QX200TM Droplet Reader
and QX Manager Software
Premium Edition
User Guide

QX200 Droplet Reader
and
QX Manager Software
Premium Edition
User Guide
Version 2.2

For Research Use Only

User Guide | c

Bio-Rad Technical Support Department
The Bio-Rad Technical Support department in the U.S. 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 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.
AUTODG, BIO-RAD, DDPCR, DROPLET DIGITAL, DROPLET DIGITAL PCR, QUANTASOFT, 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 ddPCR 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

QX200 Droplet Reader and QX Manager

DecemberSoftware, Premium Edition User Guide

2023

Description of Change
Update content for Version 2.2

Software Version 2.2
DIR No. 10000163733 Ver B
QX200 Droplet Reader and QX Manager
Software, Premium Edition

September
2023

Add EcoTank functionality to
Instrument Maintenance section

Software Version 2.1
DIR No. 10000163733 Ver A
QX200 Droplet Reader and QX Manager
Software, Premium Edition User Guide

May

Update the user guide with new and2023

improved features for Version 2.1;
add new legal statement andSoftware version 2.1

Managing Waste section; update
DIR on back cover to reflect edition

DIR No. 10000163733 Ver A

name change to Premium

QX200 Droplet Reader and QX Manager
Software Regulatory Edition User Guide

August 2022

Update document with newfeatures in QX Manager with the
QX200 instrument

Software version 2.0
DIR No. 10000107224 Ver D

User Guide | iii

This page intentionally left blank.

iv QX200 Droplet Reader and QX Manager Software, Premium Editioon

Table of Contents
Front Cover
Revision History

Safety and Regulatory Compliance

a
iii

11

Regulatory Compliance11

Safety Warning Labels

13

Safe Use Specifications

14

Personal Protective Equipment
Hazards

15
16

Biohazards

16

Chemical Hazards

17

Explosive or Flammability Hazards

17

Electrical Hazards

17

Surface Decontamination18

Decommissioning and Disposal

18

Transport

19

Warranty

19

Chapter 1 Introduction to Droplet Digital PCR

21

ddPCR Workflow

22

Finding Out More

22

Chapter 2 About the QX200 Droplet Reader

23

Instrument Specifications

25

Environmental Requirements

26

Included Components

27

Additional Components

28

Compatible ddPCR Process Instruments

30

Connecting and Starting the Instrument

31

Status Indicator Lights

32

User Guide | v

Table of Contents

Chapter 3 About QX Manager Software

33

Chapter 4 Getting Started

35

Signing In, Viewing Privileges, and Changing Preferences

35

Signing into the Software

36

Selecting the Instrument and Droplet Volume38

Viewing User Privileges

39

Managing Your Preferences

41

Signing Out or Changing Users

42

Instrument Status Bar

43

Tabs to Functional Windows

44

Compatible File Types

45

Chapter 5 Running Experiments

47

Assembling a Plate

47

Inserting an Assembled Plate into the Instrument

48

Adding the Plate in QX Manager Software

49

Configuring the Plate

50

Plate Information Tab

50

Well Selection Tab

53

Well Information Tab

54

Starting the Run

59

Run Prerequisites Checklist

60

Running the Experiment

63

Tracking the Run Status

64

Using Live Analysis

66

Canceling a Run

67

Chapter 6 Creating or Editing Templates

69

Creating or Modifying Plate Templates

70

Template Plate Editor Window

73

Creating and Storing Plate Templates from CSV Files82

Creating or Modifying Report Templates

84

Chapter 7 Lot and APF Management

87

Managing Consumable Lots

88

Managing Reagent Lots

89

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Table of Contents

Managing Assay Protocol Files

90

Importing Assay Protocol Files

92

Modifying Variables in an Assay Protocol File

93

Deleting Assay Protocol Files

94

Chapter 8 Data Analysis Module Overview

95

Opening a Data File for Analysis

97

Saving a Data File99

Analysis Display and Output Options

100

Universal Options

101

Expanding or Reducing the Chart

104

Selecting Chart Display Preferences

105

Selecting Chart Scale and Label Options

106

Using Chart Menu Options

108

Using Table Menu Options

110

Analysis Dashboard

113

Modifying the Dashboard Display

114

Dashboard Options

115

APF Results Dashboard

117

Reanalyzing the Run File
Plate View Windows

118
119

Plate Editor — Analysis View

119

Plate View

120

2D Plate View

121

Data Windows

122

Data Table Tab

122

Plate Editor Well Data Table

129

Analysis Windows

130

Viewing Run, Lot, and Audit Information

131

Showing Lots in Run Information Reports

132

Viewing the Audit Log

133

Chapter 9 Data Analysis Methodology
Amplitude Plot Analysis Options

135
136

1D Amplitude

141

2D Amplitude

146

User Guide | vii

Table of Contents

Data Visualization Chart Analysis Options

149

Concentration

152

Copy Number

155

Ratio

158

Fractional Abundance

160

Event Counts

162

Linkage Analysis

163

Chapter 10 Analysis Module Reporting
Creating Analysis Reports

Chapter 11 Gene Study Module

165
165

167

Gene Study Options

169

Setting up the Gene Study

170

Adding Data Files

172

Removing Data Files

172

Selecting Data Files for Analysis

172

Showing the Plate View

173

Using the Study Analysis Features

174

Gene Study Reports

176

Creating a Gene Study Report

Chapter 12 System Utilities

177

179

System Settings Tab

180

Preferred Location

181

Shared Settings

182

Instrument and Droplet Volume Settings

183

Software Settings

185

System Log Files

186

Event Log

186

Maintenance Log

188

Maintenance Reports

189

System Data

190

Archiving Raw Data

190

Troubleshooting Data

192

Recovering Data

194

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Table of Contents

Reprocessing Data

196

System Calibration and Tools

197

Chapter 13 Managing Users

199

Adding Users

200

Adding or Removing User Privileges

202

Modifying User Preferences

204

Removing Users

204

Appendix A Experiment Examples

205

Direct Quantification Multiplexed

206

Setting Up Experiment Parameters

206

Viewing and Adjusting Results

207

Copy Number Variation Triplexed

209

Setting Up Experiment Parameters

209

Viewing and Adjusting Results211

Drop-Off Assays for Genome Edit Detection

212

Setting Up Experiment Parameters

213

Viewing and Adjusting Results214

Direct Quantification with the Advanced Classification Method

215

Setting Up Experiment Parameters

215

Viewing and Adjusting Results

217

Appendix B Instrument Maintenance219

Fluid Maintenance and Waste Management

220

Changing the Droplet Reader Oil Bottle

221

Emptying the Waste Container

222

Using an EcoTank Oil and Waste Container

223

Priming and Flushing the Instrument

229

Managing Waste

230

Recovery From Idle Mode

231

Cleaning or Decontaminating the Instrument

231

Instrument Maintenance Log

232

Appendix C Troubleshooting

233

Event Log

233

Instrument Errors

233

User Guide | ix

Table of Contents

Appendix D Ordering Information

235

Back Cover243

x QX200 Droplet Reader and QX Manager Software, Premium Editioon

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 61326-1:202012 (Class A), EN 61326-1:2013 (Class A). Electrical equipment for measurement,
control, and laboratory use. EMC requirements, Part 1: General requirementsn

IEC 61010-2-081:20195, 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 2081: Particular requirements for automatic and semi-automatic laboratory equipment for analysis andother 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.)n

EN 61326-1:2006 20201(Class A). Electrical equipment for measurement, control, and laboratory
use. EMC requirements, Part 1: General requirementsn

UL 61010-1:2004, Laboratory equipment, Test & Measurement Equipment and Industrial Process
Controlsn

UL 61010-2-101:2019. Safety requirements for electrical equipment for measurement, control, andlaboratory use. Particular requirements for in vitro diagnostic (IVD) medical equipmentnRestriction of hazardous substances (ROHS) directiv e (European Union)

User Guide | 11Safety and Regulatory Compliancen

Registration, evaluation, authorization and restriction of chemicals (REACH). European Chemicals
Agency (ECHA) June 1, 2007n

Waste electrical and electronic equipment (WEEE) directive 2012/19/EU

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.

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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 system 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.

User Guide | 13

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 and in Appendix B, Instrument Maintenance.
Important: 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 isintended, 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 and connection accessories supplied with the instrument, and the plug adapter
corresponding to the electrical outlets in your region.

n

For adequate ventilation and easy access to the back of the instrument, place the instrument on asolid, stable surface and provide adequate room at the back and on each side. For information, see
Environmental Requirements on page 26.

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.
For information on environmental requirements, see Environmental Requirements on page 26.

14 QX200 Droplet Reader and QX Manager Software, Premium Editioon

Safe Use Specifications

Personal Protective Equipment
Proper use of gloves is recommended with use of oils and sample plates. OSHA requirements for
personal protective equipment (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 forstandard 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.
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

User Guide | 15

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).

16 QX200 Droplet Reader and QX Manager Software, Premium Editioon

Hazards

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.

User Guide | 17

Safety and Regulatory Compliance

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 touch screennInner plate holdersnDroplet reading surfaces

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.
For more information on surface cleaning, see Appendix B, Instrument Maintenance.

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.

18 QX200 Droplet Reader and QX Manager Software, Premium Editioon

Transport

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.

User Guide | 19

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20 QX200 Droplet Reader and QX Manager Software, Premium Editioon

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, which uses a combination of microfluidics and proprietary surfactant
chemistries to divide each sample into water-in-oil droplets.
The technology uses reagents and workflows similar to those used for most standard TaqMan probebased assays, and provides absolute quantification of nucleic acid target sequences by counting nucleic
acid molecules encapsulated in discrete, 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.

User Guide | 21

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 adheres to the following workflow:nPrepare 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 thousands of nanoliter-sized droplets with target andbackground 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
Click the Help tab () on the left, and then click the Bio-Rad Website link to access links to technicalnotes, manuals, videos, product information, and technical support. The website also provides manytechnical resources on a wide variety of methods and applications related to PCR, Droplet Digital PCR,
and gene expression.

22 QX200 Droplet Reader and QX Manager Software, Premium Editioon

Chapter 2 About the QX200 Droplet Reader
Using the QX200™ Droplet Reader, you can detect rare DNA target copies, determine copy number
variation, and precisely measure gene expression levels. Applications and uses include:n

Copy number variationnAbsolute quantificationnRare sequence detectionnRare mutant detectionn

Next generation sequencing (NGS) library quantificationn

NGS sample preparationn

Viral load determination, including SARS-CoV-2 assaysn

GMO detectionnmRNA analysisnContaminant testingnGene expression analysis and single cell gene expression
analysis

Following the droplet generation and thermal cycling processes, the QX200 Droplet Reader collects
binary data for analysis as it singulates the nanoliter-sized droplets in each sample, and then streams
them in single-file past a two-color detector to determine which droplets contain target molecules (positive
reading) and which do not (negative reading).
The QX200 Droplet Reader detects targets in two selected fluorescent dyes, FAM or EvaGreen® andHEX or VIC.
Important: Your QX200 Droplet Reader performs the post-PCR droplet reading function only. A
droplet generator and a thermal cycler are required to perform a full ddPCR cycle. You can purchasea droplet generator and thermal cycler, as well as associated accessories and consumables, from
Bio-Rad. For information, see Appendix D, Ordering Information.

User Guide | 23

Chapter 2 About the QX200 Droplet Reader

The following graphic and legend illustrate the functional areas on the instrument exterior:

LEGEND
Button to open and close lid

Status indicator lights (see Status Indicator Lights on page 32)

On the back of the instrument, power and USB outlets

Oil and waste compartment (see Instrument Maintenance on page 219)

24 QX200 Droplet Reader and QX Manager Software, Premium Editioon

Instrument Specifications

Instrument Specifications
This section contains information on the instrument size and weight of the instrument. Safety information
is cited in Safe Use Specifications on page 14 and the proper environmental maintenance is cited in
Environmental Requirements on page 26.

Table 3. Instrument specifications

Element

Specifications

Weight56.6 lbs (26 kg)

Size (W x D x H)

26 x 20.5 x 11.5” (660 x 521 x 292 cm)

User Guide | 25

Chapter 2 About the QX200 Droplet Reader

Environmental Requirements
Table 4 lists the environmental requirements for the QX200 Droplet Reader.
Important: You must use the supplied shielded cables with your instrument to ensure compliancewith the Class A FCC limits.
Table 4. Conditions for safe use

Usage aspect

Requirements

Rated input power

100–240 V, 50–60 Hz, 1A 90W (plugs into standard AC receptacle)

Fuses

10A 250 V SLOW BLOW

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

85% max non-condensing

Altitude

0 to 6,560 ft (0 to 2,000 m)

Installation category

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

Ventilation and access clear

The following distances should be unobstructed for proper

space requirements

ventilation and service access
n 5 in (12 cm) on the left and right sides of the instrumentn 10 in (25 cm) behind the instrument

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Included Components

Included Components
This section identifies the functional items included with your droplet reader purchase, as well as
additional components and consumables. For information on items you may need for a full ddPCR cycle,
see Appendix D, Ordering Information.
Table 5 explains the components that ship with the QX200 Droplet Reader.
Table 5. QX200 Droplet Reader and included components

Component

Description

Catalog
Number

QX200 Droplet Reader

Droplet reading instrument, part of QX200 ddPCR system

1864003

USB cable and power

USB cable that connects the computer to the instrument

Includedcord

and power cord that connects the instrument to the powersourceNote: To obtain cables or power cords, contact
Bio-Rad technical support.

Droplet reader plate

Positions and secures the 96-well plate in the droplet

holders (2)reader plate compartment

12006834

User Guide | 27

Chapter 2 About the QX200 Droplet Reader

Additional Components
The following tables identify additional components you can purchase for use with your system or
instrument.
Table 6. Accessories and consumables

Component

Description

Catalog Number

ComputerComputer that connects to the QX200 Droplet Reader

12017458

for data collection and analysis
Software

Bio-RadQX Manager Software, Premium Edition

purchase

Standard Edition is included with your droplet reader

12012172purchase.
ddPCR 96-Well

Clear well/clear shell semi-skirted plates

12001925 (pkg of 25)

Droplet Reader

ddPCR droplet reader oil for QX600 and QX200

1863004

Oil

instruments and systems

Rainin 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

FilteredRainin GP-L10F

PlatesRainin Pipet Tips

Rainin GP-L200F

28 QX200 Droplet Reader and QX Manager Software, Premium Editioon

Additional Components

Table 7. Thermal cyclers and plate sealer
Catalog
Product

Description

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

12015392

cable, and Ethernet cable
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 8. 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)
1.2ml (2 x 0.6ml)

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),

ddPCR systems

User Guide | 29

Chapter 2 About the QX200 Droplet Reader

Table 8. ddPCR supermixes, continued
Supermix

Description

Catalog number

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)

2ml (2 x 1ml)

One-step RT-

200 or 500x 20 µl reaction kit, for absolute

1864021

2ml (2 x 1ml)

ddPCR Advanced

quantification of target RNA in a one-step

18640225ml (5 x 1ml)

Kit for Probes

format with the QX600 and QX200 ddPCR
systems

Table 9. Buffer controls

BufferCatalog
NumberddPCR Buffer Control Kit for Probes

1863052

QX200 Buffer Control Kit for EvaGreen®

1864052

Compatible ddPCR Process Instruments
Along with the QX600 Droplet Reader, you can purchase the droplet generators shown below from
Bio-Rad.
QX200 Droplet Generator

Automated Droplet Generator

QX200 Droplet Reader

Important: A thermal cycler, which can be purchased separately, is required to perform a full ddPCR
cycle. For information on additional instruments, accessories, and consumables, see Appendix D,
Ordering Information.

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Connecting and Starting the Instrument

Connecting and Starting the Instrument
To execute runs on the QX200 Droplet Reader, you must connect the instrument to a computer on which
the QX Manager Software is installed and configured. Bio-Rad recommends purchasing at least one
configured computer that can remain connected to the QX200 Droplet Reader and be used for adding andrunning plates in QX Manager Software. For information on additional items you can purchase for yourinstrument, see Additional Components on page 28.

To connect and start the instrument
1.

Connect the USB cable provided by Bio-Rad to the USB port on the back of the QX200 Droplet
Reader, and then to the computer.

2.

Press the Power button on the instrument.
The Power indicator light turns solid green to indicate that power is on.

3.

Turn on the connected computer and log in with a Windows account. For information, see yoursystem administrator.

4.

Open and log into QX Manager Software.

Important: The first time you log into the software, the Instrument window appears and you mustselect the instrument you are using. For information on selecting the correct instrument in QX
Manager Software, see Selecting the Instrument and Droplet Volume on page 38.

User Guide | 31

Chapter 2 About the QX200 Droplet Reader

Status Indicator Lights
This section describes the indicator lights on the front of the QX200 Droplet Reader.

Before you start a run, check the indicator lights to ensure the instrument is ready. For information, see
Table 10.
Table 10. Droplet Reader Status Indicator Lights

Indicator(Power)Solid GreenPower is on(Plate)(Fluids)
Fluid levels OK

Plate loaded(Run
Status)Complete

properly
Flashing GreenN/An Less than 40% oil is

N/A

In progress

N/A

Error during

availablen More than 70% waste incontainer
Flashing

N/A

Amber

n Less than 10% oil available

runn More than 90% waste incontainer

No color

Power is off

N/A

No plate loaded

Instrument isidle

If the bottle indicator light is solid green or flashing green, there is enough oil in the bottle to complete a run
on 96 wells. You can configure the full plate in QX Manager Software for your run. Once the low levelsensor is triggered, the Add Plate button is disabled and you cannot continue to run plates (less than10%). You must replace the oil and waste bottles with new ones before the instrument can start the run.

32 QX200 Droplet Reader and QX Manager Software, Premium Editioon

Chapter 3 About QX Manager Software
QX Manager Software, when connected to your QX200 Droplet Reader, provides the necessaryfunctionality to create, run, and analyze droplet reading experiments on your samples.
QX Manager Software, Premium Edition, provides features to permit operation in compliance with Title 21of the U.S. Code of Federal Regulations Part 11 (21 CRF Part 11) within a closed system, which is defined
as “an environment in which system access is controlled by the persons who are responsible for thecontent of electronic records that are on the system” (Section 11.3(b) (4)).
Note the following:n

The security controls built into QX Manager Software, Premium Edition, must be properly configured
and administered by the software administrators in your organization in order to be secure and incompliance with 21 CFR Part 11.

n

Bio-Rad makes no claim that QX Manager Software, Premium Edition, is CFR-compliant in and of
itself, nor does the company guarantee compliance for the user. Your organization must establish
policies and Standard Operating Procedures that work in conjunction with the tools provided by
Bio-Rad to ensure compliance with 21 CFR Part 11.

Using the instrument and software, you cann

Set up customized, real-time ddPCR experiments for plate runsnRead standard dropletsnChoose between two droplet volumesn

See the available disk space and number of plates you can processn

Use the live analysis function during the droplet reading processnAnalyze your data files in a variety of charts and tables in the Analysis modulen

Reprocess data with updated color calibration valuesnCreate and store plate and report templates, and produce reports on your datan

Use Assay Protocol Files (APFs) to automatically configure your run with a range of predefinedsettings

nManage lots and assaysnView audit logs and produce an audit log report on old and new data values after reprocessing a file

User Guide | 33

Chapter 3 About QX Manager Software

The following image highlights functional areas.

LEGENDThe status bar displays information about the instrument and user. For information on specificfunctionality, see Instrument Status Bar on page 43.
Tabs provide access to the main functional windows.
The main pane displays the details of the selected tab.
The buttons allow you to configure the plate and start the run.
The dropdown list allows you to select an Assay Protocol File (APF).

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Chapter 4 Getting Started
Use the information in this chapter tonSign into the software or change usersnSelect the instrumentnChange the droplet volumenBecome familiar with the instrument status bar and main functional windowsn

Understand the compatible file types for your software edition

Tip: If QX Manager Software goes into standby mode after being idle, click in the lockout screen tolog into the software again.

Signing In, Viewing Privileges, and Changing Preferences
Typically, a system or software administrator sets up users and privileges for QX Manager Software, andcommunicates the information to you.
Note the following:n

When you sign in the first time after the software is installed, you must select the instrument to which
the computer is connected. See Selecting the Instrument and Droplet Volume on page 38 for
information.

n

You cannot change your user privileges unless you are assigned the Add/Manage Users privilege.
For information, see Viewing User Privileges on page 39.

n

You can change your user preferences, which are set to defaults. For information, see Managing
Your Preferences on page 41.

User Guide | 35

Chapter 4 Getting Started

Signing into the Software
Important: The Premium Edition includes audit capabilities. For auditable actions, you are prompted
to sign in again before continuing.

To sign in
1.

Right-click the software icon on the desktop and select Open to display the Sign in dialog box.

2.

Do one of the following to enter your user name:n

If the Sign in to: label shows the correct domain name, enter only the user name and password.

n

If the Sign in to: label is blank or shows a different domain, then enter it as <computer or
domain name\user name>, followed by the password.

