Droplet Digital PCR

QX ONE™ Droplet Digital™ PCR (ddPCR™) System
Workflow Tips for SuccessInstrument Power-Up Sequence■ Turn on the back switch, then the front switch, and wait
5 min before launching the QX ONE Software. Do not touch
the instrument or screen while the instrument is initializing■

 fter 5 min, launch the QX ONE Software and log in. TheA
instrument will switch from busy to ready in 2–3 minutes. Do nottouch the instrument or screen while the instrument is initializing

Sample Loading to the GCR96 Cartridges■■■Note: If the instrument is being power cycled, turn off the back
instrument switch and wait a full 3 min before following thepower-up sequence.
Starting a New Set of Experiments■ If the QX ONE instrument is already powered on and has
previously been running experiments, it is recommended that
the QX ONE Software be fully closed, then reopened after
3 min. This ensures a fresh instance of the software for theupcoming run
Plate Preparation
Sample Preparation■■■

 lways refer to the supermix product insert for instructions onA
sample handling, preparation, reaction setup, thermal cycling
conditions, and sample fragmentation, specific to the supermix
being used

 ortex samples and reagents well as outlined in the productVinsert for the supermix being usedEnsure the supermix concentration is 1x in final reaction■

Use RAININ tips for all sample handling and reaction setup steps

■

■

■

 nsure pipets are calibrated according to the manufacturer’sE
recommendations
 ortex the master mix on high for a minimum of 15 seconds
Vwhen using the 2x supermix and 30 sec when using the 4x
multiplex supermix entrifuge tubes and/or plates to settle contents andC
eliminate bubbles

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

 o not press the pipet plunger beyond the initial stop, as it willD
introduce unwanted bubbles inside the well he GCR96 Cartridge contains 6 individual DG16 Cartridges
Trepresenting 6 sets of 16 wells (2 columns per DG16 Cartridge).
Each set of 16 must be filled with either a sample or 1:1 ratio ofwater and ddPCR Buffer Control for Probes (catalog #1863052).
Do not use water or leave empty wells blank. Correct backfillingwith ddPCR Buffer Control is required for successful andefficient droplet generation in all wells
 o not vortex the GCR96 Cartridges. You should vortex
Dthe samples/reagents/master mix before loading into theGCR96 Cartridges
 oad only 20 µl per GCR96 well. GCR96 Cartridges are notL
designed for more than a 20 µl reaction volumePlate Sealing■■ or DNA applications, thaw samples and reagents completely atF
room temperature for 15–30 minutes

■

■

■

 ransfer 20 µl of the ddPCR reaction to the bottom of each wellTwithin the GCR96 Cartridge■■■

 ake sure the PX1 PCR Plate Sealer is set at 180°C for 0.5 sec.
MConfirm settings, specifically if you have a QX200™ Droplet Digital
PCR (ddPCR) System nearby ake sure the foil seal is squarely centered on top of theM
GCR96 Cartridge with no overhangs. Double red stripes
should be visible se only a 1-foil seal. Double-foil seals will create issues
U
assessing contents in the wells
 efore sealing the GCR96 Cartridge, ensure the support block
Bis oriented correctly. Position the block so that the overhanging
edge faces away from the user
 eal the GCR96 Cartridge with a foil seal, rotate the cartridge
S180 degrees, place back on the support block, and seal asecond timeCentrifuge■

Centrifuge the GCR96 Cartridge for 30 sec at 1,150 rcf■

Do not centrifuge for more than 1 minuteQX ONE Droplet Digital PCR (ddPCR) System: Workflow Tips for Success

Plate Layout■ For software version 1.0–1.2, when running fewer than 96 wells,
fill the remaining wells in the GCR96 plate with ddPCR Buffer
Control for Probes (#1863052). For software version 1.3 or later,
DG16 strips not containing samples may be left empty

Automatic Plate Recovery■ In a case of a failure during a run, follow the automatic plate
recovery process detailed in the QX ONE System User Guide(Automatically Recovering Plates from Failed Runs section
or Recovering Plates from Failed or Canceled Runs section)

Protocol Setup■ 
Unlike the QX200 ddPCR System, a 30 min hold at 4°C
is not recommended to increase droplet counts. There islittle positive impact on droplet count from a 4°C hold on
the QX ONE ddPCR System■Oil Bottles■ Keep all droplet generation (DG) oil, droplet reader (DR) oil, andwaste bottles loaded during operation to improve run outcomes
and reduce errors

Loading Plates into the System■ When loading GCR96 plates into the new plate hotel, ensure thatplates click into place and the position-indicator LEDs switchfrom yellow to green■■ hen scanning the radio frequency identification (RFID) tag
Won a GCR96 Cartridge, the software will automatically open
and close the inbox hotel door. Alternatively, users can use theInbox/Outbox buttons in the software to manually control thehotel doors. Do not physically manipulate the hotel doors■■

