Droplet Digital PCR

Initiating and Managing a
QX ONE™ Droplet Digital™ PCR System Run
Quick Start Guide

Adding a Plate(s) (GCR96 Cartridge) to the
QX ONE Droplet Digital (ddPCR™) System1 	Sign into QX ONE Software using the touch screen orkeyboard. The software will notify the user when the QX ONE
ddPCR System can accept cartridges by changing the systemstatus from Busy to Ready, as shown.
2 	In the QX ONE Software window, select Add Plate, as shown.

4 	Scanning the RFID tag will initiate the inbox hotel to open.

Alternatively, the user can select Open Inbox located in thetop banner of the software window. Place the sealed plate
into an open slot with the RFID tag facing toward the insideof the hotel (barcode should be facing the operator). Correct
installation of the GCR96 Cartridge will induce a color change
in the LED lights that border the open slot, from amber togreen, as shown. Incorrect installation will induce red lights
to alert you to reattempt cartridge installation.
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QX ONE Droplet Digital PCR System

111255RFID5 	
After installing the plate, the inbox hotel door will automatically3 	Scan the cartridge radio frequency identification (RFID) tag

close in approximately 30 seconds. Select Configure Platein the touch-screen window.
Project Title: QX ONE Images
Vendor: Troutt Visual Services
File Name: Scanning_02
Date: 05/30/19
Proof: 5(located on the side of the GCR96 Cartridge with labels A–H)
with the RFID scanner (located on the front lower left panel ofthe QX ONE ddPCR System), as shown.
Note: The RFID tag on each plate allows the instrument totrace each individual plate independently of others, as wellas generate protocol-specific data for each unique cartridge.
Cartridge barcodes are reserved for barcode scanners thatallow users to change the name/identification of the individual
cartridge (optional).

Visit bio-rad.com/QXONE for more information.

Project Title: QX ONE Images
Vendor: Troutt Visual Services
File Name: Hotel_3_w/_plate_K_w/_green_
Date: 09/18/19
Proof: 2

Project Title: QXOne Manual_Version1.1Vendor: Troutt Visual Services
File Name: 02_QX_One_front
Date: 08/11/20
Proof: 1

Initiating and Managing a QX ONE Droplet Digital PCR System RunConfiguring a Plate Using QX ONE Software3 	
Edit the remaining wells by selecting Edit and annotating

Managing Plate Template File(s)the wells with appropriate Experiment Type, Sample
Description(s), Sample Type, Supermix, Assay Type, andTarget Info, as shown. Users do not have to annotate all
fields available for the wells. Select Apply or press Enteron the keyboard after making any annotations to save theedits. Save the new plate template file by selecting Save andassigning the template a name. Saved files will be accessible
in the Choose Existing dropdown menu located in the Plate
Template section in the QX ONE Software plate configuration
window (see image in Managing Plate Template File(s) step 1).

1 	In the QX ONE Software plate configuration window, choose

one of three possible options shown:■■■ elect an existing plate template file (use the dropdown
Smenu to select an existing file)Create a new plate template file (select Create New) ame the plate, select the appropriate Supermix (dropdownNmenu), and forego selecting/creating a plate template file
(template files can be created after running a plate)Note: All template edits introduced prior to the run can bedeleted, amended, and/or edited following run completion
except for the supermix.

2 	When selecting Create New, QX ONE Software willautomatically navigate the user to the Plate Setup tab. Using
the touch screen, select wells to exclude from the current
run by selecting Exclude and indicating what processes toexclude (Droplet Generation and Droplet Reading or DropletReading), as shown. Bio-Rad™ recommends backfilling
any unused wells in a GCR96 Cartridge with a 1:1 ratio ofddPCR Buffer Control for Probes (Bio-Rad Laboratories, Inc.,
catalog #1863052) and water. All wells containing either ddPCR
reactions or buffer control and water should undergo droplet
generation; however, excluding backfilled wells from droplet
reading will save time.

