Thermo Scientific Applied Biosystems QuantStudio User manual

For Research Use Only. Not for use in diagnostic procedures.
QuantStudio™3D Digital PCR System
USER GUIDE
for use with:
QuantStudio™3D Digital PCR Instrument
ProFlex™2 × Flat PCR System or Dual Flat Block GeneAmp™PCR
System 9700
QuantStudio™3D Digital PCR 20K Chip v2
QuantStudio™3D Digital PCR Master Mix v2
QuantStudio™3D Digital PCR Chip Loader
Catalog Number A29154
Publication Number MAN0007720
Revision E.0

Manufacturer:
Life Technologies Holdings Pte Ltd |
Block 33 |
Marsiling Industrial Estate Road 3 |
#07-06, Singapore 739256
Products:
QuantStudio™3D Digital PCR Instrument
ProFlex™2 × Flat PCR System
Dual Flat Block GeneAmp™PCR System 9700
QuantStudio™3D Digital PCR Chip Loader
Manufacturer:
Life Technologies Corporation |
6055 Sunol Blvd |
Pleasanton, CA 94566
Products:
QuantStudio™3D Digital PCR 20K Chip v2
Life Technologies Corporation |
7335 Executive Way | Frederick, MD
21704 | USA
Products:
QuantStudio™3D Digital PCR Master Mix v2
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. MAN0007720
Revision Date Description
E.0 18 March 2020 Removed the v1 chip and master mix. Updated template and legal
information. Updated “Prepare the dPCR reaction mix for each sample”
on page 23. Updated thermal cycling parameters. Reformatted “Install
the GeneAmp™PCR System 9700” on page 73.
D.0 15 July 2015 Updated for v2 chips, lids, and master mix. Also updated with changes
to instrument rmware, including adjusting for the different well volumes
between v1 and v2 chips. Includes improvements to the chip loading and
imaging workows.
C.0 February 2015 Updated for rmware and software revisions, including changes to
instrument networking, thermal cycling, chip analysis, maintenance,
software access, and computer requirements. Updated to latest
corporate boilerplate. Updated general sample and chip preparation,
system installation, troubleshooting, and parts and materials.
B.0 April 2014 Added support for the ProFlex™PCR System and revised the chip
loading instructions.
A.0 December 2013 Updated the manual chip preparation and added procedures for chip
preparation using the QuantStudio™3D Digital PCR Chip Loader and
wireless network installation.
02 June 2013 Updated general chip preparation and instrument networking.
01 March 2013 Initial version
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.
Trademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TaqMan is a
registered trademark of Roche Molecular Systems, Inc., used under permission and license.
©2020 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ....................................... 8
About the QuantStudio™3D Digital PCR System .................................... 8
Instruments, kits, consumables, and accessories ................................... 9
Required materials not supplied ................................................. 10
Power line regulator ........................................................ 12
Surge protector ............................................................ 12
About the instrument ........................................................... 12
Data collection ............................................................ 13
Supported dyes ........................................................... 13
About the software ............................................................. 13
System requirements ....................................................... 13
About the chip ................................................................. 14
■CHAPTER 2 Getting Started ........................................... 15
Operational workow ........................................................... 16
Connect the QuantStudio™3D Digital PCR Instrument to a network .................. 17
Connect the QuantStudio™3D AnalysisSuite™Software ............................ 17
Choosing a thermal cycler ....................................................... 17
Compatible thermal cyclers ................................................. 17
■CHAPTER 3 Prepare the digital PCR reaction and load
the chips .................................................................. 19
Guidelines for loading and sealing chips .......................................... 19
Prepare the DNA samples ....................................................... 20
Quality of DNA ............................................................ 20
Quantity of DNA ........................................................... 20
Sample dilution ............................................................ 21
QuantStudio™3D Digital PCR System User Guide 3

