Protective Equipment

Personal Protective Equipment
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 thechemicals and factors such as duration of exposure, storage, and temperature when deciding to reusechemically exposed gloves.
Listed below are features to aid glove selection for handling of machines, assays, oils, and cleaning
solvents:nButyl gloves are made of a synthetic rubber and protect against peroxide, hydrofluoric acid, strong
bases, alcohols, aldehydes, and ketonesnNatural (latex) rubber gloves are comfortable to wear and feature outstanding tensile strength,elasticity, and temperature resistancen

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

Instrument Guide | 11Safety and Regulatory ComplianceHazards
The instrument is designed to operate safely when used in the manner prescribed by the manufacturer. If
the instrument or any of its associated components is used in a manner not specified by the manufacturer,
the inherent protection provided by the instrument may be impaired.
Bio-Rad Laboratories, Inc. is not liable for any injury or damage caused by the use of this equipment in
any unspecified manner, or by modifications to the instrument not performed by Bio-Rad or an authorized
agent. Only trained Bio-Rad personnel should perform service on the system.

Biohazards
The instrument is a laboratory product. However, if biohazardous samples are present, adhere to thefollowing guidelines and comply with any local guidelines specific to your laboratory and location.
Note: No biohazardous substances are expended during normal operations of this instrument.

General Precautionsn

Always wear laboratory coat, laboratory gloves, and safety glasses with side shields or goggles.

n

Keep your hands away from your mouth, nose, and eyes.

nCompletely protect any cut or abrasion before working with potentially infectious materials.

nWash your hands thoroughly with soap and water after working with any potentially infectious
material before leaving the laboratory.

nStore all infectious or potentially infectious material in unbreakable leak-proof containers.

nBefore leaving the laboratory, remove protective clothing.

nChange gloves frequently. Do not use a gloved hand to write, answer the telephone, turn on a lightswitch, or touch anything that other people may touch without gloves. Remove gloves immediately
when they are visibly contaminated.

n

Do not expose materials that cannot be properly decontaminated to potentially infectious material.

nUpon completion of an operation involving biohazardous material, decontaminate the work area with
an appropriate disinfectant (for example, a 1:10 dilution of household bleach).

12 QX200 Droplet Generator

Surface Decontamination

Disposal of Biohazardous Material
Dispose of the following potentially contaminated materials in accordance with laboratory local, regional,
and national regulations:nClinical samples

nReagents

n

Used reaction vessels or other consumables that may be contaminatedChemical Hazards
The instrument contains no potentially hazardous chemical materials.

Explosive or Flammability Hazards
The instrument poses no uncommon hazard related to flammability or explosion when used in a proper
manner as specified by Bio-Rad.

Electrical Hazards
The instrument poses no uncommon electrical hazard to operators if installed and operated properly
without physical modification and connected to a power source of proper specification.

Surface Decontamination
WARNING! To prevent electrical shock, always turn off and unplug the instrument
before performing decontamination procedures.
Important: Do not use abrasive or corrosive detergents or strong alkaline solutions. These agentscan scratch surfaces and damage the system.
The following areas can be cleaned with 10% bleach solution:nOuter area and chassisn

Inner plate holdersnsurfaces

To prepare and apply the disinfectant, refer to the instructions provided by the product manufacturer. For
questions regarding the use of other cleaning agents, contact Bio-Rad Technical Support.
Important: Do not clean the handler Y-axis rail when the front door is open. This is a lubricatedsurface, and failures will occur if the lubrication is removed.

Instrument Guide | 13

Safety and Regulatory Compliance

Decommissioning and Disposal
The instrument contains electrical materials that should be disposed of as unsorted waste and must becollected separately, according to European Union Directive 2012/19/EU on waste electrical andelectronic equipment — WEEE Directive. The purpose of decommissioning is to make sure that theequipment is electrically and environmentally safe for disposal. Before disposal, contact your local
Bio-Rad representative for country-specific instructions.

Transport
You must perform the specified decontamination procedures before moving or shipping the system.
Always move or ship the instrument with the supplied packaging materials, which will protect the
instrument from damage. If appropriate containers cannot be found, contact your local Bio-Rad office.

Warranty
Important: The instrument is for research use only, and not for use in diagnostic procedures.
The instrument and its associated accessories are covered by a standard Bio-Rad warranty. Contact yourlocal Bio-Rad office for the details of the warranty. Follow the safety specifications listed in this chapter
and throughout this guide.
The instrument is intended for laboratory use only. Bio-Rad Laboratories, Inc. is not responsible for any
injury or damage caused by use of this instrument for purposes other than those for which it is intended, orby modifications of the instrument not performed by Bio-Rad Laboratories or an authorized agent.
Alteration of this instrument voids the warranty and safety certification, as it creates a potential safety
hazard.
Use of unapproved supermixes or additives may harm the instrument and voids the warranty.
Use only the power cord supplied with the instrument, using only the plug adaptor that corresponds to theelectrical outlets in your region.

