BIO RAD QX100 User manual

QX100™Droplet Generator
Instruction Manual
Catalog #186-3002

Preface
QX100 Droplet Generator Instruction Manualii |
Copyright © 2012 by Bio-Rad Laboratories, Inc. All rights reserved.
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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
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Notice regarding Bio-Rad thermal cyclers and real-time systems:
Purchase of this product conveys a limited, non-transferable
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counterparts owned by Eppendorf AG: U.S. Patent Numbers
6,767,512 and 7,074,367.

Preface
QX100 Droplet Generator Instruction Manual QX100 Droplet Generator Instruction Manual | iii
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
QX100 Droplet Generator Instruction Manualiv |
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.

QX100 Droplet Generator Instruction Manual | v
PrefacePreface
QX100 Droplet Generator Instruction Manual
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 Manualvi |

QX100 Droplet Generator Instruction Manual | 1
QX100™Droplet
Generator
1
1.1 Introduction
The 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 Manual2 |
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™) cartridge. The loaded cartridge is covered with a gasket and placed in the QX100 droplet
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).
QX100 droplet generator.
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

QX100 Droplet Generator Instruction Manual QX100 Droplet Generator Instruction Manual | 3
Chapter 1 QX100 Droplet GeneratorChapter 1 QX100 Droplet Generator
Table 1.2. Additional materials required for droplet generation.
Component Recommended Catalog #
PCR supermix (required) ddPCR supermix for probes 186-3010, 186-3026,
186-3027, 186-3028
One-Step RT-ddPCR kit for probes 186-3021, 186-3022
Control Buffer control kit 186-3052
Droplet generator oil Droplet generator oil (10 x 7 ml) 186-3005
Pipets 20 μl pipet for sample loading Rainin L-20
50 μl pipet for droplet transfer Rainin L-50, L8-50
8-channel, 200 μl pipet for oil Rainin L8-200
Pipet tips Filtered Rainin GP-L10F, GP-L200F
96-well PCR plates twin.tec semi-skirted 96-well plate Eppendorf 951020362
Reagent trough For droplet generator oil Thermo 95128095
Foil plate seals Easy Pierce foil plate seals Thermo AB-0757
Plate sealer Eppendorf 951023078
8-cap strips Any
1.3 Installation and General Operation
 Connect the QX100 droplet generator to a power source using only the power cord provided. Ensure the
ground is reliably connected before plugging in the instrument
 Leave 10" (5 cm) space clear behind and 5" (2.5 cm) clear to the right and left for proper ventilation
 Power on the droplet generator by plugging it in. The status indicator turns solid green to indicate power is on
 Open and close the instrument by pressing the button on top of the green lid
U.S. Standard power cord set with grounded plug
(Type 5-15P) and C5 connector (10 A/125 V)
Power supply to 5 mm DC power jack inlet

QX100 Droplet Generator Instruction Manual4 |
Chapter 1 QX100 Droplet Generator

QX100 Droplet Generator Instruction Manual | 5
Droplet Generation
2
2.1 Sample Preparation
Prepare the PCR reaction by combining 2x PCR supermix, 20x primers and
probe, and DNA sample. Mix by vortexing in short pulses, and centrifuge briefly.
 The concentration of intact human genomic DNA should be <66 ng per
20 µl reaction. If using higher concentrations, digest DNA with a restriction
endonuclease that does not cut target or reference amplicons
 Use either the ddPCR™supermix for probes or the One-Step RT-PCR kit
for probes, which contain reagents required for droplet generation. Follow
the instructions in the product inserts to prepare the samples for droplet
generation
 Vortex the supermixes thoroughly to ensure homogeneity, as a concentration
gradient may form during –20°C storage. Alternatively, pipet up and down
>5 times to mix. Centrifuge briefly to collect contents at the bottom of the tube
before dispensing
 Thaw 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 (~3 minutes) before loading
into the DG8™cartridge for droplet formation
 Assemble reaction mixtures in vials or in 96-well PCR plates. The advantage
of using a PCR plate is that samples can be loaded into the DG8 cartridge
using an 8-channel pipet
 Use standard lab precautions to avoid contamination of the reaction mix and
sample: wear gloves, clean pipets, work in a clean area such as a PCR hood,
and use low protein binding tubes

