ThermoFisher Scientific QuantStudio 12K Flex OpenArray AccuFill... User manual

For Research Use Only. Not for use in diagnostic procedures.
QuantStudio™12K Flex OpenArray™AccuFill™
System
USER GUIDE
Use and maintenance
for use with:
OpenArray™AccuFill™Instrument
OpenArray™AccuFill™Software v2.0
Catalog Number 4471021
Publication Number MAN0025669
Revision A.0

Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition.
The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE
LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR
ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
Revision history: Pub. No. MAN0025669
Revision Date Description
A.0 30 November 2021 New document for the QuantStudio™12K Flex OpenArray™AccuFill™System (for
OpenArray™AccuFill™Software v2.0).
For documentation for OpenArray™AccuFill™Software v1.2, see “Related
documentation” on page 99.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these
products, you accept the terms and conditions of all applicable Limited Use Label Licenses.
NOTICE TO PURCHASER: DISCLAIMER OF LICENSE: Purchase of this software product alone does not imply any license under any
process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by
Thermo Fisher Scientific, either expressly, or by estoppel.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TaqMan is a
trademark of Roche Molecular Systems, Inc., used under permission and license. Microsoft and Windows are trademarks of Microsoft
Corporation. Symantec is a trademark of Symantec Corporation. McAfee is a trademark of McAfee, LLC.
©2021 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information .................................................. 7
Product description ............................................................. 7
About the instrument ............................................................ 8
Overview of the instrument ................................................... 8
About the software ............................................................. 10
Network and password security requirements ................................. 10
Overview of the software ................................................... 10
Installation of or upgrade to OpenArray™AccuFill™Software v2.0 ................ 10
File formats ............................................................... 11
Workflow ..................................................................... 13
■CHAPTER 2 Basic operations and one-time procedures ..................... 14
Basic instrument operations ..................................................... 14
Important guidelines for handling an OpenArray™Plate ............................. 15
Set the preferences ............................................................ 15
Set the general settings .................................................... 15
Set the folder defaults ...................................................... 15
Set the plate mapping defaults (full run workflow) ............................. 16
■CHAPTER 3 Initialize the system ................................................. 18
Start the system ............................................................... 18
Set up the system .............................................................. 19
Perform a system self-test ...................................................... 19
Overview of the Deck screen .................................................... 21
Reconnect the instrument ....................................................... 22
Recover from a power failure .................................................... 22
■CHAPTER 4 Download or prepare TPF or SPF files ............................ 23
Download TPF or SPF files ...................................................... 23
Create TPF or SPF files from a template .......................................... 24
QuantStudio™12K Flex OpenArray™AccuFill™System User Guide 3

■CHAPTER 5 Map plates ........................................................... 25
Overview of Map Plates features ................................................. 25
Configure the experiment design to map the plates ................................. 25
Sample plate layouts ....................................................... 27
Map a 384-well plate from 96-well plates .......................................... 30
Set up a 384-well sample plate .................................................. 35
Options to view a plate layout ................................................... 36
Export plate files ............................................................... 38
■CHAPTER 6 Set up and start the run with the quick run workflow ........... 40
Overview of the quick run workflow .............................................. 40
Overview of the Quick Run screens .............................................. 41
Before you begin—quick run workflow ............................................ 42
Configure the run—quick run workflow ........................................... 43
Configure the run with sample plate information ............................... 43
Configure the run without sample plate information ............................ 44
Verify the run setup and start the run—quick run workflow .......................... 45
■CHAPTER 7 Set up and start a run with the full run workflow ................ 47
Overview of the full run workflow ................................................. 47
Overview of the Full Run screens ................................................ 48
Before you begin—full run workflow .............................................. 50
Configure the experiment design for the full run workflow ........................... 51
Add or edit sample names—full run workflow ...................................... 52
Verify the run setup and start the run—full run workflow ............................. 52
■CHAPTER 8 Monitor run progress ............................................... 55
Deck screen during a run ....................................................... 55
Run progress .................................................................. 56
Cancel a run ................................................................... 56
Instrument disconnection during run ............................................. 57
■CHAPTER 9 Prepare the OpenArray™Plate for PCR ........................... 58
Remove the OpenArray™Plate from the instrument ................................. 58
Seal the OpenArray™Plate ...................................................... 61
Contents
4QuantStudio™12K Flex OpenArray™AccuFill™System User Guide