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Signing In, Viewing Privileges, and Changing Preferences

For more information, click the How do I sign into another domain? link.

Note: If you are logging into a network domain, but don’t know the name, contact yoursystem administrator.
3.

Ensure the Do not show EULA on sign in checkbox is selected and tap I Agree.

Each user must agree to the end user license agreement on initial login in order to user the software.
If you clear the checkbox, the End User License Agreement appears the next time you log into thesoftware, and you must agree again to the terms before the software opens. If you do not agree to theEULA, the application closes immediately.
When you agree to the EULA, the dialog box closes and the application opens. Your user nameappears in the Instrument Status bar.
If you are connected to the QX200 Droplet Reader, the Add Plate window opens.
If you are opening the software on a computer not connected to an instrument, the Data Analysis
window opens.

User Guide | 37

Chapter 4 Getting Started

Selecting the Instrument and Droplet Volume
When you open the software and sign in for the first time, the instrument connection window appears andyou must select the connected instrument and a droplet volume.
This procedure assumes the instrument is connected to the computer and QX Manager Software is
installed. If you are using the QX200 Droplet Reader and the QX600 Droplet Reader in your lab, you canchange instruments and then select the connected instrument in System Settings. You can also switch
between two droplet volumes.
Note: In QX Manager Software, Version 2.0, Bio-Rad reduced the droplet volume used to calculate
concentration from .85 nL to .795 nL. The change resulted in a 7–8% higher concentration inexperiments where all other variables were identical, thereby improving accuracy. Beginning with
Version 2.1, both the legacy and the new droplet volumes were made available to facilitate resultscomparisons across versions and to maintain consistency in calculations. System precision remains
unchanged.

To select the instrument and droplet volume1.

Select QX200, and then click Save.

2.

Select a droplet volume and click Save.

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Signing In, Viewing Privileges, and Changing Preferences

Viewing User Privileges
In the User Management window, your privileges are identified by the selected checkboxes.

To view your assigned privilegesu

Select the User Management tab.

Unless you are assigned the Add/Manage Users privilege, checkboxes for your assigned privileges are
selected but not enabled, as shown in the following graphic. To request changes to your privileges,
contact your software administrator.

User Guide | 39

Chapter 4 Getting Started

Table 11 lists the available privileges, which can be assigned in any combination.
Table 11. User privileges

Privilege

PurposeAdd and manage

Add or remove users, set privileges, and change preferences.

users

Important: Users who are assigned the Add/Manage Users privilege can create
users and update privileges and preferences for any user. Only the superuser canremove this privilege from user accounts.

Create new

Save a design for a plate or analysis report as a template.

templates

Create inventories of kits, consumables, and reagents.
Import APF files.

View data files

See run files that were created from runs executed by other users.

(created by otherusers)
Overwrite

Save the file with a new file name. Files are always saved with the extension for the

existing data fileapplication you are using. For information, see Compatible File Types on page 45.

nameNote: Users without this permission can open files and perform analysis but
cannot create a new file.

System settings

View logs, reprocess data with new calibration values, and change file locations. Allusers can view the file locations.
Important: If your administrator selected the Preferred Locations checkbox in
System Settings, individual user location preferences are overridden.

Maintenance

View the event log and the system data settings.

Note: All users can reprocess data, view system folder settings, as well as themaintenance log and maintenance reports.
System Data

Move raw data from the computer to free up disk space.
Access troubleshooting data.

Manage Plate

Cancel a run while it is in process on the QX200 Droplet Reader.

APF Privileges

To use a preconfigured APF for runs, you can be assigned the following:n Manage APFs, which provides all APF privileges when selected.
n Run APFs, which gives you the option to execute a run configured with an APF.
n Only Run APFs. which allows you to only execute runs configured with an APF.

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Signing In, Viewing Privileges, and Changing Preferences

Managing Your Preferences
Use the User Management window to modify your personal user preferences. Default folder locations
appear in your preferences, but you can change them. You can also choose to keep all data files andtemplates private. The software prompts you to choose either your personal folder or the shared folder
each time you save a file or template.

To change your preferences
1.

Change any of the following preferences:nEnter a different file path for your data files and templates.

nSelect or clear the check boxes to change your data file and template privacy settings.
Important: The paths and checkboxes are disabled if your administrator has set Preferred
Locations in System Settings.

2.

3.

n

Enter a different system timeout period.

nEnter a different total of completed plates to show in the Run Status window, up to a
maximum of 100.

n

Select the Acquire all Wells By Default checkbox. If you do not select the checkbox, all wells are
excluded by default and you must manually include the wells for each droplet reading run.

Do one of the following:n

If you are setting preferences for a new user, click Add.

n

If you are updating preferences, click Save.

When the confirmation message appears, click Yes, and then click OK.

User Guide | 41

Chapter 4 Getting Started

Signing Out or Changing Users
While the instrument is idle, one user can log out and another user can log in.
Important: If User Management was not enabled during the software installation, the sign in, signout, and change users functions are not available.
Note the following:n

Do not change users while a run is in progress or data might be affected.

n

If the screen is locked and the initial user left unsaved changes, an advisory prompt appears. Click
Save before proceeding or the previous user’s work is lost.

To sign out
1.

Click the user name link in the upper-right corner and select Sign Out.

2.

Click Yes to confirm.

To change users
1.

Click anywhere in the lockout screen to display the Sign in window.

2.

Enter a user name.
n

The domain name appears below the user login fields. If you are on the same domain as theprevious user, you can enter your user name only.

n

If the user is on a different domain, enter the domain name followed by a backslash and the user
name.
<domain name>\<user name> (for example, global\john_smith)

3.

Enter the password and click Sign in.

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Instrument Status Bar

Instrument Status Bar
An instrument status bar appears above all windows except the analysis displays, which open in a
separate module.
When a computer is connected to the instrument, the status bar appears as shown below. If a computer is
not connected to the instrument, the status bar shows only the software, disk space, and user information.

If you have installed an EcoTank, the status bar appears as shown below:

LEGEND
Software name and edition
Information and status of the connected instrument
Instrument availability
Oil and waste levels
Used and free disk space
Available storage is displayed in GB, and also in number of plates that you can run before
running out of space on the computer.
Note: When QX Manager Software detects low disk space, an advisory prompt to archive
data appears.
Name of the current user, along with the current date and time.
The status bar with an EcoTank loaded in lieu of individual oil and waste bottles.
If an EcoTank is loaded into the droplet reader, oil and waste levels are displayed as a single
circle with one status for both. For information on EcoTanks, see Using an EcoTank Oil andWaste Container on page 223.

User Guide | 43

Chapter 4 Getting Started

Tabs to Functional Windows
Table 12 describes the functional areas and primary windows in QX Manager Software.
Table 12. Window Tabs

Tab

Name

PurposeAdd Platen Add and configure a plate for droplet readingn Apply Assay Protocol Files (APFs) which contain preconfigured
settings

Run Statusn In the top pane, view the run in progressn In the bottom pane, view up to 100 completed runs

Data Analysis

n Access the Data Analysis and Gene Study modules

Templates

n Set up templates for plates and reports, and search for existing
template files
n Import and manage APFs, and manage lots of consumables andreagents

Systemn View storage locations, logs, and maintenance reports
n Archive data, reprocess data with new calibration values, accesstroubleshooting information
Important: Available functionality depends on your assigned
user privileges. Instrument calibration is available only to the
Bio-Rad service engineer.

Users

n View the user privileges you have been assigned, and view andmodify your personal preferencesn Create, edit, or remove QX Manager Software users (if you areassigned the Add/Manage Users privilege)Helpn Access software version information, current calibration values,
End User License Agreement company website, and open source
software license information
Tip: You can also link the user and instrument guides to thelabeled buttons.

44 QX200 Droplet Reader and QX Manager Software, Premium Editioon

Compatible File Types

Compatible File Types
This section describes the file types you can open in QX Manager Software.
The following applies if your organization is using more than one edition of the software:n

You can open files created using Premium Edition only in Premium Edition.

n

If you open a .qlps file in QX Manager, Premium Edition, the file opens and is saved as a .ddpcrs file.

Table 13. Compatible file types

File Type

Extension

DetailsPlate.ddpltPlate template file containing setup details to perform experiments;

template
Plate

this file type opens in the Plate Editor.
.csv

template
Plate

Importable plate template file containing setup details in CSV format;
this file type opens in the Plate Editor.

.ddpltapf

Plate template containing the configuration specified in the APF. This
file type opens in the Plate Editor, but you can add wells only and they
automatically assume the APF configuration.

Plate.apfpack

APF file containing a static configuration, and which is imported into atargeted storage area for use when setting up runs

Data

.ddpcrs

Contains the results of an experiment run performed on the droplet
reading instrument and opened in QX Manager Software, Premium
Edition.

Data

.qlps

File type from earlier QuantaSoft™ regulatory versions, for twochannel experiment runs and data analysis; this file type opens in the
Analysis module.

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Chapter 4 Getting Started

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46 QX200 Droplet Reader and QX Manager Software, Premium Editioon

Chapter 5 Running Experiments
When the Start Run button is enabled, you can start the run. You can also cancel a run after it has started
if you are assigned the Manage Plate user privilege. For information, see Canceling a Run on page 67.

Assembling a Plate
The QX200 Droplet Reader accepts a solid 96-well plate that fits into a secure holder. You must assemble
the plate components before you can insert the plate into the QX200 Droplet Reader.Three separate
components comprise the plate:n

A base section to hold the platen

The plate itselfn

A top section to secure the plate

To assemble the plate
1.

Place the plate into the base section, and then raise the release tabs on the top section.

2.

Place the top section over the plate, and then lower the release tabs to secure the plate in the holder.

User Guide | 47

Chapter 5 Running Experiments

Inserting an Assembled Plate into the Instrument
This section explains how to insert an assembled plate into the QX200 Droplet Reader.
Note: You can insert the plate into the droplet reader before or after you add the plate in QX Manager
Software, but you cannot configure the plate until the software recognizes the plate in its
compartment.

To insert a plate into the QX200 Droplet Reader
1.

Press the button to open the compartment.

2.

Fit the assembled plate into the compartment. Well A1 must be in the top-left position.

Important: Make sure the tabs on the plate holder are securely clamped and the plate lays flat.
Otherwise, the sampling needle can strike the lid and damage the instrument.

3.

Press the button again to close the lid.

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Adding the Plate in QX Manager Software

Adding the Plate in QX Manager SoftwareThis section explains how to add the plate in QX Manager Software, Premium Edition when using the
QX200 Droplet Reader for your droplet reading run.

To add a plate in QX Manager Software
1.

Click the Add Plate tab.

If the Runs Available number in the Instrument Status Bar is 1, the Add Plate button is enabled.

2.

Click

next to Add Plate.

When QX Manager Software recognizes the plate holder in the compartment, the software enables
the Configure Plate button.

Note: You can insert the plate into the droplet reader before or after you add the plate in QX
Manager Software, but you cannot configure the plate until the software recognizes the plate inits compartment. If the software does not recognize the plate holder, an advisory message
appears. Remove and reinsert the plate. If necessary, contact Bio-Rad Technical Support.
3.

Click Configure Plate.

4.

When the Plate Configuration window appears, continue to Configuring the Plate on page 50.

User Guide | 49

Chapter 5 Running Experiments

Configuring the Plate
The Plate Configuration window features the Plate Information, Well Selection, Well Information, and Lot
Selector tabs.
All users can start runs using the initial plate configuration, an altered configuration, or just the plate anddata file names and the supermix. Users with the Create New Template user privilege can save theconfiguration as a template before the droplet reading run. Users with APF privileges can select an APF
file, which contains predefined settings to automatically configure the plate. For information on APFs, seeManaging Assay Protocol Files on page 90.

Plate Information Tab
The Plate Information tab is selected by default when the Plate Configuration window opens.

In the Plate Information window, you cannSelect an APFo

To follow the standard workflow, ensure that None appears in the APF field.

o

To use an Assay Protocol File (APF), select one from the dropdown list.

Important: APFs are available for use after they have been imported. For information, see
Importing Assay Protocol Files on page 92. If you selected an APF, you can select only APF
templates (.ddpltapf file extension) or .csv templates for your run. Plate layout parameters fromthe APF are grayed out and cannot be modified.
nSelect an existing template from the dropdown listnCreate a new templaten

Browse for an existing template

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Configuring the Plate

Note: When using the Browse button to select a template, the template is applied to the run, but
is not imported or saved in QX Manager Software.
nnName your plate and select a supermixo

QX Manager Software automatically enters the plate name into the data file name field, but you
can change it.

o

You can start the run with the plate name and supermix only, and then you can identify theremainder of your well information parameters in the Analysis module Plate Editor after the run
has concluded.

Select to acquire wells by columns or rows

Identifying Plate Information
To identify the plate
1.

(Optional) Select an APF from the Choose APF dropdown list.
If you selected an APF, the APF identifier appears in the banner and the Supermix field is grayed out.
The supermix defined in the APF is automatically selected and cannot be modified.

User Guide | 51

Chapter 5 Running Experiments

2.

Do one of the following:n

To choose an existing template, select a template file from the Choose Existing dropdown list.
QX Manager Software automatically populates the fields under Create New Plate.

n

To create a new template, click Create New, and see Creating or Editing Templates on page 69.

n

To browse for a template, click Browse and navigate to the folder containing your templates, andthen select a template file. QX Manager Software automatically populates the fields under
Create New Plate.
Note: When using the Browse button to select a template, the template is applied to the run,but is not imported or saved in QX Manager Software.

n3.

To identify the plate, enter a plate name and select a supermix under Create New Plate. Whenyou enter the plate name, the Save data file as field is automatically populated with the same
name, but you can change it.

(Optional) Under Acquire Wells By, select the alternative well acquisition method. The default isColumn.

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Configuring the Plate

Well Selection Tab
When you select the Well Selection tab, the Plate Editor grid appears. The wells in the plate layout areautomatically excluded and you must manually include the wells to be processed. If you typically run fullplates, you can change the setting in User Preferences to acquire all wells by default. For information, seeManaging Your Preferences on page 41.

Including or Excluding Wells in the Plate Layout
All wells are excluded by default when the plate editor appears.
Important: If you selected an APF, you can add wells if the plate is not full, but they assume thesettings from the APF. You cannot exclude the wells defined by an APF.

To include wells in the run
1.

Select the Well Selection tab.

2.

In the Plate Editor layout, select the wells to include in the run (those containing sample), and thenclick the Include Selected Wells toggle button.

3.

On the right, QX Manager Software specifies the number of wells that will be included in the droplet
reading run and the button text changes to Exclude Selected Wells.

User Guide | 53

Chapter 5 Running Experiments

Well Information Tab
When you select the Well Information tab, the Plate Editor opens. You can configure your experimentparameters for selected wells before or after the run.
Note: QX Manager Software can calculate automatic thresholds for positive control wells, but you
must select Pos Ctrl from the Sample Type dropdown list. You can make the selection before or after
the run. For information, see Sample Types on page 77.
Important: If you selected an APF in the Add Plate window, fields defined in the APF are grayed out
in the Well Information window. The APF can also enable fields that you must complete before
running the plate. If you added wells in the Well Selection window, fields that are defined in the APF
are automatically populated.

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Configuring the Plate

Defining Well Information When Using an APF
If you selected an APF to define your plate layout, wells are configured according to the well typeselected. APF well types contain predefined settings, and can be applied to one or more wells in the platelayout. In the examples shown in this section, the experiment type, sample type, assay type, and target
information fields are all predefined in three well types, with each well type containing a different set oftargets.

The predefined fields are not editable, but you can enter values in undefined fields and in some cases,
APF rules might require that you enter values in certain undefined fields. For example, a unique sample
ID might be required for each well before the Start Run button is enabled.

User Guide | 55

Chapter 5 Running Experiments

If there is room on the plate, you can also include wells on the Well Selection tab and assign well types.

Note: The graphics included herein are examples only; the array of predefined and undefined fields
might be different in your APF.

To add wells and assign well types
1.

Select the Well Selection tab and select one or more wells.

2.

Click Include Selected Wells.

3.

Select the Well Information tab.

4.

Select one or more of the included wells.

5.

From the Well Type dropdown list, select a well type and click Apply.

6.

Repeat as applicable.

To enter values in undefined fields for existing or new wells
1.

Do one of the following:n

If the undefined fields must contain a different value for each well, select one well.

n

If the undefined fields must contain the same value, select multiple wells with the same well type.
Important: If you select a group of wells with different well types, a message appears in theapplicable fields. If your entry contradicts a requirement or quality rule, you must selectdifferent wells.

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Configuring the Plate

2.

Enter applicable values into the fields and click Apply.
Important: You must click Apply for the software to recognize your new or edited information. If
you enter information in a field and need to apply earlier changes first, an advisory message
appears.

3.

Repeat as applicable.

4.

(Optional) To clear one or more wells at any time, select the wells and click Clear Selected Wells.

5.

After you have applied your entries and selections, you can pause the cursor on a well to see the wellinformation.

Defining or Editing Well Information (No APF)
You can assign different experiment parameters to each well or groups of wells.

You can apply your entries at any time. You must click Apply for the software to recognize your new oredited information. If you enter information in a field and need to apply earlier changes first, QX Manager
Software displays an advisory message.

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Chapter 5 Running Experiments

To define the configuration for the wells
1.

Select a well or group of wells.

2.

Select an experiment type; see Experiment Types on page 76.

3.

In the Sample Description fields, enter up to four words or phrases that describe the sample; see
Sample Descriptions on page 77.

4.

Select a sample type; see Sample Types on page 77.
Note: For automatic thresholding of positive control wells, you must select Pos Ctrl.

5.

Select a supermix; see Supermixes on page 78.

6.

Select an assay type.

7.

Available assay types vary, depending on the selected experiment type; see the fluorophore optionsin Assay Types and Fluorophores on page 79.

8.

(Optional) Under Target Info, change the fluorophore assigned to a channel. The fluorophore
information populates automatically for each target, with the maximum number of rows allowed forthe assay method. However, you can modify the default fluorophore assignments, if applicable.

9.

a.

Click the dropdown arrow and select an alternative.

b.

To delete a row, click the minus (-) icon next to the target.

c.

To add a row, click the plus (+) icon.

(Optional) To clear one or more wells at any time, select the wells and click Clear Selected Wells.

10. Click Apply. After you have applied your entries and selections, you can pause the cursor on a well to
see the well information.

11. When you finish configuring the plate, click Save.
12. If you are assigning lots, select the Lot Selector tab and see Lot and APF Management on page 87
for information.

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Starting the Run
When all required elements to set up a plate for a run are satisfied, QX Manager Software enables theStart Run button. You can configure the elements of the plate before you start the run, or you can run theplate with just the plate name and supermix, and define the configuration from the Analysis module.
If you selected an APF, part or all of the configuration has already been defined. You can add wells, andenter or select information in fields not already configured by the APF, but the APF configuration cannot
be altered.

To start the droplet reading run
1.

Tap Start Run.

Important: The Premium Edition prompts you to log in again and reauthenticate your user
credentials. Enter your user name and password, and then click Sign in.
The software performs a mandatory prerequisites check to ensure that the instrument is ready.
One of the following occurs:n

If the instrument passes the check, the run starts normally. Continue to Running the Experimenton page 63.

n

If the check finds issues with the instrument, the software displays a dialog box in which theissues are identified. The instrument cannot start the run until all issues are resolved. For
information, see Run Prerequisites Checklist on page 60.

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Chapter 5 Running Experiments

Run Prerequisites Checklist
If the prerequisites check on the instrument status finds one or more problems with instrument readiness,
QX Manager Software identifies them with anin the Check for Run dialog box. You must resolve allissues before the instrument can start the run.

Note: If you encounter a problem with the instrument or software that is not described here, see
Appendix C, Troubleshooting.
For information on each issue that can prevent the instrument from starting the run, see Table 14 on page
62.

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Starting the Run

Table 14. Pre-Run Error Indicators

Status Check Item

Issue

Suggested Resolution

Instrument Connection

Power connection not recognized.

Ensure the power outlet is working.
Disengage the power cord from theoutlet, and then reinsert it into theoutlet.

USB cable connection notrecognized.

Disconnect, and then reconnect, theUSB cable between the instrument
and the computer.
Ensure the correct instrument is

Fluid Levels Stability

Sufficient Oil

Sufficiently Low Waste

Instrument connection notselected in the System Settings tab >recognized.

Instrument tab.

The oil or waste is moving within

Wait until the liquid is settled, then try

the bottle so the level cannot beagain. Ensure the instrument rests on

accurately determined.

a solid, stable surface.

Oil level is below the acceptable

Remove the oil bottle and replace it

level for a run.

with a full one.

Waste level is above the

1. Empty any remaining oil from theacceptable level for a run.

bottle and then place a Waste label(provided by Bio-Rad) over the Oillabel.
2. Insert the bottle into the Waste slot.