Loading Multiple Plates into the Instrument■ When adding a plate after a run has already started and anerror occurs when scanning, follow the prompts to delete thenew plate row before attempting to rescan the RFID tag on theGCR96 Cartridge■■

 hen encountering more than 1 instance where the QX ONEW
Software misidentifies an oil bottle as empty, even thoughbottles are partially filled, please contact Bio-Rad TechnicalSupport for assistanceIf running with only 1 DG oil, 1 DR oil, or 1 waste bottle, do notremove bottles during the runIf the QX ONE System is idle for more than 1 week, please
remove the waste oil bottle(s), invert, and store until needed

Future Upgrades■ All hardware, firmware, and software upgrades to your
QX ONE System need to be performed by a Bio-Rad Field
Service Engineer
CPU/Software Compatibility■ To ensure successful compatibility between the computer/laptop
and QX ONE Software, confirm the current CPU does
not have an Iris Xe Graphics Chipset. In most cases, installing
the QX ONE Software on PCs containing Iris Xe Chipsets canlead to extreme performance degradationIf the RFID scanner does not recognize a new GCR96 plate,reboot the QX ONE Software if the system is idle and attempt torescan the plate. If the system is not idle, store the plate at 4°C
and wait until the current plates are finished processing to power
cycle the instrument

Data Analysis■ It is recommended that fully processed data files are notanalyzed on the QX ONE instrument while the instrument isrunning workflows, particularly when the instrument is running
data acquisition with the droplet reader. Data acquisition is amemory-intensive process for the computer■If you are using manual recovery, contact Bio-Rad TechnicalSupport for assistance before proceeding■■It is recommended to move the .ddpcrone/.ddpcrsone files toa separate computer for data analysis if the QX ONE instrument
is running workflows. There is an option to automatically transfer
all files to a networked drive hen installing the QX ONE Software on a laptop/PC, selectW
English as the default language. Selecting a default language
other than English can lead to unwanted errors
 o increase the speed of analysis while using all pertinent
Tsoftware features, tailor your focus and analysis to only thedesired wells utilizing the well selector. Select only the wells
that you wish to analyzeIf you wish to use live analysis of a plate that is currently running,give the system time to process. Do not click multiple times
if the computer is running slowly© 2023 Bio-Rad Laboratories, Inc.

2

Bulletin 3284

QX ONE Droplet Digital PCR (ddPCR) System: Workflow Tips for Success

Visit bio-rad.com/QXONE for more information.
BIO-RAD, DDPCR, DROPLET DIGITAL, DROPLET DIGITAL PCR, QX ONE, and QX200 are trademarks of Bio-Rad Laboratories, Inc. in certain jurisdictions.
All trademarks used herein are the property of their respective owner. © 2023 Bio-Rad Laboratories, Inc.
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://www.bio-rad.com/en-us/terms-conditions. Unless we expressly state otherwise
in additional Terms and Conditions, no rights are granted for you to distribute or resell the Products. Unless we expressly state otherwise in additional Terms andConditions, no rights are granted for the development or commercialization 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 diagnostic uses) and (ii) sale of assays for use on Bio-Rad’s dPCRand ddSEQ instruments. The Products and/or their use 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://www.bio-rad.com/en-us/trademarks.

Bio-RadLaboratories, Inc.
Website bio-rad.com USA 1 800 424 6723 Australia 61 2 9914 2800 Austria 00 800 00 24 67 23 Belgium 00 800 00 24 67 23 Brazil 4003 0399
Canada 1 905 364 3435 China 86 21 6169 8500 Czech Republic 00 800 00 24 67 23 Denmark 00 800 00 24 67 23 Finland 00 800 00 24 67 23France 00 800 00 24 67 23 Germany 00 800 00 24 67 23 Hong Kong 852 2789 3300 Hungary 00 800 00 24 67 23 India 91 124 4029300 Israel 0 3 9636050
Italy 00 800 00 24 67 23 Japan 81 3 6361 7000 Korea 82 080 007 7373 Luxembourg 00 800 00 24 67 23 Mexico 52 555 488 7670
The Netherlands 00 800 00 24 67 23 New Zealand 64 9 415 2280 Norway 00 800 00 24 67 23 Poland 00 800 00 24 67 23 Portugal 00 800 00 24 67 23
Russian Federation 00 800 00 24 67 23 Singapore 65 6415 3188 South Africa 00 800 00 24 67 23 Spain 00 800 00 24 67 23 Sweden 00 800 00 24 67 23
Switzerland 00 800 00 24 67 23 Taiwan 886 2 2578 7189 Thailand 66 2 651 8311 United Arab Emirates 36 1 459 6150 United Kingdom 00 800 00 24 67 23Life ScienceGroup

Bulletin 3284 Ver B

US/EG23-0735

1023

Sig 0123