14 QX200 Droplet Generator

Chapter 1 Introduction to Droplet Digital PCR
Droplet Digital™ PCR (ddPCR™) is a digital polymerase chain reaction method based on water-oil
emulsion droplet technology. Droplet Digital PCR™ uses a combination of microfluidics and proprietary
surfactant chemistries to divide each sample into water-in-oil droplets. The technology uses reagents andworkflows similar to those used for most standard TaqMan probe-based assays, and provides absolute
quantification of nucleic acid target sequences by counting nucleic acid molecules encapsulated indiscrete, volumetrically defined water-in-oil droplet partitions.
ddPCR is highly effective in the following areas:nAbsolute quantification — ddPCR provides a concentration of target DNA copies per input sample
without the need for running standard curves, making this technique ideal for target DNA
measurements, viral load analysis, and microbial quantification.

n

Genomic alterations such as gene copy number variation (CNV) — CNVs result in too few or
too many dosage-sensitive genes responsible for phenotypic variability, complex behavioral traits,
and disease. ddPCR enables measurement of 1.2x differences in gene copy number.

n

Detection of rare sequences — researchers must amplify single genes in a complex sample, suchas a few tumor cells in a wild-type background. ddPCR is sensitive enough to detect rare mutations orsequences.

nGene expression and microRNA analysis — ddPCR provides stand-alone absolute quantificationof expression levels, especially low-abundance microRNAs, with sensitivity and precision.

n

Next-generation sequencing (NGS) — ddPCR quantifies NGS sample library preparations toincrease sequencing accuracy and reduce run repeats. Validate sequencing results such as single
nucleotide polymorphisms or copy number variations with absolute quantification.

nSingle cell analysis — the high degree (10-fold to 100-fold) of cell-cell variation in gene expression
and genomic content among homogeneous post-mitotic, progenitor, and stem cell populations drives
a need for analysis from single cells. ddPCR enables low copy number quantification and gene
expression of individual cells.

nGenome edit detection — ddPCR enables fast, precise, and cost-effective assessment of HDR(Homology directed repair) and NHEJ (non-homologous end joining) generated by CRISPR-Cas9 orother genome editing tools.

Instrument Guide | 15

Chapter 1 Introduction to Droplet Digital PCR

ddPCR has the following benefits for nucleic acid quantification:n

Unparalleled precision — The massive sample partitioning afforded by ddPCR enables small folddifferences in target DNA sequence between samples to be reliably measured.

nIncreased signal-to-noise ratio — High-copy templates and background are diluted, effectively
enriching template concentration in target-positive partitions. This allows for the sensitive detection ofrare targets and enables a ±10% precision in quantification.

nRemoval of PCR efficiency bias — Error rates are reduced by removing the amplification efficiency
reliance of qPCR, enabling accurate quantification of targets to near zero.

n

Simplified quantification — There is no requirement for a standard curve for absolute
quantification.

ddPCR Workflow
The ddPCR process conforms to the following workflow, and the full process is performed on one wellbefore moving to the next:n

You prepare your samples for PCR by combining DNA or RNA with primers, probes dye, and
Bio-Rad ddPCR supermix.

n

A droplet generator fractionates a sample into droplets with target and background DNA distributed
randomly into the droplets during the partitioning process.

n

Following droplet generation, the droplets are run through a thermal cycler, which performs PCRamplification of the nucleic acid target in each individual droplet.

n

A droplet reader reads each droplet to determine the fraction of positive droplets in the original
sample and uses Poisson statistical formulas to determine the absolute quantity.
Note: Positive droplets containing at least one copy of the target DNA molecule exhibit
increased fluorescence compared to negative droplets.

Finding Out More
Go to https://bio-rad.com to access links to technical notes, manuals, videos, product information, andtechnical support. The website also provides many technical resources on a wide variety of methods andapplications related to PCR, Droplet Digital PCR, and gene expression.

16 QX200 Droplet Generator

Chapter 2 About the QX200 Droplet Generator
The QX200™ Droplet Generator uses microfluidics to combine oil and sample to create the droplets
required for ddPCR analysis. The instrument generates droplets from up to eight samples in a DG8
cartridge at a time in about 2 min. You can generate droplets in one cartridge at a time.