Bottle Door Closed

Bottle door is not closed properly.

Open the bottle door and ensure
there are no blockages, and thenclose the door again.

Reader Door Closed

Reader door is not closed

Open the reader door and ensure

properly.

there are no blockages, and thenclose the door again.

Reader Lid Closed

Reader lid is not closed properly.

Open the reader lid and ensure there
are no blockages, and then close thelid again.

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Chapter 5 Running Experiments

Table 14. Pre-Run Error Indicators, continued

Status Check Item

Issue

Suggested Resolution

Plate Loaded

Plate is not loaded properly.

1. Open the reader door and remove
the plate.
2. Ensure the tabs of the plate cover
are securely clamped.
3. Insert the plate again and ensure itlays flat.

Sufficient Disk Space

There is not enough storage space

Archive older data files to clear

available for the run data.

space.

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Starting the Run

Running the Experiment
The instrument allows you to do the following:n

During the run, perform real-time analysis on the droplets in each well after the well has been readn

When the run concludes, QX Manager Software moves the run to the Completed list in the Run
Status window, and saves the analysis data file. Data files are always saved to your personal filelocation or a preferred location, and can also be saved to a shared location. For information, seeManaging Your Preferences on page 41.
Important: if your system administrator has designated Preferred Locations in System Settings,
they override any file paths indicated in your preferences.

n

During and after the run, QX Manager Software displays run information in the Run Status window.

n

Cancel a run (with the Manage Plate permission).
Note: Canceling a run also shuts down the instrument.

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Chapter 5 Running Experiments

Tracking the Run Status
You can track each run from the Run Status window.

The top pane shows the run in progress. The run remains in the top pane for the duration of theprocessing.
Icons displayed in the Run Status column indicate each process point, as shown in Table 15 on page 64.
Table 15. Run status indicators
Status Icon

Description

Ready to begin droplet reading

Droplet reading run

Run completed

Run completed, plate removed

Run stopped or canceled by the system, or canceled by the user before it began

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Starting the Run

When the run is finished, the software moves the run to the bottom pane, where up to 100 completed runs
are visible.
Tip: You set the number of completed runs to display in your user preferences. See Managing Your
Preferences on page 41.
The content of each column is explained in Table 16.
Table 16. Run Information Columns

Column Name

Location

Description

Plate nameTop and bottom

Name entered under Create New Plate

panes

Note: If you selected an existing template, the templatename appears.

Run status

Top and bottom

Icons for each process step (see Table 15 on page 64)

panesTime remaining

Top pane only

Hours and minutes until the run will be finishedTime elapsed

Top pane only

Time, in hours and minutes the run has been in progress

Total time

Below the top pane

Total hours and minutes remaining for all in-progress runs

Bottom pane only

Date and time stamp showing when the instrument completed

remaining
Run completed

the runFile name

Bottom pane only

Plate name and system-generated identifier

After run completion, the software saves the analysis data file in a location designated by you or a systemadministrator.

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Chapter 5 Running Experiments

Using Live Analysis
When the QX200 Droplet Reader initiates droplet reading, QX Manager Software provides an option forreal-time analysis of the wells that have been read, while the process as a whole is still active.
QX Manager Software initially shows each well in the Plate Editor as disabled. As the software confirmsthat the instrument has acquired a well and read the droplets, the software enables the well for live
analysis in read-only mode. The process continues until all wells are enabled and the process is finished.

To use live analysis
1.

Tap the droplet reading icon () for the run in progress.

The Droplet Reading dialog box opens.

2.

Click Open Live Analysis.

3.

Select an analysis window.

4.

In the well selector, select one or more wells that are enabled.
Important: QX Manager Software displays read-only data in the selected analysis window. You
can view the data but to make changes, you must wait for the run to complete, and then change
the data in the Analysis module.

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Starting the Run

Canceling a Run
You can cancel a run if you are assigned the Manage Plate user privilege.

To cancel the run
1.

In the Run Status window, click the X on the right to cancel the run.

Note: Canceling a run also shuts down the instrument.
2.

When the Are you sure message appears, click Yes.

The instrument finishes reading the current well, stops the process and reverts to its pre-run state.
Note: If you click No, or if you do not respond to the confirmation message within 30 sec, theprocess continues without interruption.
The

icon appears in the Run Status column.

QX Manager Software creates the data file for the wells that were processed on the canceled plate
and the status in the Event Log is specified as “run aborted by user.”

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Chapter 6 Creating or Editing Templates
If you have been assigned the Create New Templates user privilege, you can create, edit, and save plateand report templates for your common experiments. Templates that are available to you appear in the
dropdown list in the Plate Information window, and also in the default view of the Template Setup tab. If
the list is long, you can use the Search field to narrow the results.

All users can select or create a template with an APF selected. For information on APFs, see Managing
Assay Protocol Files on page 90.
All users can configure a plate template in a CSV file, and then import the template into QX Manager
Software. For information, see Creating and Storing Plate Templates from CSV Files on page 82.
Note: You can select a CSV template from the dropdown list in the Plate Information window only.
They do not appear in the My Templates list.
For information on report templates, see Creating or Modifying Report Templates on page 84.
Templates you created are saved to one of the following folders:n

The path specified in your user preferences; these appear under My Templates in the Templates
window.

n

The paths specified by your administrator in the shared or preferred location fields in System
Settings.
Important: Preferred locations override personal folder settings and templates from all users
are saved there.

You can also browse for templates when you are setting up your plate for a run.

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Chapter 6 Creating or Editing Templates

Creating or Modifying Plate Templates
Important: You must be assigned the Create New Template user privilege to create or edit, and thensave, a template.

To create or edit a template1.

2.

Do one of the following:nNavigate to the Plate Information window (click Plate Setup > Add Plate > Configure Plate) andcontinue to Step 2nOpen the Templates window and then go to Step 3.

From the Plate Information window, under Plate Template, do one of the following:nSelect an existing template from the Choose Existing dropdown list.

n

Click Create New. The plate layout opens in Edit mode.

n

Click Browse and navigate to an existing template.

Continue to Step 4.
3.

From the Templates window, do one of the following:nSelect the Plate Setup tab and click Add New Plate > Edit Plate Layout.

n

Double-click an existing template from the list.

The Plate Editor opens in Edit mode. The Instrument Type field is grayed out.
Note: CSV templates do not appear in the Templates window, but are available from thedropdown list in the Plate Information tab.
Continue to Step 4.
4.

(Optional) Select an APF from the APF dropdown list.
Important: If you select an APF, you can enter or select information only for fields that have notbeen defined with static APF entries, as shown in the following graphic. All other fields are
populated with entries from the APF configuration. You can add wells, but you cannot delete
wells set in the APF. Wells that you add assume the APF settings automatically.

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5.

Click the Exclude button, and select the wells to include in the plate layout, and then click Include
selected wells.
By default, all wells in the Plate Editor are automatically excluded. You must select and include newwells in the template. If you typically run full plates, you can change the setting to Acquire all wells by
default in your user preferences. For information, see Managing Your Preferences on page 41.

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Chapter 6 Creating or Editing Templates

6.

Click the Edit button to display the layout for experiment and sample identification.
The fields are enabled when you include wells.

7.

For one or more wells at a time, complete any or all of the following substeps to include the selections
and entries that should be static. Leave blank any field that should be completed at the time of theexperiment run.
a.

Select an experiment and sample type, supermix, assay type, and enter sample descriptions.
nExperiment Types on page 76

nSample Types on page 77

nSample Descriptions on page 77nSupermixes on page 78

nAssay Types and Fluorophores on page 79

Note: For automatic thresholding of positive control wells, you must select the Pos Ctrl
sample type.
Note: If you selected an APF on the Add Plate screen, fields that are configured in the APF
for one or more wells, are grayed out.
b.

Enter a sample ID and a subject ID.

c.

If you selected Residual DNA Quantification as the experiment type, enter a conversion factor.

d.

Enter up to four sample descriptions, and any relevant well or plate notes.

e.

Edit the Target Name and Target Type fields.

8.

Click Apply.

9.

Click Save and select one of the following:n

Shared Templates. The template is saved in the folder specified in the System Settings.

n

My Templates (saves the file to the path in your user preferences) or System Templates (saves
the file to the preferred location specified by your system administrator).

n

If your system administrator has specified preferred locations for all users, templates areautomatically saved to that location.

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Creating or Modifying Plate Templates

Template Plate Editor Window
Use the Template Plate Editor tonCreate new or edit existing plate template files, and save new or modified templates for reusen

Add up to four sample descriptions per welln

Exclude wells from droplet reading
Important: When you create an experiment from a template with wells excluded in the platelayout, the instrument pierces the foil for all wells in the physical plate, but reads droplets for
active wells only.

To open the template plate editor
1.

Click the Templates tab on the left.

2.

In the Templates window, click Edit Plate Layout

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Chapter 6 Creating or Editing Templates

You can also open the template plate editor from the Add Plate window.

LEGENDThe Edit and Exclude buttons are accessible from the top of the screen.
The right pane contains the interface for defining your experiment parameters.
The left pane displays the plate grid and configuration information in each well.
The Well Data button toggles to the Well Data table, where you can see your plate setup in atabular format, and then back to the Plate Editor. When the Well Data table appears, thebutton name changes to Plate Layout.

From the dropdown list, you can select an APF to associate with the template.

Important: If you selected an APF, you can add wells to the plate layout if there is room on the plate,but the wells inherit the APF configuration. You can update fields that are not predefined by the APF.

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Creating or Modifying Plate Templates

Plate Editor Tools
Use the buttons described in Table 17 when you are creating a template or defining an experiment in the
Plate Template Editor.
Table 17. Plate Editor Buttons

ButtonEdit

Description
Allows you ton Set the experiment type, sample name and type, supermix, and assay
type
n Set the target name, type, and fluorophore for each channeln Add well or plate notes

ExcludeToggle button that allows you to include or exclude wells from droplet
reading
Note: Wells in the plate editor are initially excluded by default.

CancelAllows you to cancel and return to the Template Setup window

Save

Opens a dialog box where you can enter a file name and storage location

Clear Selected Wells

Allows you to delete information from selected wells

Undo

Allows you to reverse your last action
Note: This button is enabled only after you have applied at least one
experiment parameter (for example, the selection for Experiment Type).

Well Data or Plate Layout

Toggle button that allows you to access the Well Data table and return toPlate Layout view

Apply

Applies your entries and choices for selected wells

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Chapter 6 Creating or Editing Templates

Experiment Types
QX Manager Software offers the experiment types described in Table 18, each enabling different assay
options and analysis tools. You can assign multiple experiment types across the plate, but you can assign
only one experiment type to each well.
Table 18. Experiment types

Type

Description

Direct

DQ uses absolute quantification to determine the concentration (copies/μl) of target

quantification

DNA copies in a sample. DQ measures the number of positive and negative droplets(DQ)

for each target in a well based on their fluorescence amplitude, and uses a Poisson
algorithm to calculate the starting concentration of each target DNA molecule.
Note: The ABS experiment type created in QuantaSoft Software versions 1.4
through 1.7 is automatically mapped into the software as a DQ experiment type.

Copy number

CNV determines concentration and calculates the copy number of an unknown (CNV)

variation (CNV)target relative to a known reference or references within the same well.

Mutation

MUT determines concentration and calculates the fractional abundance of andetection (MUT)

unknown mutant present at a low frequency in a wild-type background.

Rare event

RED determines the concentration of a known mutant or a rare target species relative

detection (RED)to a given reference species within a large pool of background DNA.

Drop-off (DOF)

DOF determines absolute quantification of targets for assays designed to detect nonwild type sequences, such as indels and genome edits; DOF is designed to support anassay strategy where one probe counts all alleles and one “drop-off” probe sits on topof a predicted cut site or mutation site.

Gene expression

GEX determines concentration (as with DQ) and calculates relative expression levels(GEX)of an unknown target relative to a known reference or references within the same well.

Residual DNA

RDQ provides a precise method for residual host cell DNA quantification.

quantification

Note: Users can enter a conversion factor (1/C-value) for a given genome(RDQ)(human, mouse, etc.) to calculate the mass for a well based on the number ofcopies measured, up to three decimals. The software displays the result in pg/ulof the ddPCR well in the Molecular Weight column of the Data Table. Starting
sample concentration can then be back-calculated based on dilution factor.

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Creating or Modifying Plate Templates

Sample Descriptions
QX Manager Software allows you to enter descriptive words or phrases for your sample in up to four fields
per well. Descriptors can include information such as research type, dilution factors, and so forth.
Tip: Only the information from the first field appears in the Plate Editor layout. However, you can see
entries in the second, third, and fourth fields in the Well Data table, or you can pause on a well to
display a tool tip, as shown in the following graphic.

Sample Types
You can assign multiple sample types within the plate, but you can assign only one sample type to eachwell.
QX Manager Software provides four sample types for selection:nUnknownn

NTC (no template control)n

Pos Ctrl (positive control) where one or more targets are expectedn

Neg Ctrl (negative control), where no response is expected

Important: Beginning in v1.2, QX Manager Software can automatically calculate thresholds for
positive control wells, but you must select Pos Ctrl from the Sample Type dropdown list. You canselect Pos Ctrl during plate setup or in the Analysis module after the run is finished.

User Guide | 77

Chapter 6 Creating or Editing TemplatesSupermixes
QX Manager Software offers five PCR supermixes. Each supermix is optimized to deliver maximum PCR
efficiency and sensitivity for the amplification and detection of DNA and RNA targets.
Important: Use of unapproved supermixes can harm the instrument and void the warranty.

ddPCR Supermix

Description

Multiplex Supermix

For use in nucleic acid sample preparations to amplify and detect DNA
targets in probe-based experiments involving multiple targets.

Supermix for Probes (NoFor use in nucleic acid sample preparations, with sensitivity for thedUTP)

amplification and detection of DNA targets using hydrolysis probebased assays.

Supermix for Probes

For use in sample preparation with uracil N-glucosylase (UNG)
decontamination protocols to prevent the reamplification of carryover
PCR products between experiments.

Supermix for Residual
DNA Quantification

For use in residual DNA detection.

One-Step RT Advanced Kit for

For use in absolute quantification of target RNA molecules.

Probes
EvaGreen® Supermix

For use in gene expression.

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Creating or Modifying Plate Templates

Assay Types and Fluorophores
QX Manager Software offers the assay methods explained in Table 19.
Table 19. Assay types
Assay type

Description

Single target per

Method assuming one or two probe colors (FAM/EvaGreen® and HEX/VIC) and one

channelor two targets per well, with a single target detected per channel.
This is the default assay type, with the maximum two rows displayed. You can delete
up to three rows.

Amplitude

Method to increase multiplexing up to four targets per well, with one or two targets

multiplex

detected per channel. The maximum of eight rows are displayed. You can delete up toseven rows.

Probe mix triplex

Triplex mode that allows exactly three targets per well, with one target detected ineach of two channels and a third target detected across both channels.
Triplex mode that allows one groups of three targets each.
Group 1 has one target in FAM, one target in HEX/VIC, and one target in bothchannels. You can delete a group, but not the individual targets within the group.
Note: The channels within a group are not interchangeable; therefore FAM isalways paired with HEX/VIC and so forth.

Advanced

Method to increase multiplexing rate in any combination of targets detected perclassification

channel. This method requires manual classification of droplets.

Basic drop-off

This mode allows two groups of two targets each. The first group appears by default,
with one target in FAM and HEX/VIC and one target in FAM or HEX/VIC.
This assay type is available only for the DOF experiment type.
Note: The channels within a group are not interchangeable; therefore FAM isalways paired with HEX/VIC and so forth.

Double drop-off

This assay type is available only for the DOF experiment type, and allows one groupsof three targets.
The first group appears by default, and looks for one target in FAM and in HEX/VIC(target type reference) one target in FAM (target type unknown), and one target in
HEX/VIC (target type unknown).
By default, all reference copies are set to 2.
The channels are static:
n Channel 1 FAM is always paired with Channel 2 HEX/VIC).
n.

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Chapter 6 Creating or Editing Templates

The experiment type you select determines the available assay methods.Table 20 displays the sample
type associated with each assay method.
Table 20. Assay types by experiment type
Experiment type
Assay type
DQ

CNV

MUT

ü

ü

Amplitude multiplex

üProbe mix triplex

üSingle target perchannelAdvancedclassification

DOF

GEX

RDQ

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

RED

ü

ü

Basic drop-offüDouble drop-offü

QX Manager Software automatically populates the fluorophore in each channel for each target but you
can change the default selections.
Use Table 21 to select from the fluorophore options for each assay method listed.
Table 21. Fluorophore options
Assay method

Signal
Ch1

SignalCh2

Single target per channel, for 1 to 2 targets

FAM

HEX

EvaGreen®

VIC

None

None

Amplitude multiplex, for

FAM HiHEX Hi1 to 4 targets

FAM LoHEX LoEvaGreen® Hi

VIC Hi

EvaGreen® Lo

VIC LoNone

None

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Creating or Modifying Plate Templates

Table 21. Fluorophore options, continued
Signal
Ch1

SignalCh2

Probe mix triplex, for

FAM

HEX

3 targets

None

Assay method

VIC
None

Advanced classification

FAM

HEX

1–10

1–10

EvaGreen®

VIC

1–10

1–10

None

None

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Chapter 6 Creating or Editing Templates

Creating and Storing Plate Templates from CSV Files
You can create a plate template in a spreadsheet application, save it in .csv format (CSV), and then store
it for use in your droplet reading runs.
Note the following:nn

CSV templates do not appear in the Templates window; however, when you set up a run, you canaccess them from the Plate Information window using the following methods:oClick the Choose Existing dropdown arrow and select a CSV template file from the listo

Click Browse and navigate to the applicable storage folder, and then select the CSV template file

You can store CSV template files in any location and navigate to the file using the Browse function,
but the Choose Existing dropdown list automatically populates with templates that are stored in thefollowing locations:oThe personal templates storage folder defined in your user preferences (see Managing Your
Preferences on page 41)o

The shared or preferred location specified by your system administrator (see Shared Settings on
page 182

As shown in Fig. 1 and Fig. 2 on page 83, when you create a CSV template, the headings for thecolumns containing the experiment information must match the fields and order in the Plate Editor. Ifthey do not match, an error message appears when you select the template.
Important: After you specify the information in row 1, do not change the field entries until you
install a new software version or edition.

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Creating and Storing Plate Templates from CSV Files

To create and save a CSV template
1.

Open a spreadsheet program and enter the run settings into the template in the format shown below.
Fig. 1: Template CSV Layout Example, Columns A through H

Fig. 2: Template CSV Layout Example, Columns I through R

2.

When you finish populating the fields, navigate to your templates storage location and save thetemplate.
If you save the CSV file inn

The personal or shared templates storage location defined in your user preferences or sharedsettings, the CSV template is available from the Choose Existing dropdown list.

nAnother storage locationfolder, you can navigate to the template file using the Browse feature in
the Plate Setup Plate Information tab.

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Chapter 6 Creating or Editing Templates

Creating or Modifying Report Templates
If you are assigned the Create New Templates user privilege, you can create and save a report templateby editing the default report structure or by opening and editing an existing report.

To create or edit a report template1.

Select the Template Setup tab.

2.

Click Reports and do one of the following:n

To create a new template, click Add New Template. and click Edit Report Template.

n

To open an existing template, select the template and click Edit Report Template.

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Creating or Modifying Report Templates

3.

Click the arrow to the left of each category to expand the list of reportable items.
Important: The Audit Log checkbox is enabled in the Premium Edition only.

4.

Select and clear checkboxes to create the report structure.
Note: Use the buttons at the bottom of the screen to expand or collapse all categories at once, orto select or clear all checkboxes at once. You can also drag and drop the section to rearrange
the order of appearance in the report, and drag and drop items in the section to reorder them.

5.

Enter a name for your report in the Report Title field and click Save.

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Chapter 6 Creating or Editing Templates

6.

When the Save dialog box appears, enter a file name.

7.

Select a storage location. Choose from the following:

8.

nSystem Templates (preferred location, if specified by the administrator)n

My Templates (personal storage location specified in user preferences)n

Shared Templates (files saved to this location are available to all users)

Click Save again to save the report format as a template.

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Chapter 7 Lot and APF Management
From the Templates tab in the Premium Edition, you can add lots by lot number, catalog number, andexpiration date to track your usage, and import preconfigured assay protocol files (APFs) that you can use
to expedite configuration of your droplet reading runs.

The following options are available:nFrom the Lot Management tab, you can manage your inventory and track use of lots for test-specifickits, consumables, and reagents. You can select lots on a per well basis. If you selected an APF, lot
fields are defined if they are required before you can start the run.

n

From the APF Management tab, if you are assigned the Manage APFs user privilege, you can importassay packages that contain preconfigured plate and run settings. You can also modify variables inan APF and delete APFs.