4 	
After creating and saving a new plate template, the QX ONE

Software will automatically navigate the user back to the plate
configuration window.
Managing Thermal Cycling Protocol(s)In the QX ONE Software plate configuration window (see imageshown), select an existing thermal cycling protocol in the Choose
Existing dropdown menu or create a new protocol by selecting
Create New.

Note: The Plate Setup tab can be directly accessed/selected,
independent of initiating a run, to create and save new plate
template files for later use. To select the Plate Setup tab, click
the icon(see image).

© 2022 Bio-Rad Laboratories, Inc.

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1 	Selecting Create New will automatically navigate the user tothe Plate Setup tab, where a new protocol can be createdby selecting the Thermal Cycling Protocol tab under Plate
Setup (see image shown).
Note: The Thermal Cycling Protocol tab can be directly
accessed/selected, independent of initiating a run, to createand save new protocol files for later use. To access theThermal Cycling Protocol tab directly, click the Plate Setup
tab icon(see image) and then click the Thermal Cycling
Protocol tab under it. Users can edit existing protocols and/oradd new protocols and then save them to access for future runs.
Accessing saved thermal cycling protocols can be accomplishedas outlined in step 2.

Recovering Cartridges from the QX ONE ddPCR System
If the run fails during the droplet generation or the droplet reading
phase, QX ONE Software moves the run to the lower pane in theRun Status screen and displays a red exclamation point underRun Status.

To recover or discard the cartridge in QX ONE Software, try oneof the following options that best suits your situation:■2 	
Choose/edit the appropriate steps (see Temperature, Time,Ramp Rate, Increment, and Extend fields, as shown) for
the desired thermal profile. Always use a Ramp Rate of
2.0°C/sec for all ddPCR applications, as shown. Save thethermal cycling protocol for future use (saved protocols canbe accessed in the Choose Existing dropdown menu in theThermal Cycling Protocol section of the QX ONE Software
plate configuration window).

■If the error stopped the plate run, select Open Outbox,
manually remove the plate from the outbox, and then restart theinstrument. When the instrument restarts, the Recover Plates
screen appears automatically. Select the Recover checkbox
and then select OK. Follow the screen prompts for scanning therecovered plate. QX ONE Software will automatically resume theddPCR experiment where it was interrupted lastIf the cartridge failed during thermal cycling, Bio-Rad
recommends discarding this cartridge and rerunning theexperiment as the contents within the wells will likely beunstable/unusable for accurate analysis downstream3 	
Saving the thermal cycling protocol will automatically navigate

the user back to the QX ONE Software plate configuration
window (see image in Managing Plate Template File(s) step 1).
Select Start Run.
Note: When programing subsequent thermal cycling protocols(protocols that succeed the initial run), Bio-Rad recommends
adding two additional steps to these protocols: add a step
preceding the user’s protocol at 25°C for 3 min, and an additional
step succeeding the user’s protocol at 25°C for 1 min.

Refer to the QX ONE Droplet Digital PCR System and QX ONE
Software User Guide (10000116512) for additional details.

© 2022 Bio-Rad Laboratories, Inc.

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Visit bio-rad.com/QXONE for more information.
BIO-RAD, DDPCR, DROPLET DIGITAL, and QX ONE are trademarks of Bio-Rad Laboratories, Inc. in certain jurisdictions. All trademarks used herein are theproperty of their respective owner. © 2022 Bio-Rad Laboratories, Inc.
The QX ONE Droplet Digital PCR System, and the consumables and reagents designed to work with this system, and/or their use is covered by claims of U.S.
patents and/or pending U.S. and non-U.S. patent applications owned by or under license to Bio-Rad Laboratories, Inc. See bio-rad.com/en-us/trademarks fordetails. Purchase of the product includes a limited, non-transferable right under such intellectual property for use of the product for internal research purposesin the field of digital PCR only. No rights are granted for diagnostic uses. No rights are granted for use of the product for commercial applications of any kind,including but not limited to manufacturing, quality control, or commercial services, such as contract services or fee for services. Information concerning a license
for such uses can be obtained from Bio-Rad Laboratories. It is the responsibility of the purchaser/end user to acquire any additional intellectual property rights that
may be required.

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