■APPENDIX A Cleaning and maintenance of the OpenArray™
AccuFill™Instrument .............................................................. 63
Cleaning schedule and instructions ............................................... 63
Clean the outside of the instrument .......................................... 63
Clean the inside of the instrument ........................................... 63
Spill accidents ................................................................. 64
■APPENDIX B Required materials not supplied ................................. 65
■APPENDIX C Site requirements .................................................. 67
Dimensions and weights ........................................................ 67
Components (packaged) .................................................... 67
Components (unpackaged) ................................................. 68
Configured system dimensions and connections .................................. 68
Component clearances required for installation and maintenance .................... 69
Environmental requirements ..................................................... 70
Electrical requirements ......................................................... 71
Electrical protective devices ..................................................... 72
Network requirements .......................................................... 73
Printer requirements ....................................................... 73
Safety requirements ............................................................ 74
Safety practices ........................................................... 74
Required safety equipment ................................................. 74
Third-party software ............................................................ 74
Computer requirements ......................................................... 75
Antivirus software requirements .................................................. 75
■APPENDIX D Manage the service settings ...................................... 76
View the instrument statistics .................................................... 76
Copy or save the instrument statistics ............................................ 77
View the status of the sensors ................................................... 77
Enable or disable the presence sensors ........................................... 78
Perform diagnostics tests ....................................................... 78
Perform a door lock test .................................................... 78
Perform a motion test ...................................................... 79
Perform a tip ejection test ................................................... 80
Perform a tip pickup test .................................................... 80
Perform a plate holder test .................................................. 81
Perform a loading test ...................................................... 81
View loading history log ......................................................... 83
Copy or export the loading history log ............................................ 83
Contents
QuantStudio™12K Flex OpenArray™AccuFill™System User Guide 5

View the instrument log ......................................................... 84
Copy or export the instrument log ................................................ 84
Perform a system self-test (manual start) .......................................... 84
■APPENDIX E Safety ............................................................... 85
Symbols on this instrument ..................................................... 85
Standard safety symbols ................................................... 86
Location of safety labels on the instrument .................................... 86
Control and connection symbols ............................................. 87
Conformity symbols ........................................................ 87
Safety information for instruments not manufactured by Thermo Fisher Scientific ...... 89
Instrument safety .............................................................. 89
General instrument safety ................................................... 89
Physical injury ............................................................. 91
Electrical safety ........................................................... 93
Cleaning and decontamination .............................................. 94
Instrument component and accessory disposal ................................ 94
Safety and electromagnetic compatibility (EMC) standards .......................... 94
Safety standards .......................................................... 95
EMC standards ............................................................ 95
Environmental design standards ............................................. 96
Chemical safety ................................................................ 97
Biological hazard safety ......................................................... 98
■APPENDIX F Documentation and support ...................................... 99
Related documentation ......................................................... 99
Customer and technical support ................................................. 99
Limited product warranty ...................................................... 100
Index ..................................................................................... 101
Contents
6QuantStudio™12K Flex OpenArray™AccuFill™System User Guide