Important: If you select the Show Expired and Uses Lots checkbox in the lower-left corner, lots thatare expired or empty are displayed.

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Chapter 7 Lot and APF Management

Managing Consumable Lots
If you are using a Bio-Rad droplet generation instrument, you can manage your inventory of consumables
packs, cartridge, and pipet tips, as well as your plate and seal inventory.

To enter a consumables lot
1.

Select the Template Setup icon.

2.

Select Lot Management.

3.

Select the Consumables tab, and then select the applicable consumable.

4.

(Optional) To display expired or used lots, select the checkbox at the bottom-left side of the window.

5.

Click in each field and enter the corresponding information

6.

If the consumable was used in a run, select the Used checkbox.

7.

Repeat until all lots are added, and then click Save.

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Managing Reagent Lots

Managing Reagent Lots
You can manage your inventory of supermixes, droplet generation oil, droplet reader oil, buffers andassays. You can purchase ready-to-use assays, such as the SARS-CoV-ddPCR kit, or, if you know yourassay sequences, you can request custom ddPCR assays from Bio-Rad.

To enter a reagent lot
1.

Select the Template Setup icon.

2.

Select Lot Management.

3.

Select the Reagents tab, and then select the applicable reagent.

4.

(Optional) To display expired or used lots, select the checkbox in the lower-left corner.

5.

Click in each of the fields and enter the corresponding information.

6.

If the consumable was used in a run, select the Used checkbox.

7.

Repeat until all lots are added, and then click Save.

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Chapter 7 Lot and APF Management

Managing Assay Protocol Files
An Assay Protocol File (APF) is a package containing preconfigured settings applied to a plate run. Alongwith allowing you to streamline the configurations of your droplet reading runs, APFs can be set to apply
more rigor to quality controls and positive versus negative determinations in each well. APFs can specify
any combination of settings for different wells.
Fields configured in the APF are not editable in the configuration windows. You can add wells if there isroom on the plate, but they automatically inherit the settings specified in the APF. If the APF contains rules
for validation that must be met before you start the run, then QX Manager Software, Premium Edition
validates information or patterns you enter into enabled fields. If they do not match, an error message
appears.
From the APF Management tab in the Templates window, you cannImport APFs into QX Manager SoftwarenModify variables defined in the APF

nDelete APFs

Important: You must be assigned the Manage APFs user privilege to upload, modify, or delete an
APF. To create your own APF configurations, you can purchase the QX Designer companion
application from Bio-Rad Laboratories, Inc.

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Note the following:nAfter an APF is imported, it is available for selection in the Add Plate window by users with Manager
APFs, Run APFs or Only Run APFs user privileges.

nWhen an APF is selected in the Add Plate window, the APF name appears in the gray banner at the
top of the window.

n

When you click Configure Plate, the wells configured in the APF appear as shown in the following
example.

For analysis information, see APF Results Dashboard on page 117.

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Chapter 7 Lot and APF Management

Importing Assay Protocol Files
APFs must be imported into the APF Packages window before they are available to use for a run.
Important: Only a user with the Manage APFs user privilege can import APFs.

To import an APF
1.

Select the Template Setup icon.

2.

Select APF Management, and then click Import Package.

3.

When the APF Packages dialog box appears, locate the APF to import.

4.

Select the file and click Open.
QX Manager Software, Premium Edition imports the APF into the APF Packages window.

Important: You cannot import multiple versions of the same APF. Each APF is assigned aversion number. When you import a newer version of the same APF, QX Manager Software will
ask if you would like to upgrade your existing APF. If yes, the earlier version is overwritten.

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Managing Assay Protocol Files

Modifying Variables in an Assay Protocol File
When you select an APF under Assay Protocol name, the APF package details appear in the bottom-leftcorner. You can modify any or all variables for your specified targets, or you can restore the variables totheir APF predefined values.

To modify a variable1.

Select the Template Setup icon.

2.

Select APF Management, and then select the row for the applicable APF package to display the
Variables grid.

3.

Click in a field under Modified, and the enter the new variable value.

4.

(Optional) To cancel your entries and restore the default variable values, click Reset.

5.

To save your changes, click Save.
The modified values are saved, and will apply for all runs using this APF.

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Chapter 7 Lot and APF Management

Deleting Assay Protocol Files
To delete an APF from the Assay Management window
1.

Select the Template Setup icon.

2.

Select APF Management, and then select the checkbox on the right for the APF to be deleted.

3.

Click Delete Package to remove the APF package from APF Management.

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Chapter 8 Data Analysis Module Overview
As the instrument reads droplets in each well, the QX200 Droplet Reader collects raw data. At the end ofeach droplet reading run, QX Manager Software uses the raw data to produce a data file, which contains
analysis information based on the number of positive and negative droplets identified for each target ineach sample. The fraction of positive droplets is fit to a Poisson algorithm to determine the starting
concentration of the target DNA molecule in units of copies/µl input.
This section summarizes the analysis functionality, and also describes the general options governing yourchart displays. More detailed information, including specific information and uses for each analysis
window, as well as information on data calculations, is contained in Chapter 9, Data Analysis
Methodology.
When you select the Data Analysis tab, you can access the Analysis module and the Gene Study module.

When you open the data file in the Analysis module, you can view the data with the automatic analysis
thresholds and calculations, or you can choose different options to recalculate, replot, or recolor the
results.

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Chapter 8 Data Analysis Module Overview

The Data Analysis module functionality allows you tonView your droplet data in 1D and 2D plotsnAnalyze multiple targets within a well using amplitude multiplexing and probe mixing strategiesnDetect genomic editing events and non-wild type events with a “drop-off assay” analysis optionnVisualize and export data with improved flexibilitynGenerate reports for different analysis typesn

The Gene Study module allows you tonCollect data by adding one or more data filesnView gene expression calculations across multiple experiments

Important: The Gene Study module is accessible from a standalone computer only. The maximum
number of samples you can analyze in a gene study is limited by the size of the RAM and virtual
memory of the standalone computer.

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Opening a Data File for Analysis

Opening a Data File for Analysis
You can open the following file types in the Data Analysis module:
n

.qlps

n

.ddpcrs

To open data files, you must be on a computer on which QX Manager Software is installed and haveaccess to the storage locations.

To open a data file for analysis
1.

In QX Manager Software, select the Data Analysis tab.

Available data files are displayed under the following headings.
nRecent Datafiles
Displays a list of files you have recently opened.

nSystem Datafiles or My Datafiles
Files are always saved to one of the following locations:no

If preferred locations are enabled, then files for all users are saved there and they appear
under System Datafiles.

o

If preferred locations are not enabled for all users, your files are saved to your personal
folder and appear under My Datafiles.

Shared Datafiles
You can also save your data files to a shared location; these appear under Shared Datafiles.

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Chapter 8 Data Analysis Module Overview

2.

Click a file to open it in the Analysis module.
Tabs for each analysis and data window appear on the left of the Analysis window.

Tip: From the computer attached to the QX200 Droplet Reader, you can also open the data filefrom the Run Status window. In the completed files section, click the completed run icon (the file, and then click Launch Analysis.

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Saving a Data File
You can save data files with or without modifications, with the same or different file names, and in thesame or different locations.
Important: When you save a .qlp.qlps file type in QX Manager Software, the software automaticallysaves the file as a .ddpcrs file. This creates a new file and does not overwrite the original.

To save a data file1.

2.

Do one of the following:n

To save the file under the same file name and in the same location, click Save.

n

To save the file under a different file name or in a different location, click Save as, and then do
one of the following:o

If you are saving the file under the same name and in the same location, QX Manager
Software saves the file immediately.

o

If you are saving the file under a different file name or in a different location, navigate to the
new location (if applicable) and enter the new file name. You must be assigned theOverwrite existing file name user privilege to change the file name.

Click Save.

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Chapter 8 Data Analysis Module Overview

Analysis Display and Output Options
QX Manager Software provides the following option that you can choose or set:n

Universal Options — available from the primary toolbar to save, import, or export data files
Note: The APF Tools button appears only when an APF was used for a droplet reading run.

nChart Display Preferences — to change how your chart appears in the analysis windownChart Scale Options — to change the scale represented on an axisnChart Menu Options — available in chart views (from theicon) to copy, save, and print chart

images. In Amplitude charts showing data points, you can show or hidenTable Menu Options — available in table views (from theicon) to copy data, export data to

Excel or CSV files, and show or hide columns
You can also expand the chart display to full-screen size and then return to the original display.

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Universal Options
Universal options appear on the top menu bar, and are available from all windows, although functionality
within the main option might differ according to the analysis window that appears.

Note: If you open a run that was executed using an APF, the APF Tools button appears in the menu
bar.

Universal options are explained in Table 22, and are available in all Analysis module windows.
Table 22. Universal options
OptionDescription

Save

Saves changes to the analysis file under its current file name or file extension

Save asSaves the file with a different name
If you open a file in the latest application that was created in an earlier application,
the file assumes the file extension of the new application. See Saving a Data File on
page 99 for information.

Import/export

n Imports or exports plate setup data to a CSV filen Imports or exports plate setup data to a plate template filen Exports visible data to a CSV filen Exports amplitude, cluster, and linkage datan Exports and prints the visible charts for the 2D plate layout

Undo

Enabled in the Plate Editor only, after you have made a change

APF Tools

Enabled only when an APF was used for the run
For information, see Reanalyzing the Run File on page 118.

User Settings

Allows you to restore your user preferences to the default settings and to show or
hide color matrix change messages

To import or export setup or analysis datau

Click Import/Export.

Table 23 describes the available import/export options.

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Chapter 8 Data Analysis Module Overview

Note: If there is unsaved data, the software prompts you to save the file before its contents can beimported or exported.
Table 23. Import/export options

Import/export option

Description

Import plate setup CSV

Import plate layout data from a CSV file to the Plate Editor
Note: This option is only available in the Plate Editor, and is notavailable for files that were run using an APF. The new plate layout
overwrites the existing layout.

Export plate setup CSVExport a configured plate layout to a CSV file
Note: This option is only available in the Plate Editor and is not available
for files that were run using an APF.

Import plate setup

Import a plate layout from a plate template (.ddplt) file
Note: This option is only available in the Plate Editor.

Export plate setup

Export the plate layout to a plate template file
Note: This option is only available in the Plate Editor.

Export visible data to CSVExport only the data from the wells you selected in the Well Selector to a CSV
file

Export amplitude data

Export the data to an Excel spreadsheet, and indicates whether or not thetarget was found (1 = yes, 0 = no)Export cluster data

Export the data to an Excel spreadsheet
Note: Includes (for each well) whether or not the target was found (1 =yes, 0 = no), the droplet count, and the mean and standard deviation foreach dye, and the cluster ID.

Export linkage data

Exports to a CSV file the number of copies of a target that are present inoverabundance, versus. the expected value in copies per µL

Export visible charts

Exports all charts that are displayed

Print visible charts

Prints all charts that are displayed

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Table 24 shows where the options are available.
Table 24. Option availability
Import/expo
rt option

APF
results

Plate
editor

Plate
view

Plate
2D

Ampl
plots

Data
visualchartsEventcounts

Data
table

ü

ü

ü

ü

Import plateü

setup from
CSV
Export plateü

setup to CSV
Import plate

ü

setup
Export plate

ü

setup
Export visible
data to CSVExportamplitude data

Export cluster
data
Export linkage
data
Export visible
chartsPrint visible
charts

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

ü

Note: Amplitude plots are available in 1D and 2D, and Data Visualization charts are Concentration,
Copy Number, Ratio, and Fractional Abundance. In the Dashboard view corresponding options areavailable for each plot or chart displayed.

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Chapter 8 Data Analysis Module Overview

Expanding or Reducing the Chart
You can expand or reduce the chart size in the following windows:nDashboardn

1D Amplituden

2D AmplitudenConcentrationn

Copy Number

n

Ratio

n

Fractional AbundancenEvent Counts

If you expand an amplitude or data visualization chart to full size, the Well Selector and the Well Data
table are hidden from view until you collapse the chart again.

To expand or reduce the chart size
1.

To increase the chart size to the full window, click the2.

To reduce the window to its original size, click theicon in the upper-right corner of the chart.
icon.

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Selecting Chart Display Preferences
The Chart Display preferences primarily control font sizes and positioning. Table 25 explains eachpreference, as well as the windows in which it is available.
Table 25. Chart display preferences
Preference

Window

Description

Channel or Dye

Plate 2D

Select Channel or Dye to identify your chart accordingly

1D Amplituden If you select Channel, the channel number appears as

2D Amplitude

the chart titlen If you select Dye, FAM or HEX appears as the chart
title

Axis Data Label

1D Amplitude

Size

2D Amplitude

Select a different font size

Concentration
Copy Number
Ratio
Fractional Abundance
Event Counts
Chart Data Label

Concentration

Size

Copy Number

Select a different font size

Ratio
Fractional Abundance
Event Counts
Chart Marker Size

Concentration

Select a different marker size

Copy Number
Ratio
Fractional Abundance
Chart Marker Label

Concentration

Position

Copy Number

Reposition the marker label

Ratio
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Chapter 8 Data Analysis Module Overview

1.

Click the Chart Display button.

To select chart display preferences
1.

Click the Chart Display button.

2.

Select your options.
The display changes immediately to reflect your choices.

3.

Do one of the following:n

To save your choices as your default settings, click Save as my default. When the successmessage appears, click OK to close the dialog.

n

To close the menu without saving the settings, click anywhere in the chart display.

Selecting Chart Scale and Label Options
Chart scale options primarily control chart scale and label displays.

Each preference, as well as the windows in which it is available, is explained in Table 26 on page 107.

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Table 26. Chart scale options

OptionDescription

Scale

Appears in options for all charts
The Scale option determines the numerical range for your chart data:
Auto — Selected by default; QX Manager Software automatically displays a scale
to match the data distribution.
Fixed — Selecting Fixed enables the Axis fields, and allows you to manually adjust
the range and increment.

Axis

Appears in options for all charts
When the Axis fields are enabled, you can manually adjust the minimum (Min) andmaximum (Max) points for the data display on each axis, as well as the increments(Incr).
X — Horizontal axis
Y — Vertical axis
Note: You can modify the x axis scale in the 2D Amplitude chart only.

Secondary Y Axis

Appears in options for Concentration only
From the dropdown list, you can select from Channel 2 concentration, ratio, copy
number, or fractional abundance to display the corresponding data in a secondaryrow on the y axis.

Log

Appears in options for all Data Visualization charts (Concentration, Copy Number,
Ratio, and Fractional Abundance)
You can select the Log checkbox to display the y axis in base 10 logarithmic
format.
Note: In the Concentration chart, you can also select Log for the secondary yaxis.

InverseAppears in options for Ratio and Fractional Abundance only
The Inverse option equals the opposing number of the Ratio data point to a total of2, and the opposing number of the Fractional Abundance data point to a total of100.

Data labels

Appears in options for all Data Visualization charts
A data label appears by default for each point in the chart, but you can clear the
checkbox to remove the labels.

Grid Lines

Appears in options for all charts
Gridlines appear by default. You can clear the check box to remove them.

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Chapter 8 Data Analysis Module Overview

To select chart scale and label options
1.

Click theicon in the upper-left corner of the chart to display the corresponding chart options.

2.

To manually define the chart scale, select Fixed.
Note: Auto is the default setting.

3.

In the Min, Max, and Inc fields, enter your lower and upper limits, and the increment, for the y axis.
For 2D Amplitude, you can also change the scale on the x axis.

4.

For Concentration, Copy Number, Ratio, Fractional Abundance, and Event Counts, select an option
for a secondary y axis display. To change to a base 10 logarithmic scale on the y axis, select the Log
checkbox.

5.

For Ratio and Fractional Abundance, to view an inverse calculation, select the Inverse checkbox.

6.

To remove the data labels or grid lines from the display, clear the Data Labels or Grid Linescheckbox.

Using Chart Menu Options

Chart menu options are explained in Table 27.
Table 27. Chart menu options
OptionDescription

Copy

Copies the chart to the clipboard, which you can paste into a separate
document, such as an MS Word file

Save Image as

Saves the chart as an image file

Print

Prints the image

Show Point Values

Shows corresponding point values when you pause on a data point

Tip: Select the Show Point Values checkbox to see the data.

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Chart menu options are available in the following windows:n

1D Amplituden

2D AmplitudenConcentrationn

Copy Number

n

Ratio

n

Fractional AbundancenEvent Counts

To use the chart menu options
1.

Select one or more wells in the Well Selector.

Corresponding data appears in the Well Data table and the chart.

2.

3.

In the upper-right corner of the chart, click the menu icon () and select from the dropdown list.

nSelect Copy to copy the chart to the Clipboard. To paste the data, navigate to the location (suchas a Word file), right-click and select Paste.

n

Select Save Image As and follow the prompts to save the file.

nSelect Print and follow the prompts to print the image.

Click anywhere in the display to close the dialog box.

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Chapter 8 Data Analysis Module Overview

Using Table Menu Options

Table menu options are explained in Table 28.
Table 28. Table options

OptionDescription

Copy

Copies the information from the selected wells to the clipboard

Export to Excel

Exports the data to an .xlsx file

Export to CSVExports the data to a .csv file

Show/HideAdd or remove columns from a table display

Columns

When you select Show/Hide Columns, the following dialog box opens. Select or clear
check boxes to show or hide columns in the data table.

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Table menu options are available in the following windows:n

1D Amplituden

2D AmplitudenConcentrationn

Copy Number

n

Ratio

n

Fractional AbundancenEvent Counts

Tip: You can access the menu icon from the individual windows, or from the windows in the
Dashboard display.

To use the table menu options
If you are using these options in the Data Table, skip to Step 3.
1.

Select wells in the Well Selector.

Corresponding data appears in the Well Data table.

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Chapter 8 Data Analysis Module Overview

2.

In the upper-right corner of the table, click the menu icon (n) and select from the dropdown list.

To copy the data from the selected wells to the Clipboard, select Copy.
Note: To paste the data, navigate to the location (for example, an Excel file) and thenright-click and select Paste.

n

To export your data, select Export to Excel or Export to CSV, and then follow the prompts to savethe file.
Note: Exporting to Excel exports the data in spreadsheet format, while Exporting to CSV
exports the data in comma-delimited format.

n3.

To show or hide the corresponding column in the table, select Show/Hide Columns, and thenselect or clear checkboxes.

Click anywhere in the display to close the dialog box.

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Analysis Dashboard

Analysis Dashboard
When you open a data file, the Analysis module opens to a Dashboard window containing default analysis
and data panes in a summary view. You can customize the view to change panes, or increase or
decrease the number of panes.

Note: If you open a .qlps file, the Plate Editor opens as the default view and you must select the
Dashboard tab to open it.
From the tabs on the left, you can access plate views, amplitude charts, data visualization distribution
charts, droplet counts, and a complete data table. You can also view data specific to the run in the Run
Information window, and run reports on any of the analysis charts from the Reports window.

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Chapter 8 Data Analysis Module Overview

Modifying the Dashboard Display
You can modify the column number and row number to display any or all of the analysis windows
simultaneously.

To change the number of windows in the display
1.

Click the dropdown arrow for Rows and then select a different number.

2.

Click the dropdown arrow for Columns, and then select a different number.

You can also use the dropdown menus to change the windows that appear in the Dashboard.

To display a different window in a particular Dashboard slot
1.

Click the dropdown arrow in the upper-right corner to display the list of available windows, and thenselect a window. The dropdown list closes and the window changes immediately.

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Dashboard Options
From the Dashboard window, depending on the individual dashboard window you have selected, you can
use a range of options as described below:nWhen you select a window, the options that appear in the menu bar correspond to the options you
see if you open the same window from the side menu. For example, if you select the Concentration
chart in the Dashboard, the Concentration menu options appear.

n

You can reset the entire dashboard display by adding or removing rows or columns to display more or
fewer individual windows. For information, see Modifying the Dashboard Display on page 114.

Click Default View to return to the default display of two rows and two columns.
nFrom any window you canoExpand or collapse the windowoCopy, save, or print the imageoSelect display, scale, axis, and logarithmic optionso

Use the dropdown list to replace the current display with a different displayo

Use the menu bar options for the particular chart type

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Chapter 8 Data Analysis Module Overview

Table 29 describes the option sets identified in the following graphic.

Table 29. Dashboard options

Item

Description
Border to identify selected window
Toolbar corresponding to the selected window type in the Dashboard
Dropdown arrow to replace the current display with a new display
Chart options

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APF Results Dashboard

APF Results Dashboard
The APF Results tab appears in the Analysis module tab layout if the experiment was run using an APF.
When you select APF Results, the corresponding window opens in a dashboard layout. In the following
example, the plate is color-coded in accordance with the visual setup in the APF. For information on
setting up an APF, see the QX Designer User Guide.

The dashboard displays the following windows:nPlate layout (upper-left) showing processed wells.

nResults (upper-right) for the selected wells.

nToggle button to the Results Data Table, and then back to APF Results (top-right).