Following reaction preparation using the appropriate ddPCR supermix, the prepared samples and droplet
generation oil (or buffer for wells without sample) are transferred to the DG8 cartridge. The loaded
cartridge is covered with a gasket and placed in the QX200 Droplet Generator, which combines the
samples and oil within the microchannels of the cartridge to create an emulsion of approximately 20,000
monodisperse, nanoliter-sized droplets for each sample.

Instrument Guide | 17

Chapter 2 About the QX200 Droplet Generator

Included Items
This section identifies the functional items included and shipped with your purchase.
Table 3. QX200 Droplet Generator included items

Component

Description

Catalog Number

QX200 Droplet

Instrument used for droplet generation

1864002

U.S. standard power cord with grounded plugContact Bio-Rad Technical(type 5-1SP) and CS connector (10A/125V), andSupportGenerator
Power cord

power supply to 5mm DC power jack inlet
DG8 droplet generator

Microfluidic cartridge used to mix sample and oil

cartridges and gaskets

to generate droplets; gaskets seal the cartridge

1864007 (pkg of 24)

to prevent evaporation and apply pressure
required for droplet formation
Droplet generator

Positions and holds the droplet generator

cartridge holder

cartridge in the instrument for droplet generation

1863051

Instrument Specifications

Table 4. Instrument size and weight
Specification

Description

Weight10 lb (4.5 kg)

Size (W x D x H)

11 in x 14 in x 5 in (28 cm x 36 cm x 13 cm)

For information on required environmental conditions, see Environmental Requirements on page 22.

18 QX200 Droplet Generator

Additional Components

Additional Components
The following tables identify additional components you can purchase for use with your system or
instrument.
Table 5. Accessories and consumables

Component

Description

Catalog Number

ddPCR 96-Well

Clear well/clear shell semi-skirted plates

12001925 (pkg of 25)

DG8 Cartridge

Droplet generation cartridge holders for the QX200

1863051

Holders

Droplet Generator

DG8 Cartridges

Droplet generation cartridges and gaskets for theand Gaskets

QX200 Droplet Generator

DG8 Cartridges

Droplet generation cartridges for the QX200 Droplet

Plates1864007 (pkg of 24)

17005222 (pkg of 24)

Generator

DG8 Gaskets

Gaskets for the DG8 cartridges

17005223 (pkg of 24)

Dropletn Droplet Generation Oil for Probes, 70 ml

1863005 (10 x 7 ml)

Generation Oilsn Droplet Generation Oil for EvaGreen®, 14 ml

1864005 (2 x 7 ml)n Droplet Generation Oil for EvaGreen®, 70 ml

1864006 (10 x 7 ml)

Droplet generation oils for the QX200 Droplet
Generator.

Droplet Reader
Oil

ddPCR droplet reader oil for QX600 and QX200
instruments and systems

1863004

Rainin Pipets

n 20 µl pipet for sample loading

Rainin L-20

n 50 µl pipet for droplet transfer

Rainin L-50, L8-50

n 8-channel 200 µl pipet for oil

Rainin L8-200

FilteredRainin GP-L10F

Rainin Pipet Tips

Rainin GP-L200F
Reagent trough

Any

N/A

8-cap strips

Any

N/A

Instrument Guide | 19

Chapter 2 About the QX200 Droplet Generator

Table 6. Thermal cyclers and plate sealer

Product

Description

Catalog
Number

C1000 Touch Thermal Cycler with

Includes the C1000 Touch Thermal Cycler

1851197

96-Deepwell Reaction Module

chassis, 96-deepwell reaction module, USB
flash drive

PTC Tempo Deepwell Thermal Cycler

Includes the thermal cycler, power cord,
USB cable, and Ethernet cable

12015392

PX1 PCR Plate Sealer

PCR plate sealer, includes heat sealing

1814000

instrument, plate support block that holds 96well and 384-well plates, sealing frame,
power cord
Pierceable Foil Heat Seal

Heat seal for the PX1 PCR Plate Sealer

1814040

Table 7. ddPCR supermixes
Supermix

Description

ddPCR
EvaGreen®
Supermix

2x supermix, for use in nucleic acid sample
preparation with the QX600 and QX200
ddPCR systems

Catalog number
1864033

2ml (2 x 1ml)

1864034

5ml (5 x 1ml)

1864035

25ml (25 x 1ml)

1864036

50ml (50 x 1ml)
2ml (2 x 1ml)

ddPCR Supermix

2x supermix, for use in nucleic acid sample

1863023

for Probes (nopreparation with the QX600™ and QX200

18630245ml (5 x 1ml)

dUTP)

ddPCR systems

1863025

25ml (25 x 1)

ddPCR Supermix

2x supermix, for use in sample preparation

1863026

2ml (2 x 1ml)

for Probeswith the QX600 and QX200 ddPCR systems

18630105ml (5 x 1ml)