Product information
■Product description .................................................................... 7
■About the instrument ................................................................... 8
■About the software ................................................................... 10
■Workflow ............................................................................ 13
IMPORTANT! Before using this product, read and understand the information in the “Safety” appendix
in this document.
Product description
The QuantStudio™12K Flex OpenArray™AccuFill™System is the automated system for loading DNA
samples and PCR master mix from a 384-well plate to OpenArray™Plates. After the OpenArray™Plates
are loaded, they are ready for real-time PCR on a compatible Applied Biosystems™real-time PCR
instrument.
The QuantStudio™12K Flex OpenArray™AccuFill™System includes the following components:
•OpenArray™AccuFill™Instrument
•OpenArray™AccuFill™Software
•Computer
The following items are key features of the OpenArray™AccuFill™Software v2.0:
•Flexible workflow options, including a full run workflow and quick run workflows
•Download or generation of TPF or SPF files from within the software
•Creation of 384-well DNA sample plate files, or mapping 384-well plate files from 96-well plates,
with easy sample renaming and recovery from pipetting errors
•Export of 96-well and 384-well sample plate files
•Export of OpenArray™Plate files in CSV or XLSX format
•Generation of loaded transcript plate file (TPF) or SNP plate file (SPF) (integrate the assay
information with the DNA sample information), and export of the files for import into a compatible
real-time PCR system
•Dispensing of PCR master mix and DNA sample across the surface of the OpenArray™Plate
For more information, see “Overview of the instrument” on page 8 or “Overview of the software” on
page 10.
1
QuantStudio™12K Flex OpenArray™AccuFill™System User Guide 7

About the instrument
Overview of the instrument
The instrument draws the PCR master mix and sample across the surface of an OpenArray™Plate.
The PCR master mix and sample do not need to be dispensed in specific volumes because the
through-holes of the OpenArray™Plate are self-metering. The PCR master mix and sample also do not
need to be specifically dispensed into the through-holes because the through-holes draw the liquid in
by capillary action.
No bubbles are trapped during the dispensing process because there are no closed wells.
For more information about OpenArray™technology, go to thermofisher.com/openarray.
For a description of the software, see “Overview of the software” on page 10.
1
2
3
Figure 1 Parts of the instrument
1Enclosure door
2instrument deck (see Figure 2 on page 9)
3Emergency stop button
Chapter 1 Product information
About the instrument
1
8QuantStudio™12K Flex OpenArray™AccuFill™System User Guide

4
3
2
1
Figure 2 Instrument deck
1Tip box holders (2); tip box installed in left holder
2OpenArray™Plate holders (4)
3Sample plate holder with sample plate installed
4Waste bin
1
2
3
Figure 3 Left side panel
1Power switch
2Power cord outlet
3USB port
Chapter 1 Product information
About the instrument 1
QuantStudio™12K Flex OpenArray™AccuFill™System User Guide 9

About the software
Network and password security requirements
Network configuration and security
The network configuration and security settings of your laboratory or facility (such as firewalls, anti-
virus software, network passwords) are the sole responsibility of your facility administrator, IT, and
security personnel. This product does not provide any network or security configuration files, utilities, or
instructions.
If external or network drives are connected to the software, it is the responsibility of your IT personnel
to ensure that such drives are configured and secured correctly to prevent data corruption or loss. It
is the responsibility of your facility administrator, IT, and security personnel to prevent the use of any
unsecured ports (such as USB, Ethernet) and ensure that the system security is maintained.
Password security
Thermo Fisher Scientific strongly recommends that you maintain unique passwords for all accounts in
use on this product. All passwords should be reset upon first sign in to the product. Change passwords
according to your organization's password policy.
It is the sole responsibility of your IT personnel to develop and enforce secure use of passwords.
Overview of the software
The v2.0 software performs the following functions:
•Sets up the OpenArray™AccuFill™Instrument to load OpenArray™Plates with samples from 384-
well plates
•Creates sample plate files for 384-well plates, which are used to set up the instrument to load the
OpenArray™Plates
•Maps 384-well plates from 96-well plates if samples were prepared in 96-well plates, creating a
384-well sample plate file
•Allows the download of TPF or SPF files from thermofisher.com/OA-platefiles
•Generates TPF or SPF files from a template
•Generates loaded TPF or loaded SPF files for a compatible real-time PCR system
•Generates OpenArray™Plate files in CSV format to import into a compatible real-time PCR system
•Corrects for loading the 384-well sample plate in a reversed orientation with the plate rotation
feature
Installation of or upgrade to OpenArray™AccuFill™Software v2.0
•Operating system requirement: Windows™10. See also “Computer requirements” on page 75.
•New users: download v2.0 software from thermofisher.com/us/en/home/global/forms/
quantstudio-12k-flex-software-download. Follow the installation wizard.
•Existing v1.2 software users: see the software release notes for v2.0.
Chapter 1 Product information
About the software
1
10 QuantStudio™12K Flex OpenArray™AccuFill™System User Guide