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Chapter 8 Data Analysis Module Overviewn

2D Amplitude display for the selected wellsnOther information specified in the APF, including sample ID, quality rule failures, and lot information
recorded for the plate run

The APF Results dashboard is a static display and the windows cannot be changed. In the Universal
Options toolbar, you can also select APF Tools and choose to reanalyze the file. See Reanalyzing the
Run File for more information.

Reanalyzing the Run File
You can use the reanalysis tool if an APF was selected for the run.

To reanalyze the run file1.

In the Analysis module, click APF Tools > APF Reanalysis.

The APF Reanalysis window appears, with the APF package used in the run selected by default.

Note: If you select the Browse for APF package, you must select a package with the same plate
configuration or you will receive an error message.
2.

(Optional) Under Output and filename, enter a new file name.

3.

(Optional) Select the run thresholding algorithm and click Apply.

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Plate View Windows

Plate View Windows
In the QX Manager Software Analysis module you can open the following windows that contain data on all
wells in the run:n

Plate Editor (analysis view) — Displays the experiment type, sample names, sample types,
supermixes, and assay type for each well in the run (similar to the Template Setup Plate Editor)n

Plate View — Displays concentration results in a text format for each processed welln

2D Plate View — Displays a two-dimensional amplitude chart for each processed well

Plate Editor — Analysis View
You can use the Plate Editor tab in the Analysis module to select wells, and then view or change theexperiment parameters. Similar to other Plate Editor displays, the Analysis Plate Editor displays theexperiment information for each well in the run.
Wells you select in the Analysis Plate Editor determine the data initially displayed in other analysis
windows.

Note: If an APF was selected for the run, fields that were automatically populated from the APF aregrayed out.

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Chapter 8 Data Analysis Module Overview

Plate View
The Plate View tab provides, within the plate layout grid, a text view of the calculated concentration foreach target in each well processed in the run. For information on the concentration results in chart format,
see Concentration on page 152.

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Plate View Windows

2D Plate View
To facilitate comparisons of amplitude in the processed wells, the Plate 2D tab provides a
two-dimensional amplitude view in a separate chart for each well in a single display. To see a larger
representation of a well, select the well in the 2D Amplitude view.

To view different color arraysu

Select the channel combination from the dropdown on the left, and then click Update Grid.

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Chapter 8 Data Analysis Module Overview

Data Windows
Important: For information on the APF Results table, see APF Results Dashboard on page 117.
QX Manager Software provides the following table views for your well and run data:nData Table — available from the main tabs on the left, shows your configured experimentparameters, plus all calculations from the run
Note: You can display the data in individual well format, merged format, or both.

nPlate Well Data Table — available in plate setup windows (including the Analysis module Plate
Editor), shows only your configuration information for each individual wellnAnalysis Well Data Table — available in the Analysis module, shows a subset of configuration andrun data for the wells selected in the Well Selector

Data Table Tab
The Data Table window contains columns of data generated for each target in each well, as droplet
clusters are identified through thresholding or manual clustering tools.

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Data Table Column Definitions
Table 30 defines each field in the Data Table.
Table 30. Data Table columns

Column nameContent description

Well

The well location in the plate
Note: The instrument accepts 96-well plates only.

Well TypeAPF only — user can select Plate, Well, or Sample, acalculation basis for analysis data

Sample ID

APF only — a unique ID for a particular sample

Patient ID

APF only — a secondary ID to align with a first-level ID

Sample description 1

Words or phrases to describe the sample in each wellSample description 2

Note: Only the sample description 1 data appears in plate

Sample description 3

layout views but you can pause on a well in the Plate

Sample description 4

Editor to display a tool tip containing the entries in allcompleted Sample description fields.

TargetTarget name from Plate Editor tab

Conc(copies/µL)

Concentration of the target molecules recorded as copies per
microliter

pg/µL
StatusMass concentration of DNA in the well in pg/µL
Contains either Check, OK, Multi, or Manualn If Check, either the automatic analysis for the well failed or
fewer than 10,000 droplets were counted in the welln If OK, enough droplets were counted to trigger automatic
analysisn If Multi, the data was automatically analyzed as part of amulti-well selectionn If Manual, the droplets were analyzed manually

Status Reason

Identifies the reason for the status (unsuccessful automatic
analysis, not enough droplets counted, or droplets analyzed
manually)

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Table 30. Data Table columns, continued

Column nameContent description

Experiment

Experiment type selected for the well in the Plate Editor

SampleType

Sample type selected for the well in the Plate Editor

TargetType

Target type selected for each dye (FAM or EvaGreen® andHEX or VIC) in the Plate Editor

Supermix

Supermix selected for the well in Plate Editor

DyeName(s)Dye assigned to channels 1 and 2, respectively, for the well in
the Plate Editor

Copies/20µLWell

Concentration of the target normalized to a volume of 20 µL

TotalConfMax

For merged wells the high error bar for the target concentrationof the combined wells at a 95% confidence interval

TotalConfMin

For merged wells the low error bar for the target concentrationof the combined wells at a 95% confidence interval

PoissonConfMax

Maximum target concentration normalized for the high error
bar of the droplet Poisson distribution for the 95% confidence
interval

PoissonConfMin

Minimum target concentration normalized for the low error barof the droplet Poisson distribution for the 95% confidence
interval

Accepted Droplets

Total number of droplets accepted by quality algorithm

Positives

Number of droplets that contain the target

Negatives

Number of droplets that do not contain the target

Copies/µl linked molecules

Shows number of copies of a target that are present inoverabundance versus the expected value in copies per µL

CNV

Copy number calculated for the target relative to the reference

TotalCNVMax

For merged wells, the high error bar for the copy number of the
combined wells at a 95% confidence interval

TotalCNVMin

For merged wells, the low error bar for the copy number of the
combined wells at a 95% confidence interval

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Data Windows

Table 30. Data Table columns, continued

Column nameContent description

PoissonCNVMax

Maximum copy number normalized for the high error bar of thedroplet Poisson distribution for the 95% confidence interval

PoissonCNVMin

Minimum copy number normalized for the low error bar of thedroplet Poisson distribution for the 95% confidence interval

ReferenceCopies

Copy number identified for the reference target in the Plate
EditorDefault is 2, indicating 2 copies per diploid genome.

UnknownCopies

This field is currently unused in QX Manager Software

Threshold1

Threshold value of first threshold line from left to right andbottom to top

Threshold2

Threshold value of second threshold line from left to right andbottom to top

Threshold3

Threshold value of third threshold line from left to right andbottom to top

ThresholdSigmaAbove

Distance of the threshold from the mean of the negative
cluster, as a multiple of the negative cluster standard deviation

ThresholdSigmaBelow

Distance of the threshold from the mean of the positive cluster,
as a multiple of the positive cluster standard deviation

ReferenceUsed

Identifies which target was used as a reference

Ratio

The ratio of the target against the identified reference

TotalRatioMax

For merged wells the high error bar for the ratio of the unknown
against the reference of the combined wells at a 95%
confidence interval

TotalRatioMin

For merged wells the low error bar for the ratio of the unknown
against the reference of the combined wells at a 95%
confidence interval

PoissonRatioMax

Maximum ratio of the unknown against the reference
normalized for the high error bar of the droplet Poisson
distribution for the 95% confidence interval

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Table 30. Data Table columns, continued

Column nameContent description

PoissonRatioMin

Minimum ratio of the unknown against the reference
normalized for the low error bar of the droplet Poisson
distribution for the 95% confidence interval

FractionalAbundance

Calculation of fractional abundance of this unknown target vs.
the reference target

TotalFractionalAbundanceMax

For merged wells the high error bar for the fractional
abundance of the combined wells at a 95% confidence interval

TotalFractionalAbundanceMin

For merged wells the low error bar for the fractional abundanceof the combined wells at a 95% confidence interval

PoissonFractionalAbundanceMax

Maximum fractional abundance normalized for the high error
bar of the droplet Poisson distribution for the 95% confidence
interval

PoissonFractionalAbundanceMin

Minimum fractional abundance normalized for the low error barof the droplet Poisson distribution for the 95% confidence
interval

MeanAmplitudeOfPositives

Mean amplitude value of all droplets that contain the target

MeanAmplitudeOfNegatives

Mean amplitude value of all droplets that contain no target

MeanAmplitudeTotal

Mean amplitude value of all droplets

ExperimentComments

Data populates this field only from files created in
QuantaSoft™ versions 1.4 – 1.7, if comments were added.

MergedWells

Identifies which wells were merged together

TotalConfidenceMax68

For merged wells the high error bar for the target concentrationof the combined wells at a 68% confidence interval

TotalConfidenceMin68

For merged wells the low error bar for the target concentrationof the combined wells at a 68% confidence interval

PoissonConfidenceMax68

Maximum target concentration normalized for the high error
bar of the droplet Poisson distribution for the 68% confidence
interval

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Table 30. Data Table columns, continued

Column nameContent description

PoissonConfidenceMin68

Minimum target concentration normalized for the low error barof the droplet Poisson distribution for the 68% confidence
interval

TotalCNVMax68

For merged wells the high error bar for the copy number of the
combined wells at a 68% confidence interval

TotalCNVMin68

For merged wells the low error bar for the copy number of the
combined wells at a 68% confidence interval

PoissonCNVMax68

Maximum target concentration normalized for the high error
bar of the droplet Poisson distribution for the 68% confidence
interval

PoissonCNVMin68

Minimum target concentration normalized for the low error barof the droplet Poisson distribution for the 68% confidence
interval

TotalRatioMax68

For merged wells the high error bar for the ratio of the unknown
against the reference of the combined wells at a 68%
confidence interval

TotalRatioMin68

For merged wells the low error bar for the ratio of the unknown
against the reference of the combined wells at a 68%
confidence interval

PoissonRatioMax68

Maximum ratio of the unknown against the reference
normalized for the high error bar of the droplet Poisson
distribution for the 68% confidence interval

PoissonRatioMin68

Minimum ratio of the unknown against the reference
normalized for the low error bar of the droplet Poisson
distribution for the 68% confidence interval

TotalFractionalAbundanceMax68

For merged wells the high error bar for the fractional
abundance of the combined wells at a 68% confidence interval

TotalFractionalAbundanceMin68

For merged wells the low error bar for the fractional abundanceof the combined wells at a 68% confidence interval

PoissonFractionalAbundanceMax68

Maximum fractional abundance normalized for the high error
bar of the droplet Poisson distribution for the 68% confidence
interval

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Table 30. Data Table columns, continued

Column nameContent description

PoissonFractionalAbundanceMin68

Minimum fractional abundance normalized for the low error barof the droplet Poisson distribution for the 68% confidence
interval plate list after correcting the issue

TiltCorrected

Indicates if tilt correction was applied to the well
Note: Tilt correction rotates the angles from the doublenegative cluster centroid to each droplet, such that thetwo single positive cluster centroids are orthogonal withthe double-negative cluster centroid.

Ch1+Ch2+

Number of droplets that contain both channel 1 and channel 2targets

Ch1+Ch2-

Number of droplets that contain just the channel 1 target

Ch1-Ch2+

Number of droplets that contain just the channel 2 target

Ch1-Ch2-

Number of droplets that contain neither channel 1 nor channel
2 targets

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Plate Editor Well Data Table
A well data table containing both configuration and run data appears in the analysis windows, next to theWell Selector. This table displays a subset of data columns for only the wells selected in the Plate Editor
or Well Selector. Table 31 defines each column in the consolidated table.
Table 31. Fields in the Analysis Well Data table

Column nameContent description

Well

The well location in the plate the sample is from

Perform Droplet Reading

Yes or No

Experiment Type

Experiment type from the Plate Editor

Sample description 1 – 4The sample name used to identify the well in the Plate Editor tab

SampleType

Sample type from the Plate Editor

Supermix Name

Supermix from the Plate Editor

Assay type

Assay type selected in the Plate Editor

Target Name

Target Name from Plate Editor tab

TargetType

Target type assigned to the target in the Plate Editor

Signal Ch1

Selected fluorophore in Channel 1

Signal Ch2

Selected fluorophore in Channel 2

Reference Copies

Copy number identified for the reference target in the Plate Editor tab

Well Notes

Entries by the user

Plot?

If selected, target will be used to calculate the copy number for the well

RDQ Conversion Factor

The Residual DNA Quantification conversion factor for the well
Note: RDQ is only available in Residual DNA Quantification
experiments.

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Chapter 8 Data Analysis Module Overview

Analysis Windows
In its Analysis module, QX Manager Software provides amplitude displays and data visualization charts in
the Analysis module. For more information on each chart, see Chapter 9, Data Analysis Methodology.

Amplitude Charts
Amplitude charts illustrate the droplets by degree of dye fluorescence. QX Manager Software displays
fluorescence for positive and negative targets identified with FAM/EvaGreen® and HEX/VIC fluorophores
in the following analysis windows:n

1D Amplituden

2D Amplitude

Data Visualization Charts
Data visualization charts show calculations based on positive droplet concentrations. QX Manager
Software counts the number of positive and negative droplets for each fluorophore in each sample, andthen fits the fraction of positive droplets to a Poisson algorithm to determine the starting concentration of
the target DNA molecule in units of copies/µl input in the following analysis windows:nConcentrationn

Copy Number

n

Ratio

n

Fractional Abundance

When you open the analysis data file in QX Manager Software and select one or more wells in the grid,
the software plots each calculated Poisson distribution average as a data point in the grid. You can pause
on the data point to see the high, median, and low numbers.
Note: You can display the data using a confidence level of either 68% or 95% (default setting).

Event Counts
Event counts record the number of droplets in which the target was found (positive) and was not found(negative). The Event Counts tab shows a bar chart view of the number of positive, negative, and total
droplets for each of the targets in each of the selected wells.

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Viewing Run, Lot, and Audit Information
Use the Run Information window to view the information about the plate and run. You can also view or add
post-run notes regarding the plate. In Premium Edition, you can also view lots used, the audit logs, and
APF information.

If an APF was used in the run, then the Run Information windows displays the APF information on theright.

For information on displaying your used lots in the Run Information window, see Showing Lots in Run
Information Reports on page 132.
You can also view the Audit Log. For information, see Viewing the Audit Log on page 133.

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Chapter 8 Data Analysis Module Overview

Showing Lots in Run Information Reports
After you have set up your lots, you can ensure they appear in the Run Information screen when you open
a file for analysis.

To show the lots in Run Information
1.

Click Add Plate, then click Configure Plate.

2.

Select the Lot Selector tab.

3.

For kit lots, consumables, and reagentsa.

Select a tab.

a.

Select a lot for the run.

b.

Click Select Lots.

4.

Continue setting up the plate until the Start Run button is enabled.

5.

Click Start Run.

6.

When the run is completed, open the analysis file.

7.

Click the Run Information tab to see the used lots.

To show the lots in a reportuEnsure the Lot Information check box is selected in the report elements before running .the report.

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Viewing the Audit Log
You can view the audit log entries for the data file using the Audit Log viewer found in the Run Information
tab in the Analysis module.

To view the Audit Logu

In the Analysis module, select the Run Information tab, and then select the Audit Log tab to display
the audit log entries.

If the run used an APF, the APF package identifier appears in the gray banner above the window, but thecolumns are the same as the display for a standard run.
Tip: To expand the table to display more rows, click Expand All.

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Chapter 9 Data Analysis Methodology
As summarized in Chapter 8, Data Analysis Module Overview, the software presents analysis data inseveral different formats. When you open the data file in the Analysis module, you can view the data withthe automatic analysis thresholds and calculations or you can choose different options to recalculate,
replot, or recolor the results.
Data is shown in the following formats:n

Amplitude, which shows each droplet in each well in a scatter plot, in one-dimensional or twodimensional viewsnData visualizations, which show estimated target molecule concentration, ratio, and fractional
abundance of one target against another target based on selected error model and confidence
interval
Note: Copy number variation is also calculated if the user ran a CNV experiment.

nEvent counts, which are precise counts of positive and negative droplets for each target in each well

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Chapter 9 Data Analysis Methodology

Amplitude Plot Analysis Options
QX Manager Software provides two amplitude plot displays in which you can view the data with automaticthresholding where applicable, or choose different options to replot or recolor the results.
In the 1D amplitude and 2D amplitude plots, you cannShow well calculations
Note: The 1D amplitude plot shows the data for each selected well in its own section, while the2D amplitude plot shows all selected wells together.

nModify automatic thresholds calculated by QX Manager Software
Important: If the data file contains calculations defined in an APF, they are displayed in the topright table of the APF Results dashboard. If you manually change thresholds in the amplitudedisplays, those calculations are affected and the original data in the table is overwritten.

nView data in a heat mapnView histograms (1D amplitude tab only)nRe-apply automatic analysisnApply tilt correction to automatic analysis

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Table 32 explains the analysis options that are available in both 1D amplitude and 2D amplitude plots.
Table 32. 1D and 2D amplitude tool options

Icon

Mode

Description
Data appears with the thresholds or clusters

View mode

assigned by QX Manager Software.
When this icon is selected, the view is locked andyou cannot modify the thresholds.

Heat map

Shows the distribution of droplets, with higher
density of droplets shown as hot.

Automatic analysis

Disables tilt correction and automaticallyreanalyzes the data.
Enables tilt correction and automaticallyreanalyzes the data.

Automatic analysis withtilt correction

Note: Tilt correction rotates the angles fromthe double-negative cluster centroid to each
droplet, such that the two single positive
cluster centroids are orthogonal with the
double-negative cluster centroid.

Reset

Resets the data to the original automaticallyanalyzed data.
Choose whether to display axis with channel

Chart display options

number or fluorophore, and change the size ofaxis markers, data labels, and axis labels.

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Chapter 9 Data Analysis Methodology

Table 33 explains the analysis options available only for 1D amplitude plots.
Table 33. 1D amplitude tool options

Icon

Mode

Automatic thresholding

Description
Individual Wells: Clusters are generated for each selected well
separately.
Combined Wells: Droplets from all selected wells are combined, andclusters are generated on that combined set.
Positive Control Wells: Thresholds are generated for each channel
based on any positive controls currently selected, and applies thosethresholds to all currently selected wells.
Note: If you change the thresholds manually, you can click
Reset to return to the automatic thresholds.

Threshold, single

For a single well or multiple wells, the user can manually input

wellthresholding values in the 1D amplitude plot.
You can click anywhere in the plot to apply threshold lines to the data.

Threshold, multiple

Important: Thresholding options are disabled if an APF was

wells

used in the run, and was configured to disallow manual data fileanalysis.

To adjust the threshold valuesn Drag the lines horizontally in the plot arean Enter a new threshold value in the boxes at the end of eachthreshold linen Click the up and down arrows to incrementally adjust the numbers
Threshold, single

For a single well or multiple wells, QX Manager Software

well SD

automatically calculates and populates thresholding values withThreshold, multiple

standard deviations (SD).

wells SD

Important: SD thresholds are not recommended for RMD, sincethese clusters are not typically located at right angles to eachother.
Note: The SD thresholds are set at a limit that is less than themean number of positive targets, and more than the mean
number of negative targets. Starting from where the user clicks
in the plot, SD locates the threshold between the positive andnegative clusters such that the classification error is minimized.

Show histogram

Hides or displays histogram plots for 1D amplitude

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Table 34 explains the analysis options available only for 2D amplitude plots.
Table 34. 2D amplitude tool options

Icon

Mode

Automatic thresholding

Description
Individual Wells: Clusters are generated for each selected well
separately.
Combined Wells: Droplets from all selected wells are combined, andclusters are generated on that combined set.
Positive Control Wells: The software generates thresholds for eachchannel based on any positive controls currently selected, and applies
those thresholds to all currently selected wells.
Note: If you change the thresholds manually, you can click Resetto return to the automatic thresholds.

Threshold line

Use the Threshold line icons to establish thresholds across a pair ofchannels, dividing droplets into distinct clusters separated by different
colors.
You can click anywhere in the plot to apply threshold lines to the data.
To adjust the threshold values, you cann Drag the lines horizontally or vertically in the plot arean Enter a new threshold value in the boxes at the end of eachthreshold linen Click the up and down arrows to incrementally adjust the numbers

Threshold line SD

QX Manager Software automatically calculates and populates
threshold line values with standard deviations (SD).
Important: SD thresholds are not recommended for RMD, sincethese clusters are not typically located at right angles to eachother.
Note: The SD thresholds are set at a limit that is less than themean number of positive targets, and more than the mean
number of negative targets. Starting from where the user clicks inthe plot, SD locates the threshold between the positive andnegative clusters such that the classification error is minimized.

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Chapter 9 Data Analysis Methodology

Icon

Mode

Description

Threshold cluster

Use the Threshold Cluster icons to establish thresholds across a pairsquareof channels, dividing droplets into distinct clusters separated byThreshold cluster

different colors.

circleTo classify your droplets, you canThreshold clustern Click any of the three Threshold Cluster Mode buttons (square,

freeform

circle, or free form)n Draw the chosen shape around the cluster of droplets
Note: When using the cluster mode tools to draw a shape arounda cluster of droplets, a dialog box with color selections by target
appears in the window to help you select the correct target
combination.