1863027

25ml (25 x 1ml)

1863028

50ml (50 x 1ml)

ddPCR Multiplex

4x supermix especially suited for probe-

12005909

1.2ml (2 x 0.6ml)

Supermix

based detection of multiple targets in DNA

12005910

3 ml (5 x 0.6 ml)

samples using the QX600 and QX200

1200591112.5 ml (5 x 2.5 ml),

ddPCR systems

20 QX200 Droplet Generator

Additional Components

Table 7. ddPCR supermixes, continued
Supermix

Description

ddPCR Supermix

2x supermix, for use in residual DNA

1864037

for Residual DNA

detection with the QX600 and QX200 ddPCR

1864038

5ml (5 x 1ml)

Quantification

systems

1864039

25ml (25 x 1ml)

1864040

50ml (50 x 1ml)

1864021

2ml (2 x 1ml)

18640225ml (5 x 1ml)

One-step RTddPCR Advanced
Kit for Probes

200 or 500x 20 µl reaction kit, for absolute
quantification of target RNA in a one-stepformat with the QX600 and QX200 ddPCR
systems

Catalog number
2ml (2 x 1ml)

Table 8. Buffer controls

BufferCatalog
NumberddPCR Buffer Control Kit for Probes

1863052

QX200 Buffer Control Kit for EvaGreen®

1864052

Instrument Guide | 21

Chapter 2 About the QX200 Droplet Generator

Environmental Requirements
Table 9 lists the environmental requirements for the QX200 Droplet Generator.
Important: You must use the supplied shielded cables with your instrument to ensure compliancewith the Class A FCC limits.
Table 9. Conditions for safe use

Usage aspect

Requirements

Rated input power

100–240 V, 50–60 Hz, (plugs into standard AC receptacle)

Voltage fluctuations± 10% for the included external power supply
Note: Use only the power cord supplied with the equipment.

Pollution degree

2Usage temperature

18–30° C

Relative humidity

non-condensing

Altitude

0 to above sea level

Installation category

II (external power supply plugs into a standard AC receptacle)
Indoor use only

Ventilation requirements

The following distances should be unobstructed for proper
ventilation:

22 QX200 Droplet Generator

General Maintenance

General Maintenance
When surfaces of the instrument require general cleaning, use deionized/distilled water to wipe down witha slightly dampened cloth. For decontamination, you can use 10% bleach followed by 70% ethanol and/or
deionized/ distilled water.
Important: Do not use acetone or tap water.
Inspect the equipment regularly for damaged external components or wiring. Do not use if damaged.
Note the following:n

Bio-Rad droplet generation and reader fluids are based on fluorinated hydrocarbon chemistry, andshould be disposed of in accordance with institutional, state and local regulations.

n

Avoid release to the environment and prevent entry into sewer systems or bodies of water.

n

As a disposal alternative, incinerate in a permitted high-temperature waste incineration facility.

n

Do not use the droplet generator with biohazardous material.

n

Do not replace detachable power cord with an uncertified or an inadequately rated cord.

Instrument Guide | 23

Chapter 2 About the QX200 Droplet Generator

Managing Waste
You must apply standard Material Safety Data Sheet (MSDS) and OSHA practices when handling anddisposing of generated waste. A typical waste profile should contain the following:
Table 10. Managing Waste
Chemical name

Weight %Fluorinated fluids

>50%

Water

<50%

Bleach<10%

Other materials (proteins, nucleic acids, fluorescent dye)

<10%Note: The chemical identities and exact percentages in the above table are withheld as trade
secrets.
Bio-Rad droplet generation and reader fluids are based on fluorinated hydrocarbon chemistry, and should
be disposed of in accordance with institutional, state and local regulations. Avoid release to theenvironment and prevent entry into sewer systems or bodies of water. As a disposal alternative, incinerate
in a permitted high-temperature waste incineration facility.
These nonflammable fluids are inert and have low environmental impact and low toxicity.
Toxicological Information
Chemical name: (mixture)
Oral LD50: >5000 mg/kg (Rat)
Dermal LC50: >5000 mg/kg (Rabbit)
Inhalation LD50: >8838 ppm (Rat/8-hr)
Ecological Information
Acute aquatic hazard: LC50 > 500 mg/l (96-hr./static; Pimephales promelas/Fathead minnow)
Chronic aquatic hazard: No information available (GHS Chronic 4)

24 QX200 Droplet Generator

Connecting the QX200 Droplet Generator

Connecting the QX200 Droplet Generator
To connect the instrument
1.

Position the instrument so it can be easily disconnected from the power source.

2.

For proper ventilation, leave 10 in (25.4 cm) clear space behind the instrument, and 5 in (12.7 cm)
clear space to the right and left.