QX100 Droplet Generator Instruction Manual6 |
Chapter 2 Droplet Generation
2.2 Operation of the QX100™Droplet Generator
1. Insert the DG8 cartridge into the holder with the
notch in the cartridge at the upper left of the
holder:
a. Open the cartridge holder by pressing the
latches in the middle.
b. Slide the DG8 cartridge into the right half of
the holder, then drop it down.
c. Press the halves of the holder together to
snap it closed.
Inserting the DG8 cartridge into the cartridge holder.
The QX100 droplet generator prepares droplets for eight samples at a time. Droplet generation takes
2 minutes for each set of eight samples (20–30 minutes for a 96-well plate).
 All 8 sample wells in the DG8 droplet generator cartridge must contain sample (or 1x buffer
control), and all 8 oil wells must contain droplet generator oil
 Do not load the DG8 cartridge with sample or oil unless it is already inserted in the holder
Press
Press to open Slide to close
Notch
Top wells (droplets)
Middle wells
(20 μlsample)
Bottom wells (70 μloil)
DG8 cartridge

QX100 Droplet Generator Instruction Manual | 7
Chapter 2 Droplet Generation
QX100 Droplet Generator Instruction Manual
Air bubbles can cover the bottom of the well and result in 2,500–7,000 fewer droplets and poor
data quality. They are difficult to see. To avoid creating air bubbles, use the following pipetting
techniques, which also ensure samples wet the bottoms of the wells so they are wicked into the
microchannels (necessary for proper droplet generation).
 Use only 20 μl aerosol-barrier (filtered) Rainin pipet tips; do not use 200 μl pipet tips (see Table 1.2)
 Gently slide the pipet tip down the side of the well at a ~15° angle until it passes over the ridge near
the bottom. Holding the 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
 After dispensing about half the sample, slowly draw the tip up the wall while dispensing the rest of the
sample; do not push the pipet plunger past the first stop
4. Dispense the droplet generator (DG) oil in the reagent trough. Use 700 μl DG oil per 8 samples (one DG oil
bottle contains enough oil for a 96-well PCR plate).
3. Transfer 20 μl of each prepared sample to the sample wells (middle row) of the DG8 cartridge.
DG8 cartridge
Reagent trough and droplet generator oil.
Transferring sample to the sample wells (middle row) of the DG8 cartridge. Hold the pipet tip at a 15°angle and at the bottom of
the well (middle and right panels); do not dispense sample onto the wall or side of the well.
15°angle
Tip
Ridge in well

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Chapter 2 Droplet Generation
QX100 Droplet Generator Instruction Manual
5. Using a multichannel pipet, fill each oil well (bottom row) with 70 μl DG oil from the reagent trough.
Filling the oil wells with droplet generator oil.
6. Hook the gasket over the cartridge holder using the holes on both sides. The gasket must be securely
hooked on both ends of the holder; otherwise, sufficient pressure will not build up for droplet generation.
Correct placement of the gasket over the cartridge holder.
7. Place the cartridge holder into the QX100 droplet generator and initiate droplet generation:
a. Open the instrument by pressing the button on the green top
b. Place the cartridge holder into the instrument. When the holder is in the correct position, both the
power (left light) and holder (middle light) indicator lights are green (Table 2.1)
8. Press the button on the top again to close door. This initiates droplet generation: a manifold positions itself
over the outlet wells, drawing oil and sample through microfluidic channels where droplets are created.
Droplets flow to the droplet well, where they accumulate. The droplet indicator light (at right) flashes green
after 10 sec to indicate droplet generation is in progress.

QX100 Droplet Generator Instruction Manual | 9
Chapter 2 Droplet GenerationChapter 2 Droplet Generation
9. When droplet generation is complete, all three indicator lights are solid green. Open the door and remove
the holder (with DG8 cartridge still in place) from the unit. Remove the disposable gasket from the holder
and discard. The top wells now contain droplets, and the middle and lower wells are nearly empty with a
small amount of residual oil.
QX100 Droplet Generator Instruction Manual
Table 2.1. Status indicator lights on the QX100 droplet generator. If the central LED flashes amber, the gasket is
not placed on the holder correctly or is missing and no seal was made. If the right LED flashes amber, a process error
occurred because the volume is too low in at least one well.
Solid green Power on DG8 cartridge holder in place Run complete
Flashing green ___ ___ Run in progress
Flashing amber --- No gasket; empty well or seal Low volume in well
Off Power off No DG8 cartridge holder Idle
QX100 droplet generator with DG8 cartridge in place.
Keep the DG8 cartridge in the holder.
Press to open and close Status indicator llights