Target names are shown along the two axes based on the signal
values assigned during plate setup. Click the colored box that best
represents the location of the cluster of droplets selected toautomatically classify the droplets as positive or negative for eachgiven target.
Note: The Cluster dialog box display varies according to the plexmode.

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1D Amplitude
Use the 1D Amplitude analysis window to view droplet amplitudes for each channel, in selection order, foreach well selected in the Well Selector.

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Chapter 9 Data Analysis Methodology

The 1D Amplitude plots illustraten

All accepted droplets, with a visual representation of the positive and negative droplets in each welloPositive droplets appear in color, while negative droplets appear in gray.

o

The Well Selector displays an A in each well where QX Manager Software automaticallythresholded the droplet data. An M appears in any well in which you manually changed thethreshold.

n

Amplitude in a histogram plot

Note: The Histogram icon is enabled by default so a Histogram plot appears automatically foreach fluorophore (channel).
n

Amplitude in a Heat Map view

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When you select the 1D Amplitude tab, the toolbar options that allow you to change thresholds and showor hide the heat map and histogram appear above the plots.

Note: For detailed information on each toolbar option, see Amplitude Plot Analysis Options on page
136.
Default color assignments for 1D amplitude plots are
Positive FAM

=

Blue

Positive HEX

=

Green

Negative=

Gray

The images in this section display data from a direct quantification experiment involving two targets:
Negative droplets appear in grayscale in each plot.

For experiments where enough droplets are recognized, QX Manager Software automatically configures
an amplitude threshold, which distinguishes between positive and negative droplets.
Note: Well data must meet certain quality metrics (minimum of 10,000 droplets) before the software
will automatically calculate a threshold above which droplets are considered positive. You can use
the manual thresholding tools to ensure correct quantification of positive and negative droplets.

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Chapter 9 Data Analysis Methodology

By default, the Histogram icon (.

) is enabled so the Histogram plot automatically appears with theamplitude plot.

To manually adjust the thresholds
1.

Select one or more wells.

2.

Click any of the threshold icons () to set manual thresholds:nRegular threshold for a single well; when multiple wells are selected, you can set a different
threshold for each welln

Regular threshold for multiple wells, where you can set one threshold for all selected wellsnStandard deviation threshold for a single well; when multiple wells are selected, you can set a
different threshold for each wellnStandard deviation for multiple wells, where you can set one threshold for all selected wells

3.

Click on the location in the plot where you want to draw the new threshold.

4.

When the line appears, use the up or down arrows, or click and drag the threshold, to adjust thelocation.

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QX Manager Software displays the manual threshold and changes the color of the droplets that are
now above or below the threshold.
Note: You can also manually enter a threshold number.
When you manually modify a threshold, the well selector displays an M for manual instead of the A for
Automatic.

5.

(Optional) To reset to the automatic threshold, click Auto.

6.

(Optional) To adjust the automatic threshold to consider tilt correction, click Auto with Tilt.

7.

(Optional) To reset everything to the original display, click Reset.

To view a heat map representation of the plot datau

Click the heat map () icon.

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Chapter 9 Data Analysis Methodology

2D Amplitude
For the wells you select in the analysis view of the Plate Editor, the 2D Amplitude window illustrates
fluorescence for two targets. The images in this section display data from an experiment involving twotargets. The plot shows individual cluster representations for first and second target positive droplets,
droplets containing both targets, and droplets containing neither target.

When you select the 2D Amplitude tab, the toolbar options allow you to change thresholds, manuallycluster wells, and show or hide the heat map above the plots.

For detailed information on each toolbar option, see Amplitude Plot Analysis Options on page 136.

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Default color assignments for 2D amplitude plots are:
Positive FAM

=

Blue

Positive HEX/VIC

=

Green

Positive FAM and HEX/VIC=

Orange (may appear brown on some monitors)

Double negative

=

Gray

Note: Well data must meet certain quality metrics (minimum of 10,000 droplets) before QX Manager
Software will automatically calculate a threshold above which droplets are considered positive. You
can use the manual thresholding tools to ensure correct quantification of positive and negative
droplets.

To use the 2D amplitude tools
1.

Open your data file in the Analysis module and select the 2D Amplitude tab.

2.

Choose a threshold line or cluster option.
Note: Use the cluster option when the data is not orthogonal and the threshold lines do notadequately divide the populations of droplets.
n

To adjust threshold lines, select a threshold line type () and then click in the plot to apply

crosshair lines. Use any of the following methods:oDrag the lines horizontally or vertically in the plot area.

oEnter a new threshold value in the boxes at the end of each threshold line.

o

Tap the up and down arrows to incrementally adjust the numbers.

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Chapter 9 Data Analysis MethodologynTo adjust thresholds using the cluster option, select a cluster type () and draw thechosen shape around the cluster of droplets to classify.

3.

(Optional) To reset to the automatic threshold, click Auto.

4.

(Optional) To adjust the automatic threshold to consider tilt correction, click Auto with Tilt.

5.

(Optional) To reset everything to the original display,click Reset.

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Data Visualization Chart Analysis Options
QX Manager Software also provides chart displays where you can view the data from the original
calculations, or choose different options to recalculate the results.
In charts reflecting Data Visualization distributions, you cannShow individual or merged well datan

Change the error model and confidence level

Note: For event counts, you can also alter the view mode to see positive, negative, or all droplet
counts.
Table 35 explains the available options.
Table 35. Chart tool options for Data Visualization distribution charts
Icon

Mode

Description

Show bothShows the calculated total or
percentage as a merged calculation for
all selected wells and as an individual
calculation for each selected wellShow merged

Shows the calculated total or
percentage as a combined number for
all selected wells with the same
parameters
Note: Well setup must match foreach well before the software canmerge them.

Show individualShows the calculated total or
percentage as an individual calculationfor each selected well

X-axis wellShows the well number on the x axis

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Chapter 9 Data Analysis Methodology

Icon

Mode

Description

X-axis sample

Shows a partial sample name on the xaxis
Note: You can select Well andSample simultaneously.

Error model andSelect an error model and confidence

confidence interval

level
Note: The default choices are
Poisson and 95%, to yield thehighest confidence in the results.

Important: The software uses thefollowing multipliers in its
calculations:n For 95% confidence interval, thesigma multiplier is 1.96
n For 68% confidence interval, thesigma multiplier is 1.0

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Table 36 identifies the additional options available in the Event Count window. These options areavailable for event counts only.
Table 36. Additional options for event counts
Icon

Mode

Description

View mode

Displays in a bar chart the number of positive droplets for each target inpositiveeach well

View mode

Displays in a bar chart the number of negative droplets for each target innegativeeach well

View mode

Displays in a bar chart the number of total droplets in each well

total

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Chapter 9 Data Analysis Methodology

Concentration
Concentration measures the number of copies of the target molecules in each µl of sample based on thedefault settings. Use the toolbar to merge or separate the calculated results for each well, and torecalculate your results based on a different error model and confidence interval.
For information on toolbar options, see Data Visualization Chart Analysis Options on page 149.

QX Manager Software plots the averaged concentration for each target as a data point. Pause on a data
point to see the high, median, and low numbers.

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Concentration Calculation
The software uses the formula and variables shown below.

Where:-ln

Negative natural logarithm

Vdroplet

Volume of droplet

Nneg

Number of negative dropletsN

Total number of droplets

Note the following:n

The droplet volume used by QX Manager Software, v1.2 and earlier, is defined as 0.85 nL.

n

The droplet volume used by QX Manager Software, v2.0 is updated to 0.795 nL.

nBoth volumes are available in QX Manager Software, v2.1.

This droplet volume change provides improved accuracy of measurements on the QX200 Droplet
Reader, and can result in concentrations that are 7% to 8% higher in experiments where all othervariables are identical. System precision is unchanged.

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Chapter 9 Data Analysis Methodology

Confidence Interval Calculation
Note: If you select a 68% confidence interval, the multiplier is changed from 1.96 to 1.00.

Where:

Vdroplet

Volume of droplet

Nneg

Number of negative dropletsN

Total number of dropletsp

p-value (probability of finding the target in the sample)

¶∂

Delta

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Copy Number
Important: To see copy number variation data, you must run a copy number variation (CNV)
ddPCR experiment.
Copy number measures the count of the target gene, relative to the reference gene, to calculate thenumber gene targets per genome. Use the toolbar to merge or separate the calculated results for eachwell, and to recalculate your results based on a different error model and confidence interval. For
information on toolbar options, see Data Visualization Chart Analysis Options on page 149.

The following image displays copy number data, across a sequence of wells.

QX Manager Software plots each copy number variation as a data point. Pause on a data point to see thehigh, median, and low numbers.

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Chapter 9 Data Analysis Methodology

Copy Number Calculation
The software uses the formula and variables shown below.

Where:A

Target concentration

B

Reference concentration

NB

Number of reference copies in genome (usually 2)

Confidence Interval Calculations
Note: If you specify the lesser confidence interval when you define your error model, the softwareuses 68% in its calculations instead of 95%.

.

Where:A

Target concentration

B

Reference concentration

NB

Number of reference copies in genome (usually 2)

CIA

Poisson confidence interval of target (95% max - 95% min)CIB

Poisson confidence interval of reference (95% max - 95% min)

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Notes:
Copy Number analysis involves determining the number of copies of a given target DNA sequence ascompared to an invariant reference DNA sequence. Use the CNV analysis to determine structuralvariations, such as ploidy changes (addition or deletion of chromosomes), deletions (missing partial
chromosomes) or duplications (repeated target sequences) in the genome.
The ability to discriminate between consecutive CN states has been a technical challenge in copy number
assessment. Fundamentally, as CN state increases, the percentage difference in target genomic material
between states decreases. For example, for a given target locus, a CN of 3 is 50% more abundant inconcentration per genome than a CN of 2, while a CN of 5 is only 25% more abundant per genome than a
CN of 4, and so on.
Due to the massive partitioning of the reaction across up to 20,000 droplets per well, and the absolutenature and precision of the ddPCR concentration measurement, ddPCR CNV analysis enables thequantitative discrimination required to resolve consecutive copy number states beyond CN 3. For
example, a 20% difference in target concentration between a CN 5 versus CN 6 sample can be
reproducibly resolved using ddPCR. This discrimination is both a function of concentration differences
between consecutive CN states, as well as the amount of DNA assayed per well.

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Chapter 9 Data Analysis Methodology

Ratio
Ratio determines the quotient of two target molecules in each µl of sample based on the default settings.
T1:T2
Use the toolbar to merge or separate the calculated results for each well, and to recalculate your results
based on a different error model and confidence interval. For information on toolbar options, see Data
Visualization Chart Analysis Options on page 149.

The following image displays ratio data, across a sequence of wells.

QX Manager Software plots each ratio as a data point. To see the confidence level numbers, pause on thedata point.

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Ratio Calculation
The software uses the formula and variables shown below.

Where:A

Target concentration

B

Reference concentration

Note: If no reference is selected, the target with the highest dye concentration in the highest channel
will automatically be considered as the reference. If multiple references are selected, the geometricmean is used.

Confidence Interval Calculations
Note: f you specify the lesser confidence interval when you define your error model, the softwareuses 68% in its calculations instead of 95%.

Where:A

Channel 1 target concentration

B

Channel 2 target concentration

CIA

Confidence interval of Channel 1 target (95% max - 95% min)

CIB

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Chapter 9 Data Analysis Methodology

Fractional Abundance
Fractional Abundance determines the relative abundance of your targets in each µl of sample based on
the default settings. Use the toolbar to merge or separate the calculated results for each well, and torecalculate your results based on a different error model and confidence interval. For information on
toolbar options, see Data Visualization Chart Analysis Options on page 149.

The following image displays fractional abundance data across a sequence of wells.

QX Manager Software plots the fractional abundance as a data point. To see the high and low confidence
interval numbers, pause on the data point.

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Data Visualization Chart Analysis Options

Fractional Abundance Calculation
The software uses the formula and variables shown below.

Where:A

Target concentration

B

Reference concentration

Note: If no reference is selected, the target with the highest dye concentration in the highest channel
will automatically be considered as the reference. If multiple references are selected, the geometricmean is used.

Confidence Interval Calculations
Note: If you specify the lesser confidence interval when you define your error model, the softwareuses 68% in its calculations instead of 95%.

Where:A

Channel 1 target concentration

B

Channel 2 target concentration

CIA

Confidence interval of Channel 1 target (95% max - 95% min)

CIB

Confidence interval of Channel 2 target (95% max - 95% min)User Guide | 161

Chapter 9 Data Analysis Methodology

Event Counts
The Event Counts tab shows a bar chart view of the number of positive and negative droplets for each of
the targets in each of the selected wells.

Use the toolbar to change the display by combining or separating data for each well. You can also show
data by well name or by sample name, and you can show any combination of positive, negative, or
combined droplet counts.

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Data Visualization Chart Analysis Options

Linkage Analysis
In ddPCR, physical linkage of two targets can occur in one of the following patterns:nTandem repeats if the same target sequencenProximity of two target sequences physically linked on the same piece of DNA

QX Manager Software uses the formulas and variables shown below.
n

The following formula presents the linkage in copies per µL:n

The following formula presents the linkage in copies per droplet.

Where:
N

Total number of dropletslnNatural logarithm-ln

Negative natural logarithm

n00

Number of negative droplets for both channels

n01

Number of negative droplets in channel 1 and positive droplets in channel 2

n10

Number of positive droplets in channel 1 and negative droplets in channel 2

Where:

Confidence Interval Calculation

Where:σStandard deviation

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Chapter 10 Analysis Module Reporting
Use the Reporting function to create a variety of reports in the QX Manager Software Analysis module.
You can create reports on the fly from any analysis file or, if you need to generate specific reports on aregular basis, you can set up report templates for reuse.
This section contains information on how to create analysis reports.

Creating Analysis Reports
You can create reports with or without a template. For information on creating templates for reports you
generate often, see Creating or Modifying Report Templates on page 84.

To create a report
1.

Select the Reports tab to display the Reports window.

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Chapter 10 Analysis Module Reporting2.

Do one of the following:n

To create a report from a template, click the Template dropdown arrow and select a templatefrom the listn

To create a custom report, click the arrows to expand reporting categories, and then select thecheckbox for each report element to include, and clear checkboxes for elements to eliminate.
Note: Use the buttons at the bottom of the screen to expand or collapse all categories atonce, or to select or clear all checkboxes at once. You can also drag and drop the section torearrange the order of appearance in the report, and drag and drop items in the section toreorder them.
or

3.

Enter a report title.

4.

(Optional) To restrict viewing, select the Password Encrypt Report checkbox and then enter apassword.

5.

Click Generate Report to generate a PDF report.

6.

To save the report, click Save.

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Chapter 11 Gene Study Module
You access the Gene Study module from the Data Analysis window.

To create a gene study, you add one or more data files and then compare gene expression data from one
or more ddPCR experiments.
Note: The maximum number of samples you can analyze in a gene study is limited by the size of thecomputer’s RAM and virtual memory.

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Chapter 11 Gene Study Module

To open the Gene Study moduleu

Click Gene Study.

The Gene Study dialog box includes two tabs:nStudy Setup — manages the run files in the gene study
Important: Adding or removing data files in a gene study does not change the data in theoriginal file.

nStudy Analysis — displays the gene expression data for the combined runs.

From these tabs you can add files to set up a gene study, analyze your data in charts and plots, and run
reports on the gene study data.

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Gene Study Options

Gene Study Options
The Gene Study module provides the menus and corresponding options described below.
nFile — Open, save, and close the gene study, and add filesnSettings — Restore the default layoutnTools — Create a report

To open a gene study file1.

Click File Ú Open.

2.

In the Open dialog box, navigate to and select the data file, and then click Open.

To save a gene study file1.

Click File and select Save or Save As.

2.

If prompted, enter a file name and click Save.

3.

If prompted to overwrite an existing file, click Yes or No.

To close a gene study fileu

Click File Ú Close.
Note: If you have not saved the file, an advisory prompt appears.

To add data files
1.

Click File Ú Add Data Files.

2.

In the Open dialog box, navigate to the data files to be added to the study.

3.

Select one or more files and then click Open to add the files to the Gene Study window.

To restore default settingsuClick Settings Ú Restore default settings.
Note: At least one modified data file must be open.

To generate a reportu

See Gene Study Reports on page 176.

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Chapter 11 Gene Study Module

Setting up the Gene Study
Use the Study Setup window ton

Add data files to include in the studynRemove data files from the studynSelect data files for viewing and analysisnShow the plate view for a data file

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Setting up the Gene Study

Table 37 defines each column in Study Setup.
Table 37. Gene Study Setup Fields
Column Title

Description

File Name

Name of the data file

Date Created

Date the file was imported into the Gene Study module

Plate View

Opens a map of the plate with the data for each dye in each well included in theGene Study

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Chapter 11 Gene Study Module

Adding Data Files
To add data files
1.

On the Study Setup tab, click Add Data Files.

2.

In the Open dialog box, navigate to the data files to be added to the study.

3.

Select one or more files and then click Open.
The files are added to the Study Setup window.

Removing Data Files
To remove data filesuSelect the checkbox next to the file and then click Remove.
The file is removed from the Study Setup window.
Note: The Remove button is disabled until you select a file.

Selecting Data Files for Analysis
To select data files for analysis
1.

Select the checkboxes next to the files to be included in the analysis.

2.

Select the Study Analysis tab to see the analysis results.

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Setting up the Gene Study

Showing the Plate View
To show the plate view
1.

In the Plate View column, click the button for the plate view to be displayed.

The Plate view appears.

2.

Click Close to close the view.

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Chapter 11 Gene Study Module

Using the Study Analysis Features
The Study Analysis tab displays the data from all runs in the gene study in the views described in Table
38.

Table 38. Analysis Toolbar

ButtonDescription

Bar Chart

Size of bars correspond to normalized expression or relative quantity

Clustergram

Data is arranged in a hierarchy based on the degree of similarity of expression fordifferent targets and samples

Scatter Plot

Dot plot of normalized expression of targets for a control versus an experimental
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Using the Study Analysis Features

Table 38. Analysis Toolbar, continued

ButtonDescription

Volcano Plot

Dot plot of change in expression (regulation) of a target for an experimental sample
compared to a control

Heat Map

Plate layout grid showing target regulation for an experimental compared to a control
sample based on relative normalized expression
Note: If the same targets are in the same location on multiple plates but withdifferent samples, use the dropdown menu to select a particular plate for analysis.

Results Table

Provides results in a tabular format

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Chapter 11 Gene Study Module

Gene Study Reports
Use the Gene Study Report dialog box to arrange the gene study data into a report. Table 34 lists all theoptions available for a gene study report.
Table 39. Gene Study Report Categories
Category

OptionDescription

Report Information

Date, user name, data file name, data file path, and the

Headerselected well group
Gene Study File List

List of all the data files in the gene study

Notes

Notes about the data report

Study Analysis Bar Chart
Analysis Settings

List of the selected parameters

Chart

Gene expression bar chart showing the data

Target Names

List of targets in the gene study

Sample Names

List of samples in the gene study

Data

Spreadsheet that shows the data

Target Stability

Target stability data

Inter-run Calibration

Inter-run calibration data

Study Analysis Clustergram, Scatter Plot, Volcano Plot, and Heat Map
Analysis Settings

Settings for each chart type

Chart

Gene expression chart showing the data

Data

Spreadsheet listing the data in each target

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Gene Study Reports

Creating a Gene Study Report
Before creating a report, make any needed adjustments to the gene study data and charts.

To create a gene study report
1.

Select Tools Ú Reports in the Gene Study menu to open the Report dialog box.

2.

Select the options you want to include in the report.
The report opens with default options selected. Select or clear the checkboxes to change wholecategories or individual options within a category.
For information on the available options to display, see Gene Study Reports on page 176.

3.

Change the order of categories and items in a report.
Drag the options to the required position. Note that Items can be reordered only within the categories
to which they belong.

4.

Click Update Report to update the Report Preview window with any changes.

5.

Print or save the report:a.

Click the Print Report button on the toolbar to print the current report.

b.

Select File Ú Save to save the report in PDF, MHT or MHTML file format and select a location tosave the file.
Note: MHT and MHTML are Microsoft formats.

c.
6.

Select File Ú Save As to save the report with a new name or in a new location.

(Optional) To save the current report settings as a template, select Template Ú Save or Save As.

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Chapter 12 System Utilities
From the System tab, you can manage tasks related to the instrument, software, data, and storage.
nSystem Settings — View shared and assigned storage locations, select an alternate graphics
rendering method, and change the instrument and droplet volume.

n

Event Log — View logged data about all software activities.

n

Maintenance Log — Record maintenance activities.

n

Maintenance Reports — PDF maintenance records from Bio-Rad maintenance.

nSystem Data — Archive raw data to clear up space in your primary storage areas, access data fortroubleshooting, and use the data recovery function.

n

Reprocess Data — Reprocess a .data file using new calibration values.

nTools — Flush or prime the instrument.