3.

Ensure the ground is reliably connected before plugging in the instrument.

4.

Connect the instrument to the power source to power it on.
The status indicator turns solid green to indicate power is on.
Important: Use only the power cord and power adapter provided.

5.

To open and close the lid, press the button on the lid.

Status Indicator Lights
This section describes the indicator lights on the top of the QX200 Droplet Generator.
Table 11. Droplet Generator Status Indicator Lights

Indicator(Power)(Cartridge)

Solid GreenPower is on

Cartridge is positioned properly(Status)
Droplets generated; runcomplete

Flashing Green

N/A

N/A

Droplets generating; run inprogress

Flashing Amber

N/A

N/A

Error during run (no seal, nogasket, or an empty well)

No color

Power is off

No cartridge loaded

Instrument is idle

Instrument Guide | 25

Chapter 2 About the QX200 Droplet Generator

26 QX200 Droplet Generator

Chapter 3 Droplet Generation
Preparing the Sample
Prepare the PCR reaction by combining 2x PCR supermix, 20x primers and probe, and DNA sample. Mix
by vortexing in short pulses, and then briefly centrifuge.
Note the following:n

The concentration of intact human genomic DNA should be less than 66 mg per 20 µl reaction. If
using higher concentrations, digest DNA with a restriction endonuclease that does not cut target orreference amplicons.

n

Use one of the PCR supermixes recommended in Appendix B, Ordering Information. These
supermixes contain reagents required for droplet generation. Follow instructions in the productinserts to prepare the samples for droplet generation.

nVortex the supermixes thoroughly to ensure homogeneity, since a concentration gradient may form
during -20° C storage. Alternatively, pipet up and down more than 5 times to mix. Before dispensing,centrifuge briefly to collect contents at the bottom of the tube.

nThaw and equilibrate reaction components to room temperature. If the sample is prone to thermal
degradation, prepare the reaction mix on ice, but equilibrate the reaction mix to room temperature(approximately 3 min) before loading in the DG8 cartridge for droplet formation.

nAssemble reaction mixtures in vials or in 96-well PCR plates. Note that using a PCR plate, you canload samples into the DG8 cartridge using an 8-channel pipet.

n

Use standard lab precautions to avoid contamination of the reaction mix and sample. Wear gloves,work in a clean area (such as a PCR hood) and use clean pipets and low protein binding tubes.

Instrument Guide | 27

Chapter 3 Droplet Generation

Operating the QX200 Droplet Generator
The instrument prepares droplets for up to eight samples at a time. Each DG8 cartridge contains eightsample wells. Each well must contain sample or 1x buffer control. Wells containing sample must also
contain droplet generation oil. Droplet generation takes approximately 2 min for each full cartridge.

Inserting the Cartridge into the Cartridge Holder
To insert the cartridge
1.

Press the latch on each side of the cartridge to open it.

2.

Slide the cartridge to the right, and then drop it into the holder.

3.

Press the halves of the holder together to close it.

28 QX200 Droplet Generator

Operating the QX200 Droplet Generator

Filling and Preparing the Cartridge for the Run
Air bubbles can cover the bottom of the well, resulting in 2,500 to 7,000 fewer droplets and poor data
quality. Use the pipeting technique described in this section ton

Avoid air bubblesnEnsure samples wet the bottom of the wells so they are wicked into microchannels (necessary forproper droplet generation)

To fill the cartridge
1.

Transfer 20 µl of each prepared sample to the sample wells (middle row) of the DG8 cartridge.
Important: Use only 20 µl aerosol-barrier (filtered) Rainin pipet tips. Do not use 200 µl pipet tips.
a.

Gently slide the pipet tip down the side of the wall at a 15-degree angle until it passes over the
ridge near the bottom. .

b.

Holding the 15-degree angle, ground the pipet tip against the bottom edge of the sample well,while slowly dispensing a small portion of the sample.
Do not pipet directly onto the side wall of the well.

c.

After dispensing about half the sample, slow draw the tip up the side wall while dispensing therest of the sample.
Do not push the pipet plunger past the first stop.

Instrument Guide | 29

Chapter 3 Droplet Generation2.

Dispense the droplet generation oil into the reagent trough.
Use the following volume guide:3.

n

For 8 wells, use 700 µl of oiln

For 24 wells, use 1,820 µl of oiln

For 48 wells, use 3,500 µl of oiln

For 96 wells, use 6,860 µl of oil

Using a multichannel pipet, fill each oil well (bottom row) with 70 µl of droplet generator oil from thetrough.

To prepare the cartridge for the droplet generation runu

Hook the gasket over the cartridge holder using the holes on the sides.