IMPORTANT! OpenArray™AccuFill™Software v1.2 and OpenArray™AccuFill™Software v2.0 cannot
be installed on the same computer at the same time.
File formats
The following file formats are used or generated by OpenArray™AccuFill™Software v2.0.
File Description
Sample plate file (CSV) Contains the sample layout information for the plate. It can be set up
for 96-well plates, 384-well plates, or OpenArray™Plates.
A sample plate file is used for the quick run workflow with sample
information and for the full run workflow.
•Serial number (optional)
•Well, for example, A1, A2
•Sample ID
•Description (optional)
•Dilution (optional)
•Selected area index (optional), defines the location in the sample
plate that is divided into eight sections
Note: The file must contain column headers that match the items
listed above. The sample ID is populated in the OpenArray™AccuFill™
Software. The other values are edited in Microsoft™Excel™software.
Transcript plate file (TPF) Contains OpenArray™Plate information for gene expression runs. It is
required for the quick run workflow with sample information and the full
run workflow.
•Reagent information
•Number of samples per subarray
•Target information
•Thermal protocol
SNP plate file (SPF) Contains OpenArray™Plate information for genotyping runs. It is
required for the quick run workflow with sample information and the
full run workflow.
•Reagent information
•Number of samples per subarray
•Target information
•Thermal protocol
Chapter 1 Product information
About the software 1
QuantStudio™12K Flex OpenArray™AccuFill™System User Guide 11

(continued)
File Description
Loaded TPF (XML format) •Contains the information in the original TPF file, plus the sample
information
•Generated by the instrument during a run, based on the original
TPF file
•Contains the prefix Loaded
•Imported into the compatible real-time PCR system to perform the
real-time PCR run
Loaded SPF (XML format) •Contains the information in the original SPF file, plus the sample
information
•Generated by the instrument during a run, based on the original
SPF file
•Contains the prefix Loaded
•Imported into the compatible real-time PCR system to perform the
real-time PCR run
OA.csv •Contains the sample layout for the OpenArray™Plate with sample
information
•Generated in the map plates workflow
•Used for the quick run workflow without sample information
•Used for data analysis on the QuantStudio™12K Flex System
Chapter 1 Product information
About the software
1
12 QuantStudio™12K Flex OpenArray™AccuFill™System User Guide

Workflow
1
OpenArray™AccuFill™Software v2.0 workflow
Initialize the system (page 18)
(Optional) Download or prepare TPF or SPF files (page 23)
(Optional) Map plates (page 25)
•(Optional) Create an OpenArray™Plate file (CSV)
•(Optional) Create a 384-well sample plate file (CSV)
•(Optional) Map samples from a 96-well plate to a 384-well sample plate file (CSV)
Set up and start the run
•Set up and start the run—quick run workflow
2
(page 13)
•Set up and start the run—full run workflow
3
(page 13)
2
Set up and start the run—quick run workflow
Configure the run
•Configure the run with sample plate information (page 43)
•Configure the run without sample plate information (page 44)
Verify the run setup and start the run—quick run workflow (page 45)
3
Set up and start the run—full run workflow
Configure the experiment design for the full run workflow (page 51)
Add or edit sample names—full run workflow (page 52)
Add or edit the sample names and other information associated with each sample.
Verify the run setup and start the run—full run workflow (page 52)
Chapter 1 Product information
Workflow 1
QuantStudio™12K Flex OpenArray™AccuFill™System User Guide 13