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Chapter 12 System Utilities

System Settings Tab
When you select the System tab, the System Settings window opens by default.

n

Use the Datafile and Template Storage tab to view storage locations:oPreferred Locations — if the checkbox selected, storage for all users is limited to a single folder
for data files and a single folder for templates.

oShared Settings — if the Preferred Locations checkbox remains cleared, then shared locations
can be defined, but remain optional. Users can choose to save their files to their personal folders
specified in User Preferences or to the shared location.

Note: The system administrator specifies shared and preferred storage locations, and can also
define a backup location for data file storage if the priority folder is full.
n

Use the Instrument tab to select the instrument model that is connected to QX Manager Software.

n

Use the Software Settings tab to change the graphics rendering method.

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System Settings Tab

Preferred Location
If the administrator sets Preferred Location file paths, then data files and templates for all users areautomatically saved to the specified folders. Preferred Locations override selections in individual user
preferences.
Important: Only users assigned the System Settings user privilege can set preferred locations.

To specify preferred locations
1.

Select the Use for all users checkbox.

2.

(Optional) Keep the default paths or modify them to alternative secure storage locations.

3.

Click Save.

4.

When the confirmation message appears, click OK.

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Chapter 12 System Utilities

Shared Settings
Under Shared Settings, you can choose to save your files to locations that are available to all users.

The software allows the software administrator to set a primary storage folder and a backup storage
folder. Bio-Rad recommends routinely checking available storage space and if necessary, using theArchive function.
Important: Only users assigned the System Settings user privilege (typically your software
administrator) can change storage locations in the System Settings window.

To specify shared folder locations
1.

In each of the storage path fields, enter a file path or click Browse to search for the folder.

2.

Click Save.

3.

When the confirmation message appears, click OK.

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System Settings Tab

Instrument and Droplet Volume Settings
When you open QX Manager Software for the first time after installation, the Instrument connection
window appears and you must select the instrument you are using.

Changing the Instrument
You can choose between the QX200 Droplet Reader and the QX600 Droplet Reader.

To change the instrument
1.

Select the System Settings tab.

2.

In the System Settings window (default), select the Instrument tab.

3.

Select the instrument and then click Save.
Features associated with the selected instrument become available when the instrument isconnected.

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Chapter 12 System Utilities

Changing the Droplet Volume
From the Instrument tab, you can also choose between two droplet volumes, 0.795 nL and 0.85 nL.

To change the droplet volumeu

Select the alternate button to change the volume.
Your droplet volume selection persists until you change it again.

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System Settings Tab

Software Settings
To improve chart appearance, the Software Settings tab provides an alternate option for chart rendering.
Important: Poor rendering typically occurs with some Intel graphics cards only. Contact Bio-Rad
Technical Support for information and assistance. Do not change the setting unless instructed to do
so by Bio-Rad Technical Support.

Complete the following steps if directed to do so by Bio-Rad Technical Support.

To change the graphics rendering method1.

Under Chart Settings, click Alternate.

2.

Click Save.

3.

Close QX Manager Software.

4.

To enable the change, restart the connected computer, and then reopen the software.

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Chapter 12 System Utilities

System Log Files
From the System tab, you can access log files for system and software events (event log), andmaintenance activities (maintenance log).

Event Log
Users who are assigned the Maintenance user privilege can view the system event log, which contains
timestamped information on all software activities.

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System Log Files

To view the Event Log
1.

Select the System Utilities tab.

2.

Select Event Log.

3.

Click Open Log to choose either the debug log or the history log.

4.

Review the log entries.

5.

(Optional) To automatically generate and display a PDF document, click PDF Report.
Tip: To restrict access to the file, you can assign a password. Select the PDF Password checkbox and then enter a password in the field. The file is saved in the Log Reports folder and can be
opened only by entering the password.

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Chapter 12 System Utilities

Maintenance Log
All users can view the maintenance log, which contains a list of maintenance records. Users who areassigned the Maintenance user privilege can set up maintenance records, specify associated activities,
and generate PDF reports.
Tip: This guide also contains a form on which you can document completion of maintenanceactivities. For information, see Instrument Maintenance Log on page 232.

To add or view an activity
1.

Select the System Utilities tab.

2.

Select Maintenance Log. Note that activities that are already scheduled appear in the grid, sorted bynewest activity first.

3.

Do one of the following:n

Scroll to view a particular activity.
Important: You can view or add static activities; you cannot modify them.

n

Add an activity; click the + icon next to New Activity.

A line item appears in the bottom section, with all fields except Activity completed automatically.
4.

In the Activity field in the bottom section, type the activity into the Activity field, and click Save.

5.

Repeat to add another activity.

6.

(Optional) Click PDF Report to create a report of the added activities.

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Maintenance Reports

Maintenance Reports
Reports generated from the Bio-Rad service engineer when performing maintenance on your instrument
are stored on the Maintenance Reports tab.

To open a reportu

Click the list item.

Following is an example of a Color Calibration report:

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Chapter 12 System Utilities

System Data
In the System Data window, you cannArchive raw datan

Access troubleshooting datan

Recover data

Archiving Raw Data
When the storage space on the computer connected to the QX200 Droplet Reader approaches the limit
displayed under Disk Space, you can free up space by moving raw data to an archive storage folder in adifferent location, such as a network or USB drive.
Important: You must be assigned the System Data user privilege to archive data.

To archive raw data
1.

Select the System Utilities tab.

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System Data

2.

Select System Data.
The Archive Raw Data tab is selected by default.

3.

Under Archive Progress, click the calendar icons and select a From date and a To date to define adate span.

4.

Click Query to search for files dated within the date span.

5.

Click Browse to search for and select the target storage location.

6.

Click Archive.

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Chapter 12 System Utilities

Troubleshooting Data
If issues occur with the instrument or software, you can access data to assist in troubleshooting the
problem.
Note: You must be assigned the System Data user privilege to access troubleshooting data.
Important: To minimize the size of the zip file and ensure a smoother transfer of troubleshooting
data, delete the contents in C:\ProgramData\Bio-Rad\QXMgrPremium\Logs before you perform thefollowing procedure.

To collect data for troubleshooting
1.

Select the System Settings tab.

2.

Select System Data.
The window opens to the Archive Raw Data screen by default.

3.

Select the Troubleshooting Tab.

4.

Click the From and To calendar icons to select a date range.

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System Data

5.

6.

Select any of the following checkboxes:nSystem Logsn

Raw Plate Datan

Version DatanCalibration Data

Click Browse to navigate to a folder where the data will be stored.
QX Manager Software advises how much space you need and how much is available, and also
advises if there is no data from your specified date range.

7.

Click Collect Data.
A progress bar appears.

QX Manager Software creates a subfolder containing the data you specified and places it in thetarget location.

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Chapter 12 System Utilities

Recovering Data
If a run fails on the QX200 Droplet Reader, you can use the Data Recovery tab in System Data to recover
data that has been saved to a temporary file.
Important: You must be assigned the System Data user privilege to access the Data Recovery tab.

To create a..ddpcrs file from the data in the temporary file1.

Click the System Utilities tab.

2.

Click System Data, and then click Data Recovery.

Temporary files that are available for conversion are listed in the top pane, which is scrollable.
3.

Click a file, and then click Browse

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System Data

4.

Navigate to the target storage location on your computer or network, and then click Recover.
The following advisory message appears.

5.

Click Yes.
A dialog box appears with a progress bar, and automatically closes when the conversion is complete.

The .ddpcrs file is stored in the folder you specified.

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Chapter 12 System Utilities

Reprocessing Data
After your instrument has been recalibrated, you can reprocess a data file from a run using different color
calibration values.
Note: The instrument must be in an idle state before you can reprocess the data in QX Manager
Software If the file was created in an older software version, the software cannot reprocess the fileand displays an advisory message.

To reprocess a data file1.

Select the System Utilities tab.

2.

Click Reprocess Data.

3.

Under Datafile, click Browse and navigate to the analysis data file.

4.

In the Select Datafile dialog box, select the file and click Open.
The calibration values appear in the first Color Calibration table.

5.

Under the New calibration values heading, enter new values for the fluorophores.

6.

Click Reprocess Data.
Note: When you reprocess a data file, the software creates an audit record containing the oldand new calibration values.

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System Calibration and Tools

System Calibration and Tools
You cannot execute runs on the QX200 Droplet Reader unless the instrument is properly calibrated. Onlya Bio-Rad service engineer can calibrate your instrument and use the Instrument Calibration options in
QX Manager Software.
If your instrument requires service, contact Bio-Rad Technical Support.
The Tools functions are currently applicable only to instrument maintenance. For information, see
Appendix B, Instrument Maintenance.

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Chapter 13 Managing Users
Use the User Management window to add, change, or remove QX Manager Software users, and set orchange user privileges and preferences.

An administrative user account, with all privileges, should be set up first. You will use this user account tocreate additional users and assign user privileges. If you need assistance, contact Bio-Rad TechnicalSupport. Users who are not assigned any of the specified privileges can still execute runs and use theAnalysis module.
You can set up local or domain accounts. If the computer connected to the QX200 Droplet ReadernCannot access your company’s network, your IT department or system adminisrator can set up usernames as local Windows accounts.

n

Can access your company’s network, QX Manager Software can recognize the Active Directory usernames.

You can create user accounts with any user name convention and password character structure, as longas it complies with your organizational requirements. The software is designed to validate each user
against the name it finds in either the Active Directory or local domain, so users must log in with the proper
domain and user name.

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Chapter 13 Managing Users

Adding Users
Before you can add users to QX Manager Software, you must be logged in with the initial superuser
account, or another account that is assigned the Add/Manage Users privilege.
Important: Before you begin, ensure that all users either have local Windows user accounts on thelocal computer or user accounts in Active Directory (network domain).

To add a user
1.

Open QX Manager Software and sign into the application.

2.

Click the User Management tab on the left

3.

In the User Name field on the right, enter the user name as follows:n

If the computer is connected to a network and you are using Active Directory accounts, enter<domain name>/<user name>. For example, global/johnsmith.
Important: Active Directory users must log in every time with the domain name preceding
the user name.

n

If the computer is not connected to a network, enter <local computer name>/<user name>. For
example, analysiscomputer/johnsmith.
Important: To locate the computer name, right-click on the yellow folder in the lower menu
bar and select File Explorer. When the dialog box appears, the computer name is located at
the top of the left panel. Local users are not required to reenter the computer name after the
initial login.

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Adding Users

4.

Click Check Name.
One of the following occurs:

5.

n

If the software recognizes the network domain or computer name and the user name, thesoftware displays a validation message.

n

If the user is not recognized, an error message appears. Do one of the following:o

For network users, ensure there is a working connection to the network and then verify yourentry is accurate.

o

For local users, verify the entry is accurate. If the user is not set up locally or on the network,
contact your system administrator for assistance.

When the This user is valid message appears, click OK, and then click Add at the bottom of the pane.
An Are you sure you want to add this user? message appears.

6.

Click Yes.
A confirmation message appears.

7.

Click OK.

8.

Continue until all users are added.

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Chapter 13 Managing Users

Adding or Removing User Privileges
Only a user assigned the Add/Manage users privilege can add or remove user privileges. By default,
individual users without privileges can set up and execute a run, open files, view and analyze results.
For descriptions of all user privileges, see Viewing User Privileges on page 39.

Table 40 contains a sample set of privileges assigned by user roles common to a laboratory. User roles
can be defined and used in any scenario, but might be required in regulatory environments.
Table 40. Example User Roles

Superuser

Lab
Manager

Add/manage usersüü

Create new templates

ü

ü

ü

View data files created by

ü

ü

ü

ü

ü

ü

Privilege

Group
Lead

other users
Override existing ddPCR file
name
System settingsü

Maintenanceü

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Technician/Student InternüAdding or Removing User Privileges

Table 40. Example User Roles, continued

Superuser

Lab
Manager

Group
Lead

Technician/Student Intern

Archive data files

ü

ü

ü

ü

Access the module recovery

ü

ü

ü

ü

Manage APFs

ü

ü

ü

Run APFsüüüPrivilege

tool
APF Privileges:ü

Only Run APFs
Manage Plates

ü

ü

ü

ü

You can assign the Create new templates privilege to non-administrative roles if anyone can create andsave a template. If template formats are restricted, then you should assign this permission toadministrative or supervisory roles only.
Note: Bio-Rad recommends defining at least one additional superuser as a backup, as well as otheradministrative and standard roles based on your needs. Guest users can open shared templates,
execute runs, and perform analysis but are not typically assigned other privileges.

To add or modify privileges
1.

Click the Add/Manage Users tab to open the User Management window.

2.

Select a user from the Current Users list. The name appears in the User Name field. A network orcomputer name and backslash might appear before the user name.

3.

Select or clear the checkbox for each privilege in accordance with the user’s role in using thesoftware. You can assign user privileges in any combination.

4.

When the confirmation message appears, click Yes to save the changes, and then click OK to close
the pop-up.

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Chapter 13 Managing Users

Modifying User Preferences
Users assigned the Add/Manage Users privilege can change the preferences for other users. Individual
users can also change their own preferences.

To modify a user's preferences
1.

Click the Add/Manage Users tab, and then enter the user name.

2.

Change any of the following preferences for the user:nEnter a different file path for user data files and templates, and choose to keep them private.
Important: You can also specify Preferred Locations in System Settings, to override all filepaths specified in individual preferences. For information, see System Settings Tab on page
180.

nEnter a different default system timeout period.

nEnter a different number of completed plates to show in the Status section, up to a maximum of
100.

3.

Click Save. QX Manager Software displays a confirmation message.

4.

Click Yes to save the changes, and then click OK to close the dialog box.

Removing Users
Only a user assigned the Add/Manage Users privilege can remove users. Removing a user from thesoftware does not remove the user from other systems, such as Windows, or databases.

To remove a user
1.

Click the Add/Manage Users tab to open the User Management window.

2.

In the Current Users pane, select the user and click Remove. QX Manager Software displays aconfirmation message.

3.

Click Yes to remove the user, and then click OK to close the dialog box.

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Appendix A Experiment Examples
This section contains setup and analysis information for the following sample experiments:n

Direct Quantification, using the Amplitude Multiplex assay typen

Copy Number Variation, using the Probe Mix Triplex assay typenDrop-Off, using the Basic Drop-off Assay type for genome edit detectionnDirect Quantification, using the Advanced Classification Method assay type

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Appendix A Experiment Examples

Direct Quantification Multiplexed
You can increase the number of targets to be evaluated by using the Amplitude Multiplex option.
Optionally, to expedite plate setup you can copy and paste data from one well to another, and you canclick Undo to undo an applied well setting. You cannot change the supermix that was used during datacollection.

Setting Up Experiment Parameters
To set experiment parameters
1.

Open the analysis data file and select the Plate Editor tab.

2.

Select one or more wells to be assigned well analysis attributes.

3.

Change the experiment type to Direct Quantification (DQ), and then click Apply.

4.

(Optional) Change the sample description identifiers.

5.

(Optional) Change the sample type. The default type is Unknown.
Tip: For automatic thresholding of positive control wells, you must select Pos Ctrl.

6.

Under Assay Type, select Amplitude Multiplex and click Apply. Four target rows appear.

7.

Change the target name and type (unknown or reference) for each target in the well.
The software defaults to FAM Lo, FAM Hi, HEX Lo, and HEX Hi, respectively, for each target.

8.

(Optional) Change the high and low target identifiers.
Amplitude Multiplex allows for up to two assays in each channel, indicated by Lo and Hi labels. In thismultiplex mode, each target may have a signal for only one channel. You can

9.

nSelect a different dye, if the channel supports two dyes (for example change HEX to VIC or
VIC to HEX)n

Select a different channel for the target (for example, change FAM to HEX)n

Change Hi to Lo or Lo to Hi

Click Apply.

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Direct Quantification MultiplexedViewing and Adjusting Results
Automatic thresholding is not available for Amplitude Multiplex experiments.
For clusters that are easily identifiable across the chart, use Threshold Lines mode to set manualthresholds. If the data is not orthogonal and the threshold lines do not adequately divide the populations ofdroplets, use Threshold Clusters mode to set manual thresholds.

To set thresholds in the 2D Amplitude window
1.

Select the 2D Amplitude tab.

2.

On the toolbar, click the Threshold Line Mode button.

3.

Click anywhere on the plot to apply “best fit” threshold lines to the data.

4.

To adjust the thresholds, drag the lines horizontally or vertically in the plot area.
Tip: You can also enter a specific threshold value in the boxes at the end of each threshold line.

User Guide | 207

Appendix A Experiment Examples

To apply and adjust manual clusters
1.

Click any of the three cluster mode buttons (square, circle, or freehand).

2.

Press the left mouse button and draw the chosen shape around the cluster of droplets to be classified
first.
Tip: When you release the mouse button, a pop-up tool appears to help you select the correct
target combination. Target names are shown along the two axis based on the signal values
assigned during plate setup.

3.

To classify droplets as positive or negative for each given target, select the colored box that best
represents the location of the cluster of droplets.

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Copy Number Variation Triplexed

Copy Number Variation Triplexed
A CNV experiment with probe mix triplexing uses two targets and a reference in one groups of three toproduce analysis data. Optionally, to expedite plate setup you can copy and paste data from one well toanother, and you can click Undo to undo an applied well setting.

Setting Up Experiment Parameters
To set experiment parameters
1.

Open the analysis data file and select the Plate Editor tab.

2.

Select one or more wells to be assigned well analysis attributes.

3.

Set the experiment type to Copy Number Variation (CNV), and click Apply.

4.

(Optional) Change the sample description identifiers.

5.

(Optional) Change the sample type. The default type is Unknown.
Tip: For automatic thresholding of positive control wells, you must select Pos Ctrl.
Note: You cannot change the supermix that was used during data collection.

6.

Click Apply.

7.

From the Assay Type dropdown list, select Probe Mix Triplex and click Apply.
QX Manager Software displays three targets.
Important: You cannot add or delete triplex targets.

8.

Enter target names and select the target type (unknown or reference) for each target in the well.
This creates one group of three targets.

User Guide | 209Appendix A Experiment Examples

9.

Assign the targets as follows:

Group 1
TargetTarget Type

Signal
Ch1

Signal Ch2

Ref
CopiesPlot?

Target 1

Unknown

FAM

None

N/A

N/A

Target 2

Unknown

None

HEX/VIC

N/A

N/A

Target 3

Reference

FAM

HEX/VIC

2Yes

10. Click Apply.

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Copy Number Variation TriplexedViewing and Adjusting Results
Note: Linear thresholding is not available for Probe Mix Triplex experiments.

To see the results
1.

After all wells are configured, select the 2D Amplitude tab to evaluate the data and manually set
clusters.

2.

Click any of the three cluster mode buttons (square, circle, or freehand).

3.

Press the left mouse button and draw the chosen shape around the cluster of droplets to be classified
first.
Tip: When you release the mouse button, a pop-up tool appears to help you select the correct
target combination. Target names are shown along the two axis based on the signal values
assigned during plate setup.

4.

To classify droplets as positive or negative for each given target, select the colored box that best
represents the location of the cluster of droplets.

User Guide | 211

Appendix A Experiment Examples

Drop-Off Assays for Genome Edit Detection
Optionally, to expedite plate setup you can copy and paste data from one well to another, and you canclick Undo to undo an applied well setting.
Two configurations of drop-off assays are possible and are shown below. Assign a signal (expectedcluster position) to wild-type and NHEJ indel alleles. The signal produced by a wild-type allele will always
be positive for both FAM and HEX, while the signal produced by an NHEJ indel allele depends on theassay configuration used (as shown below left and right).
Drop-Off Probe in HEX

Drop-Off Probe in FAM

NHEJ Probe = HEX and Reference Probe =FAM

NHEJ Probe = FAM and Reference Probe =HEX

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Drop-Off Assays for Genome Edit Detection

Setting Up Experiment Parameters
To set experiment parameters
1.

Open the analysis data file and select the Plate Editor tab.

2.

Select one or more wells to be assigned well analysis attributes.

3.

Set the experiment type to Drop-Off (DOF) and click Apply.

4.

(Optional) Change the sample description identifiers.

5.

(Optional) Change the sample type. The default type is Unknown.
Tip: For automatic thresholding of positive control wells, you must select Pos Ctrl.
Note: You cannot change the supermix that was used during data collection.

6.

Click Apply.
QX Manager Software automatically assigns the assay method as Basic Drop-Off.

7.

Enter the target names, and then designate one target as Reference and the other as Unknown.
The Reference target enables ratio calculation of results.

8.

Click Apply.

User Guide | 213

Appendix A Experiment Examples

Viewing and Adjusting Results
Thresholding is not available for Drop Off experiments.

To apply and adjust clusters
1.