Important: The gasket must be hooked securely on each end or the instrument cannot reachthe required pressure.

30 QX200 Droplet Generator

Inserting the Cartridge and Generating Droplets

Inserting the Cartridge and Generating Droplets
To insert the cartridge into the instrument and generate droplets
1.

Press the button on the top of the QX200 Droplet Generator to open the instrument.

2.

Place the cartridge (in the holder) into the instrument.
When its position is correct, the power and cartridge status indicator lights turn green. For information
on indicator lights, see Status Indicator Lights on page 25.

3.

Press the button on the instrument again to close the lid.
When the lid is closed, droplet generation begins. The droplet light on the right flashes green to
indicate that droplet generation has begun.
When droplet generation is complete, all lights are solid green.

4.

Open the instrument and remove the cartridge holder and cartridge.

5.

Remove and discard the disposable gasket.
The top level of each well contains the droplets.

Instrument Guide | 31

Chapter 3 Droplet Generation

32 QX200 Droplet Generator

Appendix A Preparing For and Executing PCR
After you have generated droplets in the cartridge, you can pipet 40 µI of the contents of the top wells
containing the droplets into a single column of a 96-well PCR plate. To avoid shearing or coalescing thedroplets, use the following pipeting techniques Repeat until all droplets are transferred or the plate is full.

Aspirating Droplets from the Cartridge
To aspirate droplets from the droplet generation cartridge
1.

Use an 8-channel manual L-50 pipet with 200 µI tips.
Do not use wide or narrow-bore tips.

2.

Place the cartridge holder on a flat surface and position the pipet tips in each of the 8 top wells at a 30-45° angle to the junction where the side wall meets the bottom of the well.
Do not position the pipet tip in a vertical orientation (90°) or against any flat surface of the well. Do notallow the tips to be flat against the well bottoms.

3.

Slowly draw 40 µI of droplets into the pipet tip.
This should take 5 sec, and -5 µI air is expected. Do not aspirate more than 40 µI, as this causes air topercolate through the droplets.

4.

Pipet slowly. Apply a stable resistive force to the plunger to draw and aspirate droplets smoothly intoand out of pipet tips.

Instrument Guide | 33

Appendix A Preparing For and Executing PCR

Dispensing Droplets into the Plate
To dispense droplets into the 96-well plate
1.

Position the pipet tip along the side of the well, near—but not at—the bottom of the well, and thenslowly dispense the droplets (5 sec).

2.

To prevent evaporation and contamination with particulates, cover the plate (for example, with
8-cap strips or the lid from a pipet tip box) as you work.

Sealing the Plate
To seal the PCR plate with foil immediately after transferring droplets
Note: Use pierceable foil plate seals that are compatible with the PX1 PCR Plate Sealer and theneedles in the QX200 Droplet Reader. For information, see PX1 PCR Plate Sealer Instruction
Manual (Item #10023997).
1.

Set the plate sealer temperature to 180° C and the time to 5 sec.

2.

Touch the arrow to open the PX1 tray door, and then position the support block on the tray with the
96-well side facing up.

34 QX200 Droplet Generator

Sealing the Plate

3.

Place the 96-well plate onto the support and ensure that all plate wells are aligned with the support
block.

4.

Cover the 96-well plate with one sheet of pierceable foil seal.
Note: The yellow label on the Bio-Rad heat seal bag identifies the sealing surface.
Important: Do not attempt to place the frame over the foil-covered plate. The frame is only for
use with other seals.

5.

Once the 96-well plate is secured on the support block and covered with the pierceable foil seal,
touch the Seal button.
The tray closes and heat sealing begins. When heat sealing is complete, the PX1 door opens
automatically.

6.

Remove the plate from the block, and then remove the block from the PX1.

7.

Check that all wells in the plate are sealed.

The depressions of the wells should be visible on the foil.
Important: Begin thermal cycling (PCR) within 30 min of sealing the plate, or store the plate at 4° C
for up to 4 hr before thermal cycling. Refer to the supermix product for cycling conditions.

Instrument Guide | 35

Appendix A Preparing For and Executing PCR

Thermal Cycling and Droplet Reading
To perform thermal cycling
1.

Once the 96-well plate containing the droplets is sealed, place it into the thermal cycler for PCR
amplification.
Refer to the supermix product inserts for cycling conditions.

2.

When PCR amplification is complete, remove the 96-well plate from the thermal cycler.

To perform droplet reading
1.

Read the droplets using the QX200 or QX600™ Droplet Reader.
For information, see the QX200 Droplet Reader and QX Manager Software, Standard Edition, User
Guide (#1000107223) or the QX600 Droplet Reader and QX Manager Software, Standard Edition,
User Guide (#10000153877).