Basic operations and one-time
procedures
■Basic instrument operations ........................................................... 14
■Important guidelines for handling an OpenArray™Plate ................................... 15
■Set the preferences ................................................................... 15
Basic instrument operations
Table 1 Basic instrument operations
Operation Description
Power on or power o Toggle the power switch on or o. See Figure 3 on page 9.
Open or close the instrument
enclosure door
To open: grasp the enclosure door handle and gently, but firmly, pull
the enclosure door up.
To close: pull the enclosure door down by its handle. The door is
locked during instrument runs.
See Figure 1 on page 8.
Place a sample plate into the
sample plate holder
Insert a 384-well sample plate, with the foil seal in place and the
notched edge to the left, into the sample plate holder. Press on the
plate until you hear it snap into place. See Figure 2 on page 9.
Note: Do not remove the foil from the sample plate until prompted by
the software.
Place an OpenArray™Plate into
the OpenArray™Plate holder
Holding the OpenArray™Plate by the edges, place it into the
OpenArray™Plate holder with the barcode facing left and the serial
number facing right.
Place tip boxes on the instrument
deck
Place tip boxes with covers in their holders. See Figure 2 on page 9.
Do not stack tip boxes or use tip boxes that are past their expiration
date.
Cancel the instrument run In the Deck screen, click Cancel operation. See Figure 26 on
page 55.
Emergency stop Press the red system stop button on the front of the instrument. See
Figure 1 on page 8.
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14 QuantStudio™12K Flex OpenArray™AccuFill™System User Guide

Important guidelines for handling an OpenArray™Plate
•IMPORTANT! Do not use an OpenArray™Plate that is past its expiry date.
•Wear gloves that are one size smaller than the size you typically wear, to help prevent excess glove
material from contacting the plate while handling.
•Hold the plate by the edges, at the end opposite from the barcode.
•Do not touch the through-holes.
•After the OpenArray™AccuFill™Instrument loads each OpenArray™Plate with sample and master
mix, seal the plate immediately after loading and within one hour after opening the packaging. For
more information, see the user guide or application guide for your assay.
•If you drop a loaded plate, discard it in the appropriate waste container.
Set the preferences
Set the general settings
1. Click Preferences.
2. In the Preferences dialog box, select the General settings tab.
3. Select or deselect the Always show loading history after run completes checkbox.
If this option is selected, the loading history log is displayed after the run is complete (see “View
loading history log” on page 83).
If this option is deselected, the Deck page is displayed after the run is complete.
4. Set a selection for the Quick run default selection.
•Load with sample information
•Load without sample information
This setting defines the page that is displayed when the Quick Run page is selected. It can
be changed on the Quick Run screen when setting up a run. See “Overview of the Quick Run
screens” on page 41.
5. Click Save.
Set the folder defaults
The folder defaults set the folder that is opened when selecting a file to import into the software. A
dierent folder can be selected when importing a file.
The files are automatically saved to the selected location when files are exported.
1. Click Preferences.
2. In the Preferences dialog box, select the Folder defaults tab.
Chapter 2 Basic operations and one-time procedures
Important guidelines for handling an OpenArray™Plate 2
QuantStudio™12K Flex OpenArray™AccuFill™System User Guide 15

3. Click Change, then select the folder for the following items.
Folder Description
OpenArray Plate File Folder
(TPF or SPF files)
The folder that is opened when a TPF or SPF file
is imported to set up a run.
The folder where a new TPF or SPF file is saved
when it is downloaded or created from a template.
Default location: C:\OpenArray\OpenArray
Plates
Loaded OpenArray Plate File Folder
(Loaded TPF or loaded SPF files)
The folder where a loaded TPF or SPF file is saved
after a run is completed.
Default location: C:\OpenArray\Loaded
OpenArray Plates
Input Sample Plate Folder
(CSV files)
The folder that is opened when a sample plate file
is imported to set up a run.
Default location: C:\OpenArray\Sample
Plates
Export Data Folder
(CSV or XLSX files)
The folder where a new sample plate file or
OA.csv file is saved when mapping plates.
The folder where the instrument log or the loading
history is saved when it is exported.
Default location: C:\OpenArray\Export
Data
The selected folder for each option is the default folder in the Folders menu.
4. Click Save.
Set the plate mapping defaults (full run workflow)
This setting defines the selections when the Full Run page is selected. It can be changed on the Full
Run screen when setting up a run. See “Overview of the Full Run screens” on page 48.
1. Click Preferences.
2. In the Preferences dialog box, select the Plate mapping defaults tab.
3. Select the experiment type.
•Gene Expression
•Genotyping
•3-Sample Fixed Panel
•4-Sample Fixed Panel
4. Select the OpenArray Plate from the dropdown list.
The items in the dropdown list depend on the selection made in step 3.
Chapter 2 Basic operations and one-time procedures
Set the preferences
2
16 QuantStudio™12K Flex OpenArray™AccuFill™System User Guide