After all wells are configured, select the 2D Amplitude tab to evaluate the data and manually set
clusters.

2.

Click any of the three cluster mode buttons (square, circle, or freehand).

3.

Press the left mouse button and draw the chosen shape around the cluster of droplets to be classified
first.
Tip: When you release the mouse button, a pop-up tool appears to help you select the available
cluster assignments. Target names are shown along the two axis based on the signal values
assigned during plate setup.

4.

To classify droplets as positive or negative for each given target, select the colored box that best
represents the location of the cluster of droplets.

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Direct Quantification with the Advanced Classification Method

Direct Quantification with the Advanced Classification Method
The Advanced Classification Method analysis mode allows the user complete control of droplet
identification, and does not force or preassign any clusters. This allows a higher degree of multiplexing
through radial dye mixing. Optionally, to expedite plate setup you can copy and paste data from one wellto another, and you can click Undo to undo an applied well setting.
Important: This mode is intended for experienced users of Droplet Digital PCR.

Setting Up Experiment Parameters
To use the advanced classification method
1.

Open the analysis file and select the Plate Editor tab.

2.

Select one or more wells to be assigned well analysis attributes.

3.

Set the experiment type to Direct Quantification (DQ) or RED and click Apply.

4.

(Optional) Change the sample description identifiers and click Apply.

5.

(Optional) Change the sample type and click Apply. The default type is Unknown.
Important: For automatic thresholding of positive control wells, you must select Pos Ctrl. You
cannot change the supermix that was used during data collection.

6.

Under Assay Type, select Advanced Classification Method and use the + icon to add up to ten
targets.

User Guide | 215

Appendix A Experiment Examples

7.

Enter the target name and type (unknown or reference) for each target in the well, and then click
Apply.
If you select Reference, you can change the number of reference copies. The default is 2.
n

If no reference is selected, the target with the highest dye concentration in the highest channel isused as the reference.

n

If more than one reference is selected in the well, checkboxes appear to the right for using thereference in the plot.

Note: Each Reference target enables ratio calculations in the results.
8.

Assign the first target an expected signal in a channel.

9.

Assign your last target a signal in a channel that was not selected for your first target.
Each target in between will be assigned a signal depending on mixture ratio of the target.

10. Click Apply to confirm all well settings.

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Direct Quantification with the Advanced Classification Method

Viewing and Adjusting Results
To view and adjust results
1.

Click the 2D Amplitude tab.
All droplets are unclassified by default and are colored red. Only the Threshold Cluster mode isavailable for setting thresholds in Advanced Classification experiments in the 2D plot.

2.

Use one of the Threshold Cluster mode tools (box, circle or freehand) to assign droplet clusters totargets.
When you select a droplet cluster, a cluster assignment box appears.

3.

Select a radio button to identify the composition of the cluster.
For example, if the cluster is composed of positive droplets for Target-2, select the positive radio
button for Target-2 and the negative radio buttons for the remainder.
Important: For calculations to occur, you must have at least one positive cluster for each target,
as well as the assigned negative cluster.
Note: The software sets aside unassigned for calculation purposes. If you are unsure ofdroplet/cluster composition, leave it unassigned (red).
You can view the concentration results in the data table and in the Concentration tab.
If one of your samples was identified as a Reference under AssayType, you can view a ratio ofconcentration for unknown versus reference in the Ratio tab.

User Guide | 217

Appendix A Experiment Examples

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Appendix B Instrument Maintenance
Bio-Rad recommends regular maintenance of your equipment, which includesnKeeping the surface areas clean, post-run or as necessary
Note: Wipe down external panels and the plate holder with 70% ethanol. See Cleaning or
Decontaminating the Instrument on page 231 for information.

nRegularly checking the fluid levelsnInspecting the equipment for damaged parts or wiring

Bio-Rad also recommends that a Bio-Rad service engineer perform annual preventive maintenance on
your instrument. Contact Bio-Rad if your instrument requires service or recalibration.

User Guide | 219

Appendix B Instrument MaintenanceFluid Maintenance and Waste Management
You must ensure there is enough oil for at least one full run, and you must empty the waste container
when it approaches a full state.
You can verify your fluid levels by checking the following:nInstrument status barnInstrument indicator lightsn

The oil and waste bottles or EcoTank

Table 41 explains fluid level maintenance for your instrument.
Table 41. Fluid Levels
Fluid Level

StatusOil greater than 40% or waste

Bottle levels OK. You can start your run.

less than 70%
Oil less than 40% or waste

You may be able to start a run with fewer than 96 wells.

greater than 70%

If there is not enough oil in the dispensers to perform a run on thenumber of wells you set up in the Plate Editor, the software prevents
the run until you fill the oil dispenser and empty the waste container.
Pay attention to the fluid level by checking instrument status bar in the
QX Manager Software or by checking the oil bottles.

Oil less than 10% or waste

The software prevents the run until you fill the oil dispenser and empty

greater than 90%

the waste container.

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Fluid Maintenance and Waste Management

Changing the Droplet Reader Oil Bottle
To replace the oil bottle
1.

Slide the container carriage out using the handle on the side of the instrument.

2.

Remove the oil bottle and set it aside, to use when changing the waste bottle.
Once opened, a pop-up appears on your screen asking you to indicate which type of bottle you areinstalling on the system.

Note: If using an EcoTank, see Using an EcoTank Oil and Waste Container on page 223 for
information.
3.

Insert a new bottle of oil and tighten the cap into place.

4.

Prime and flush the instrument at least once after the new oil bottle is installed. See Priming andFlushing the Instrument on page 229 for information.
Note: If you are replacing reagents in the middle of a run, the run resumes when the bottle door
is closed and you have clicked OK in the dialog box. You can replace with the same type of bottle
only. For example, if the run started with an EcoTank loaded, you must replace the spent
EcoTank with another EcoTank.
After an EcoTank is loaded into the system, the software tracks the number of plates that have been
run with the EcoTank. Once you have run 40 plates, the software begins to warn you to replace the
EcoTank. After you have run 50 plates, you are required to replace the EcoTank before proceedingwith a new run.

User Guide | 221

Appendix B Instrument Maintenance

Emptying the Waste Container
Important: Use each empty oil bottle as a new waste bottle once and then discard it. Before
discarding, add 50 ml of 10% bleach solution to the bottle to prevent microbial growth, and then label
the bottle as waste. If you are using an EcoTank, see Using an EcoTank Oil and Waste Container on
page 223 for information.

To replace the waste bottle
1.

Slide the container carriage out using the handle on the side of the instrument and remove the waste
bottle.

2.

Place the new Waste label over the Oil label on the oil bottle.

3.

Insert the last empty oil bottle into the waste container slot.

4.

Flush the instrument after the new waste bottle is installed. See Priming and Flushing the Instrument
on page 229 for information.

For information on disposing of waste, see Managing Waste on page 230.

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Fluid Maintenance and Waste Management

Using an EcoTank Oil and Waste Container
EcoTanks are high-capacity reservoirs that you can use instead of individual oil and waste bottles in your
QX200 Droplet Reader.
The ddPCR Droplet Reader Oil EcoTank for Probes distributes and recirculates droplet reader oil, andalso collects waste generated by the instrument into a single partitioned container. This ensures thatfloating waste droplets remain on the waste side of the bottle, while the droplet reader oil can beredistributed through the instrument for another droplet reading cycle.

Usage Advisories
Note the following when using the Droplet Reader Oil EcoTank for Probes:n

The EcoTank can read up to 50 plates.

n

Do not add bleach to the EcoTank before or while it is installed in the instrument. You can add bleachafter you remove the EcoTank from the instrument and before storage or disposal.

n

Do not reuse a spent EcoTank.

n

An unused EcoTank is stable for up to 12 months when stored at room temperature (25°C).

n

You must replace the EcoTank before or at 6 months after date you install it in the instrument. QXManager Software tracks the EcoTank and locks out the user after the EcoTank passes the 6-month
limit.

n

The EcoTank for Probes is not compatible with QX200 ddPCR EvaGreen® Supermix (Catalog No.
1864033, 1864034, 1864035, 1864036).

User Guide | 223

Appendix B Instrument MaintenanceInstalling an EcoTank Bottle in the Droplet Reader
To install an EcoTank bottle
1.

Open QX Manager Software.

2.

Open the reagent door on the left side of the QX200 Droplet Digital PCR System and place an
EcoTank in front of the currently installed oil bottles.
Note: The EcoTank is symmetrical and new bottles can be loaded in either orientation. Bio-Rad
does not recommend changing the EcoTank orientation after it has been installed in the droplet
reader.

3.

Remove the caps from the EcoTank.

4.

Remove from the currently installed bottles the caps that are attached to the instrument, and attach
them to the EcoTank.

5.

Cap and remove the currently installed bottles.

6.

Place the EcoTank in the bottle tray. Maintain the orientation to prevent twisting of the oil lines.

After the bottle door has opened, QX Manager Software prompts you to select the action taking place.
Continue to the next section.

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Fluid Maintenance and Waste Management

Selecting the EcoTank in QX Manager Software
To specify an EcoTank is being used1.

Select New EcoTank is being loaded into instrument.

2.

Enter the batch number and expiration date, and then click OK.

In the Instrument Status bar, QX Manager displays the EcoTank for the droplet reader and waste oils,
as well as the number of plates remaining.

Important: If the instrument has been idle for more than a week, you must prime the instrument
before running a plate. From the Setup menu, click Tools > Prime to fill the lines with oil before
starting a run.

User Guide | 225

Appendix B Instrument Maintenance

Reinstalling the Standard Bottles
You can return the QX200 Droplet Reader to the initial two bottle configuration at any time, except when arun is in progress.
Complete the steps in the following sections to change the bottle configuration.

To exchange the EcoTank for the two-bottle configuration
1.

Open QX Manager Software.

2.

Complete the following substeps to prepare a new 1 L waste bottle for the QX200 Droplet Reader:a.

Add 50 ml 10% bleach to the Waste bottle to prevent microbial growth.

b.

Place an identifying label on the Waste bottle.

3.

Open the reagent door on the left, and then place a droplet reader oil bottle and the new waste bottle
into the space in front of the EcoTank bottle.

4.

Remove the caps from the EcoTank and bottles.

5.

Replace the oil and waste caps on the used EcoTank bottle, and then use the handle on the EcoTankbottle to move it out of position and remove it from the instrument.

6.

Place the oil and waste bottles into the corresponding slots and close the reagent door.

After the bottle door has opened, QX Manager Software prompts you to select the action taking place.
Continue to the next section.

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Fluid Maintenance and Waste Management

To specify that separate oil and waste bottles are being used in QX Manager Softwareu

Select New Oil and/or Waste bottle is being loaded into the instrument and click OK.

QX Manager displays the DR Oil and Waste indicators.

Important: If the instrument has been idle for more than a week, you must prime the instrument
before running a plate. From the Setup menu, click Tools > Prime to fill the lines with oil before
starting a run.

Disposing of Waste
Droplet generation and reader fluids from Bio-Rad are based on fluorinated hydrocarbon chemistry andshould be disposed of in accordance with institutional, state, and local regulations. For information, seeManaging Waste on page 230.

User Guide | 227

Appendix B Instrument MaintenanceDisposing of the EcoTank and EcoTank Waste
When QX Manager indicates 50 plates have been run, you must replace the used EcoTank bottle. Afterremoving the EcoTank from the instrument, you can install a new EcoTank or reinstall the standard twobottle configuration. If the EcoTank bottle is removed before 50 plates are run, discard the EcoTank bottle
and oil in accordance with institutional, state, and local regulations.

To remove and dispose of the EcoTank and EcoTank Waste
1.

Uncap one side of the EcoTank and take it to the liquid waste receptacle.

2.

Hold the uncapped opening slightly lower than the capped opening and slowly pour out as much of
the contents from the uncapped side as possible.

3.

Return the bottle to its upright position to allow the fluid trapped in the closed cap side of the bottle tomove to the open cap side, and repeat the process.

4.

Pour entire contents of spent bottle into the waste receptacle.

5.

Place the cap on the empty EcoTank bottle and then discard per waste disposal regulations.

Cleaning the EcoTank Waste Cap
Repeat the following process once per month at a minimum.

To clean the waste cap
1.

Dampen a lint-free wipe with fresh 10% bleach solution.

2.

Remove the cap on the waste side of the EcoTank.

3.

Wipe down anywhere microbial growth might occur, including along the threading and inside of the
cap .

4.

If the cleaning leaves excess liquid on the cap, dry the cap using a dry lint-free wipe.

5.

After the cleaning is done and the cap is dry, place and tighten the cap on the EcoTank.

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Fluid Maintenance and Waste Management

Priming and Flushing the Instrument
You should prime the instrument after you replace the oil bottle and you should prime and flush the
instrument when you change the waste bottle.
Important: Before you initiate a prime or flush, the lid must be closed. Do NOT press the button to
open the lid while a prime or flush is in progress.

To prime the instrument
1.

Select the System Utilities tab.

2.

Tap Prime.
A message appears, asking if you want to prime the instrument.

3.

Tap Yes to begin.

4.

A “Performing Prime” message appears.
When the priming process is finished, an operation complete message appears.

5.

Tap OK.

To flush the instrument
1.

Select the System Utilities tab.

2.

Tap Flush.
A message appears, asking if you want to flush the instrument.

3.

Tap Yes to begin.

4.

A “Performing Flush” message appears.
When the flushing process is finished, an operation complete message appears.

5.

Tap OK.

User Guide | 229

Appendix B Instrument MaintenanceManaging 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 42. 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)

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Recovery From Idle Mode

Recovery From Idle Mode
Complete the steps below if the instrument has been idle:
1.

Check the expiration date on the oil bottle. If expired, replace the oil bottle.

2.

Ensure the waste bottle is not full.

3.

If needed, add 50 ml of 10% bleach to the waste bottle.

4.

If you have changed the bottles, or if you have not used the system for a week or more, perform theprime and flush processes as specified in Priming and Flushing the Instrument on page 229.

Cleaning or Decontaminating the Instrument
Use the protocols specified below for the following:nRegular post-run instrument cleanupnInstrument decontamination, as needed

If you have questions regarding the use of cleaning agents other than those specified, contact Bio-Rad
Technical Support.

To clean the instrument
1.

Remove the plate after a run is complete and ensure it is properly discarded.

2.

Using 70% ethanol, wipe down the external panels, as well as the plate holder and its compartment.

To decontaminate the instrument
1.

Remove the plate after a run is complete and ensure it is properly discarded.

2.

Wipe down the plate holder and its compartment with 10% bleach.
Important: Do not use bleach inside the system.

3.

Wipe down all external surfaces with 10% bleach.

4.

Identify the equipment as Decontaminated.

User Guide | 231

Appendix B Instrument MaintenanceInstrument Maintenance Log

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Appendix C TroubleshootingThis section contains information on troubleshooting and correcting minor issues you may experience
with your instrument or software.

Event Log
The Event Log contains records for all system and user activities, including system errors. If you do notunderstand, or cannot find an immediate remedy to, the error event, contact Bio-Rad Technical Support.

Instrument Errors
If an error occurs during a run, the software cancels the run and displays an X in the Status column, alongwith a Run Aborted by System message as the Run End status. Table 43 contains error grouped by type.
1.

Click the X to display the corresponding error code and description.

2.

Perform the steps in the solution column before starting a new run.

3.

If the suggested solution does not resolve the problem, contact Bio-Rad Technical Support
immediately.
Note: The error code and description are also displayed in the Run Information window .

Communication errors can be caused by instrument, connectivity, or power failures.
Table 43. Communication errors

Error CodeDescription

Solution

102, 103, 104*,

Communication loss between the instrument andDisconnect and reconnect the

110*, 111

software, detector board error, loss during a run,

USB cable, and then power cycleor unable to reestablish a connection

the instrument.

Note: For codes marked with an asterisk(*), some data may be usable.
302, 308

Communication error involving pump

Power cycle the instrument.

Note: Some data might be usable.

User Guide | 233

Appendix C Troubleshooting

Table 43. Communication errors, continued

Error CodeDescription

Solution

502

Invalid checksum value

Retry.

900

Invalid commandAn electrical error is typically triggered by an invalid setting.
Table 44. Electrical error codes

Error CodeDescription

Solution

406

Electrical Error; invalid power value setting.

Power cycle the instrument.

Note: Some data might be usable.

Mechanical errors can be caused by fluid issues (low oil, high waste), instrument operation errors, or
binary data collection errors.
Table 45. Mechanical error codes

Error CodeDescription

Solution

105, 106

Fluidics or motion response was invalid.

Power cycle the instrument.

Note: Some data may be usable.
201

Motors disabled
Note: Some data may be usable.

1. Remove and reinsert the plate andplate lid.
2. Check for incorrect or multiple heatseal foil layers.
3. Check for strain on all motor axes.
4. Power cycle the instrument.

205, 207, 210,

X, Y, or Z-axis, unable to reach target

Check for motor obstructions, and then211, 212, 218

location or home in allotted time.

power cycle the instrument.

Note: Some data might be usable.

301, 303, 304,

Pump errors

305, 307, 312,

Note: Some data might be usable.

Power cycle the instrument.

316, 317

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Appendix D 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 Reader.

ddPCR System and Instrument Packages
Table 46. ddPCR system and instrument packages

Product

Description

Catalog
Number

QX200 Droplet Digital

Includes the QX200 Droplet Generator, QX200 Droplet

1864001

PCR System

Reader, computer, software, and consumables

QX600 Droplet Digital

Includes the QX200 Droplet Generator, QX600 Droplet

PCR System

Reader, computer, software, and consumables

QX200 AutoDG™

Includes the AutoDG, QX200 Droplet Reader, computer,and QX Manager Software Standard Edition

1864100

QX600 AutoDG Droplet

Includes the AutoDG, QX600 Droplet Reader, computer, QX

17008371

Digital PCR System

Manager Software Standard Edition, and consumables

Automated Droplet

Includes the AutoDG (1), cooling block accessory (1), oilGenerator

purge reservoir (1), and power cord (1)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,

1864003

Droplet Digital PCR

17007769

System1864101

and power cord
QX600 Droplet Reader

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

12013328

and power cord

User Guide | 235

Appendix D Ordering Information

Thermal Cyclers and Plate Sealer
Table 47. Thermal cyclers and plate sealer
Catalog
Product

Description

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

12015392

cable, and Ethernet cable
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

AutoDG Accessories
Table 48. Automated Droplet Generator accessories

Product

Description

Catalog
Number

Cooling block accessory

Prevents evaporation during droplet

12002819

generation
Oil purge reservoir

Collects oil waste from priming and flushing

N/A

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

Connects the AutoDG to the power source
Note: Contact Bio-Rad Technical Support
for replacement information.

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N/A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 49. 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

12006834

User Guide | 237

Appendix D Ordering Information

QX200 Droplet Reader Accessories
Table 50. 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

238 QX200 Droplet Reader and QX Manager Software, Premium Editioon

12006834

ddPCR Consumables and Other Materials
Table 51. Consumables and other materials

Product

Description

Catalog
NumberddPCR 96-Well Plates

Cear well/clear shell semi-skirted plates

12001925(pkg of 25)

DG32 Droplet Generation

Microfluidic cartridge with gasket for the AutoDG

Cartridges

1864108(pkg of 30)
1864109(pkg of 60)

Pipet Tips

Pipet tips for the AutoDG

1864120(pkg of 20)
1864121(pkg of 40)

Pipet Tip Bins

Pipet tip waste bins for the AutoDG

Automated Droplet

Automated droplet generation oils for the AutoDG:

Generation Oilsn Automated Droplet Generation Oil for Probes

1864110n Automated Droplet Generation Oil for EvaGreen®

1864112Droplet Generation Oils

Rainin Pipets

Rainin Pipet Tips

1864125

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

User Guide | 239

Appendix D Ordering Information

ddPCR Supermixes
Table 52. 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)
1.2ml (2 x 0.6ml)

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),

ddPCR systems
ddPCR Supermix

2x supermix, for use in residual DNA

1864037

2ml (2 x 1ml)

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)

One-step RT-

200 or 500x 20 µl reaction kit, for absolute

1864021

2ml (2 x 1ml)

ddPCR Advanced

quantification of target RNA in a one-step

18640225ml (5 x 1ml)

Kit for Probes

format with the QX600 and QX200 ddPCR
systems

Buffer Controls
Table 53. Buffer controls

BufferCatalog
NumberddPCR Buffer Control Kit for Probes

1863052

QX200 Buffer Control Kit for EvaGreen®

1864052

240 QX200 Droplet Reader and QX Manager Software, Premium Editioon

ddPCR Kits
Table 54. 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

1863040200x 20 μl reactions, includes 1 vial of primers and probes at 20x concentration, 2x
ddPCR Supermix for Probes (no dUTP) and positive controls

User Guide | 241

Appendix D Ordering Information

ddPCR Assays
Table 55. 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

242 QX200 Droplet Reader and QX Manager Software, Premium Editioon

100 rxns

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