2.

If the goal is to read or quantify droplets and recover material from droplets in parallel, prepare two
sets of reactions, one for each application.
For example, in a single DG8 cartridge. four wells will be read after thermal cycling and four will not
be read.

36 QX200 Droplet Generator

Appendix B Ordering Information
This appendix contains descriptions and catalog numbers for new or replacement instruments,
accessories, and consumables for Bio-Rad ddPCR products, including your QX200 Droplet Generator.

ddPCR System and Instrument Packages
Table 12. ddPCR system and instrument packages
Catalog
NumberProduct

Description

QX200 Droplet

1864002

Generator

Includes the droplet generator (1), cartridges and gaskets(24 each), cartridge holders (2), and power cord (1)QX200 Droplet Reader

Includes the droplet reader, two plate holders, USB cable,

1864003and power cord
QX600 Droplet Reader

Includes the droplet reader, two plate holders, USB cable,

12013328

and power cord

Thermal Cyclers and Plate Sealer
Table 13. Thermal cyclers and plate sealer

Product

Description

Catalog
Number

C1000 Touch Thermal Cycler with

Includes the C1000 Touch Thermal Cycler

1851197

96-Deepwell Reaction Module

chassis, 96-deepwell reaction module, USB
flash drive

PTC Tempo Deepwell Thermal Cycler

Includes the thermal cycler, power cord,
USB cable, and Ethernet cable

12015392

PX1 PCR Plate Sealer

PCR plate sealer, includes heat sealing

1814000

instrument, plate support block that holds 96well and 384-well plates, sealing frame,
power cord
Pierceable Foil Heat Seal

Heat seal for the PX1 PCR Plate Sealer

1814040

Instrument Guide | 37

Appendix B Ordering Information

QX200 Droplet Generator Accessories

Product

Description

Catalog
NumberDG8 droplet generator

Microfluidic cartridges used to mix sample and oil for droplet

1864007

cartridges and gaskets

generation, and gaskets to seal the cartridges
Note: You must seal the cartridge to prevent evaporationand to apply required pressure for droplet generation.

Droplet generator

Positions and holds the droplet generator cartridge in the

cartridge holder

instrument compartment

Power cord

Connects the QX200 Droplet Generator to the power source

1863051

N/A

Note: Contact Bio-Rad Technical Support for
replacement information.

QX600 Droplet Reader Accessories
Table 14. QX600 Droplet Reader accessories

Product

Description

Catalog
NumberComputerComputer that connects to the QX600 Droplet Reader for data

12017458

collection and analysis
USB cable andCable connecting the computer to the instrument and power

power cord

cord connecting the instrument to the power source

Included

Note: Contact Bio-Rad Technical Support for replacement
information.
Droplet reader plate

Used to position the 96-well plate in the droplet reader plate

holders (2)compartment

38 QX200 Droplet Generator

12006834

QX200 Droplet Reader Accessories
Table 15. QX200 Droplet Reader accessories

Product

Description

Catalog
NumberComputerComputer that connects to the QX200 Droplet Reader for data

12017458

collection and analysis
USB cable andCable connecting the computer to the instrument and power

power cord

cord connecting the instrument to the power source

Included

Note: Contact Bio-Rad Technical Support for replacement
information.
Droplet reader plate

Used to position the 96-well plate in the droplet reader plate

holders (2)compartment

12006834

Instrument Guide | 39

Appendix B Ordering Information

ddPCR Consumables and Other Materials
Table 16. Consumables and other materials

Product

Description

Catalog
NumberddPCR 96-Well Plates

Cear well/clear shell semi-skirted plates

12001925(pkg of 25)

Droplet Generation Oils

Rainin Pipets

Rainin Pipet Tips

Droplet generation oil for the QX200 Droplet Generator:n Droplet Generation Oil for Probes, 10 x 7 ml

1863005n Droplet Generation Oil for EvaGreen®, 2 x 7 ml

1864005n Droplet Generation Oil for EvaGreen®, 10 x 7 ml

1864006n 20 µl for sample loading

L-20, L8-20

n 50 µl for droplet transfer

L-50, L8-50

n 8-channel, 200 µl for oil

L8-200Filtered

GP-L10F
GP-L200F

Foil Plate Seals for PX1

Pierceable foil plate seals for PX1 Plate Sealer

1814040

ddPCR Droplet Reader

Droplet reader oil for the QX600 Droplet Reader and1863004

Oil

QX200 Droplet Reader

Droplet reader waste

You can use an empty droplet reader oil bottle to collectbottlethe waste from droplet reading.