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Chapter 2 Droplet Generation
QX100 Droplet Generator Instruction Manual
2.3 Preparation for PCR
1. Pipet 40 μl of the contents of the top wells (the droplets) into a single column of a 96-well plate.
Aspirating droplets from the DG8 cartridge. Dispensing droplets into a 96-well PCR plate.
Use the following pipetting techniques to avoid shearing or coalescing the droplets:
To aspirate droplets from the DG8 cartridge:
 Use an 8-channel manual P-50 Pipetman with 200 µl tips (not wide- or narrow-bore); do not use a P-20
or P-1000 Pipetman
 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, vertical into 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 not allow the
tips to be flat against the bottoms of the wells
 Slowly draw 40 µl droplets into the pipet tip (should take ~5 sec, and ~5 µl air is expected); do not
aspirate >40 µl, as this causes air to percolate through the droplets
 Pipet slowly. Apply a stable resistive force to the plunger to draw and aspirate droplets smoothly into
and out of pipet tips
To dispense droplets into the 96-well plate, position the pipet tip along the side of the well — near, but
not at, the bottom of the well — and slowly dispense the droplets (~5 sec).
Cover the plate (for example, with 8-cap strips or the lid from a pipet tip box) as you work to prevent
evaporation and contamination with particulates.

QX100 Droplet Generator Instruction Manual | 11
Chapter 2 Droplet Generation
QX100 Droplet Generator Instruction Manual
Chapter 2 Droplet Generation
2. Seal the PCR plate wells with foil immediately after transferring droplets to avoid evaporation. Use
Easy Pierce foil plate seals (compatible with the needles in the QX100 droplet reader) and a compatible
thermal plate sealer.
a. Allow the plate sealer to warm up for at least 10 min before use.
b. Place the foil seal over the plate and place the plate in the plate sealer.
c. Press the sealer firmly against plate for 3 sec, then rotate the plate 180° and seal for another 3 sec.
d. Check that all the wells in the plate are sealed. The depressions of the wells should be visible on the
foil. Once sealed, the plate is ready for thermal cycling.
3. Once droplets are removed, press the latches on the DG8 cartridge holder to open it. Remove the empty
DG8 cartridge and discard it.
Eppendorf plate sealer (left) and a sealed 96-well plate (right).
Begin thermal cycling (PCR) within 30 min of sealing the plate, or store the plate at 4°C for up to 4 hr prior
to thermal cycling. Refer to the supermix product inserts for cycling conditions.

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Chapter 2 Droplet Generation
QX100 Droplet Generator Instruction Manual

Chapter 2 Droplet Generation
QX100 Droplet Generator Instruction Manual QX100 Droplet Generator Instruction Manual | 13
Specifications and
Maintenance
3
3.1 Specifications
Weight 10 lbs. (4.5 kg)
Size (W x D x H) 28 x 36 x 13 cm (11 x 14 x 5")
Electrical requirements 100–240 V, 50/60 Hz 60 W; voltage fluctuations not
to exceed +10% of ratings
Temperature 15–30ºC
Altitude 0–6,560 ft (0–2,000 m)
Humidity 85% max (noncondensing)
Pollution degree 2 (indoor use)
Installation category II (external power supply plugs into standard AC
receptacle)
Ventilation requirement 5" (12 cm) left and right of machine and 10" (25 cm)
behind should be unobstructed for proper ventilation
5 inches
(127 mm)
11 in che s
(279 mm)
14 inches
(356 mm)

Chapter 3 Specifications and Maintenance
14 | QX100 Droplet Generator Instruction Manual
3.2 Maintenance
Surfaces of the instrument may require general cleaning. Use deionized/distilled water for general wipe down
with a slightly dampened cloth. For decontamination, 10% bleach followed by 70% ethanol and/or deionized/
distilled water may be used. Do not use acetone or tap water.
Inspect equipment regularly for damaged external components or wiring. Do not use if damaged.
Apply standard MSDS (Material Safety Data Sheet) and OSHA practices when handling and disposing of
generated waste.
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. These nonflammable fluids are inert
and have low environmental impact and low toxicity. Collect waste in a polyethylene container and dispose
within one month.
Droplets made with Bio-Rad master mix have antimicrobial properties, but microbial growth is possible. The
waste profile should contain the following: fluorinated hydrocarbons, water, fluorescent dye (from probes),
protein, and nucleic acids. The droplet generator is not intended to be used with biohazardous material.