5. Select the Pipettor.
•Fixed
•Adjustable
6. Click Save.
Chapter 2 Basic operations and one-time procedures
Set the preferences 2
QuantStudio™12K Flex OpenArray™AccuFill™System User Guide 17

Initialize the system
■Start the system ...................................................................... 18
■Set up the system .................................................................... 19
■Perform a system self-test ............................................................. 19
■Overview of the Deck screen ........................................................... 21
■Reconnect the instrument ............................................................. 22
■Recover from a power failure ........................................................... 22
Start the system
IMPORTANT! To safely operate the instrument, keep the deck clear and have enough room in the
waste bin to eject the used pipette tips. See “Set up the system” on page 19.
The instrument does not initiate a self-test immediately after starting the software. A self-test is initiated
the first time that one of the following items is clicked after starting the software:
•Full Run
•Quick Run
•Service4Diagnostics
The other features in the software can be accessed after starting the software without a self-test.
1. Ensure that the instrument door is closed.
2. Power on the instrument, if it is o.
See Figure 3 on page 9.
3. Start the OpenArray™AccuFill™Software ( ).
The software checks the computer and connections as the system starts.
Proceed to set up the system (see “Set up the system” on page 19).
3
18 QuantStudio™12K Flex OpenArray™AccuFill™System User Guide

Set up the system
IMPORTANT! To safely operate the instrument, keep the deck clear and have enough room in the
waste bin to eject the used pipette tips.
1. Open the instrument door, empty the waste bin, then place the waste bin back on the instrument
deck.
CAUTION! Wear appropriate personal protection equipment while handling the waste bin.
2. Ensure that the sample plate holder and the OpenArray™Plate holders are empty.
3. Replace the tip boxes, if necessary.
See Figure 2 on page 9.
Each tip box contains 384 tips, divided into 8 sections.
When setting up a run, the status of the tip boxes is confirmed in the software. A full tip box is
recommended when starting a run.
Do not reuse tips.
4. Remove the cover from each tip box.
Note: Ensure that the tip box covers are removed from the instrument deck.
5. Close the instrument door.
The system is ready to start a run. A self-test is initiated the first time that one of the following items is
clicked after starting the software:
•Full Run
•Quick Run
•Service4Diagnostics
See “Perform a system self-test” on page 19.
Perform a system self-test
A self-test is initiated the first time that one of the following items is clicked after starting the software:
•Full Run
•Quick Run
•Service4Diagnostics
The self-test checks the following items and performs the following test:
•The waste bin is present on the deck
•The instrument door is closed
•Axis motion test
Chapter 3 Initialize the system
Set up the system 3
QuantStudio™12K Flex OpenArray™AccuFill™System User Guide 19

To start a system self-test manually, see “Perform a system self-test (manual start)” on page 84.
1. In the Deck screen, click one of the following options:
•Quick Run
•Full Run
•Service4Diagnostics
The System self-test dialog box is displayed.
2. Prepare the instrument for the self-test (see “Set up the system” on page 19).
3. Click Start test.
The system performs a self-test. The status of the self-test is displayed in the dialog box.
The Quick Run screen, the Full Run screen, or the Statistics tab of the diagnostics screen is displayed
when the self-test is complete.
Chapter 3 Initialize the system
Perform a system self-test
3
20 QuantStudio™12K Flex OpenArray™AccuFill™System User Guide