N/A

ddPCR Supermixes
Table 17. ddPCR supermixes
Supermix

Description

ddPCR
EvaGreen®
Supermix

2x supermix, for use in nucleic acid sample
preparation with the QX600 and QX200
ddPCR systems

Catalog number
1864033

2ml (2 x 1ml)

1864034

5ml (5 x 1ml)

1864035

25ml (25 x 1ml)

1864036

50ml (50 x 1ml)
2ml (2 x 1ml)

ddPCR Supermix

2x supermix, for use in nucleic acid sample

1863023

for Probes (nopreparation with the QX600™ and QX200

18630245ml (5 x 1ml)

dUTP)

ddPCR systems

1863025

25ml (25 x 1)

40 QX200 Droplet Generator

Table 17. ddPCR supermixes, continued
Supermix

Description

Catalog number

ddPCR Supermix

2x supermix, for use in sample preparation

1863026

for Probeswith the QX600 and QX200 ddPCR systems

18630105ml (5 x 1ml)

1863027

25ml (25 x 1ml)

1863028

50ml (50 x 1ml)
1.2ml (2 x 0.6ml)

2ml (2 x 1ml)

ddPCR Multiplex

4x supermix especially suited for probe-

12005909

Supermix

based detection of multiple targets in DNA

12005910

3 ml (5 x 0.6 ml)

samples using the QX600 and QX200

1200591112.5 ml (5 x 2.5 ml),

2ml (2 x 1ml)

ddPCR systems
ddPCR Supermix

2x supermix, for use in residual DNA

1864037

for Residual DNA

detection with the QX600 and QX200 ddPCR

1864038

5ml (5 x 1ml)

Quantification

systems

1864039

25ml (25 x 1ml)

1864040

50ml (50 x 1ml)

1864021

2ml (2 x 1ml)

18640225ml (5 x 1ml)

One-step RTddPCR Advanced
Kit for Probes

200 or 500x 20 µl reaction kit, for absolute
quantification of target RNA in a one-stepformat with the QX600 and QX200 ddPCR
systems

Buffer Controls
Table 18. Buffer controls

BufferCatalog
NumberddPCR Buffer Control Kit for Probes

1863052

QX200 Buffer Control Kit for EvaGreen®

1864052

Instrument Guide | 41

Appendix B Ordering Information

ddPCR Kits
Table 19. ddPCR Kits

Product

Description

CatalognumberddPCR Mutation Screening Kits
ddPCR KRAS G12/G13 Screening Kit

1863506

ddPCR KRAS Q61 Screening Kit

12001626

ddPCR BRAF V600 Screening Kit

12001037

ddPCR NRAS Q61 Screening Kit

12001006

ddPCR NRAS G12 Screening Kit

12001094

ddPCR NRAS G12/G13 Screening Kit

12001627

ddPCR EGFR Exon 19 Deletions Screening Kit

12002392

All kits include 20x multiplex assay and 2x ddPCR supermix for probes (no dUTP).
ddPCR Residual DNA Quantification Kits
ddPCR CHO Residual DNA Quantification Kit

17000031

ddPCR E.coli Residual DNA Quantification Kit

17000032

200x 20 μl reactions, includes 20x CHO or E.coli RDQ assay and 2x ddPCR
Supermix for Residual DNA Quantification.
ddPCR Copy Number Determination Kits

ddPCR SMN1 Copy Number Determination Kit
ddPCR SMN2 Copy Number Determination Kit

1863500
1863503200x 20 μl reactions, includes assay at 20x concentration, 2x ddPCR Supermix for
Probes (no dUTP) and positive controls
ddPCR Library Quantification Kit

ddPCR Library Quantification Kit for Illumina TruSeq
200x 20 μl reactions, includes 1 vial of primers and probes at 20x concentration, 2x
ddPCR Supermix for Probes (no dUTP) and positive controls

42 QX200 Droplet Generator

1863040

ddPCR Assays
Table 20. ddPCR Assays

Product

Catalog number

ddPCR HDR Gene Edit Assay

12002312

ddPCR HDR Gene Edit Assay

12002313

500 rxns

ddPCR HDR Gene Edit Package

12003796

1,000 rxns

ddPCR HDR Ref Assay, Predesigned

12003805

100 rxns

ddPCR HDR Ref Assay, Predesigned

12003806

500 rxns

ddPCR HDR Ref Package, Predesigned

12003793

1,000 rxns

ddPCR NHEJ Gene Edit Assay

12002314

100 rxns

ddPCR NHEJ Gene Edit Assay

12002315

500 rxns

ddPCR NHEJ Gene Edit Package

12003794

1,000 rxns

100 rxns

Instrument Guide | 43

Appendix B Ordering Information

44 QX200 Droplet Generator

D094813 (10031907) Ver G US/EG

Sig 0123