Determine the optimal dilution when the target is known ........................ 21
Determine the optimal dilution when the target is unknown ...................... 22
Prepare the digital PCR reactions ................................................ 22
Required materials ......................................................... 22
Guidelines for dPCR sample preparation ..................................... 22
Recommended DNA volume and concentration ............................... 23
Prepare the dPCR reaction mix for each sample ............................... 23
Load the chips using the QuantStudio™3D Digital PCR Chip Loader ................. 24
Materials required ......................................................... 24
Chip loader status light ..................................................... 25
Prepare the chip loading workspace ......................................... 25
Prepare the syringe containing the Immersion Fluid ............................ 26
Load and seal the chips .................................................... 27
Fill the chip case with Immersion Fluid ....................................... 30
Seal the chip case with the label ............................................. 31
■CHAPTER 4 Thermal cycle the chips ................................. 32
Materials required .............................................................. 32
Prepare the thermal cycler ...................................................... 32
Guidelines for handling loaded chips ............................................. 35
Perform the PCR ............................................................... 36
Unload the thermal cycler ....................................................... 38
■CHAPTER 5 Image and analyze the chips ........................... 40
About imaging and primary analysis .............................................. 40
QuantStudio™3D System data ow .......................................... 40
About the instrument interface ................................................... 41
Chip imaging .................................................................. 42
Materials required ......................................................... 42
Guidelines for imaging multiple chips ......................................... 42
Specify the data destination ................................................. 42
Image the chips ........................................................... 43
Primary analysis ............................................................... 46
About imaging data and primary analysis ..................................... 46
About the results screen .................................................... 47
Data quality ags .......................................................... 48
About data les ............................................................ 48
Transfer the results ......................................................... 49
Using the QuantStudio™3D AnalysisSuite™Software .............................. 51
Access the software from a Connect cloud-based platform account ............. 51
Access the software from the server ......................................... 51
Obtain information from the Help system ..................................... 53
Contents
4QuantStudio™3D Digital PCR System User Guide

■CHAPTER 6 Troubleshooting .......................................... 54
Troubleshooting chip images using the Chip View .................................. 54
■APPENDIX A Install the QuantStudio™3D Digital PCR System .... 61
Time required for installation ..................................................... 61
Materials required .............................................................. 61
Before you begin ............................................................... 61
Plan the laboratory layout ....................................................... 62
Choose the instrument locations ................................................. 62
Install the QuantStudio™3D Digital PCR Instrument ................................ 63
Install the ProFlex™2 × Flat PCR System ......................................... 68
Unpack and place the ProFlex™PCR System Base Module ..................... 68
Prepare the workspace and instrument ....................................... 69
Install the Tilt Base ......................................................... 69
Unpack and install the sample block module .................................. 71
Set up the ProFlex™PCR System ............................................ 71
Install the GeneAmp™PCR System 9700 .......................................... 73
Unpack and place the GeneAmp™PCR System 9700 Base Module .............. 73
Unpack and install the Dual Flat Block Module ................................ 74
Install the Tilt Base and Chip Adapter ........................................ 75
Set up the GeneAmp™PCR System 9700 ..................................... 75
■APPENDIX B Specications and Layout ............................. 79
Component dimensions and weights ............................................. 79
QuantStudio™3D Digital PCR Instrument layout and connections .................... 80
Instrument clearances .......................................................... 80
Electrical specications ......................................................... 81
Environmental requirements ..................................................... 82
Network requirements .......................................................... 83
■APPENDIX C Maintenance ............................................ 84
Cleaning the chip tray and sample block .......................................... 84
Materials required ......................................................... 84
Clean the chip tray or sample block .......................................... 85
Congure the instrument settings ................................................ 86
(Optional) Set the instrument name .......................................... 86
Set the date and time ...................................................... 87
Check the instrument rmware .................................................. 87
Update the instrument rmware ............................................. 88
Returning your instrument for service ............................................. 89
Contents
QuantStudio™3D Digital PCR System User Guide 5

Replace the instrument fuses .................................................... 90
Materials required ......................................................... 90
Replace the fuses .......................................................... 90
Calibrate the touchscreen ....................................................... 91
View the instrument log ......................................................... 92
■APPENDIX D Networking .............................................. 94
Networking overview ........................................................... 94
About the network port and wireless adaptor .................................. 94
Networking guidelines and best practices ..................................... 95
Connect the instrument to the network ........................................... 95
Network setup workow .................................................... 96
Materials required ......................................................... 96
Required network information ............................................... 96
Connect the QuantStudio™3D Digital PCR Instrument to a network .............. 98
Create a network destination to receive run data ............................. 103
■APPENDIX E Load chips manually .................................. 106
Guidelines for loading and sealing chips ......................................... 106
Materials required ............................................................. 107
Prepare the syringe containing the Immersion Fluid ............................... 107
Load and seal the chips manually ............................................... 108
Fill the chip case with Immersion Fluid ........................................... 111
Seal the chip case with the label ................................................ 112
■APPENDIX F Safety ................................................... 113
Symbols on this instrument .................................................... 113
Conformity symbols ...................................................... 114
Safety alerts on this instrument ................................................. 115
Location of safety alerts on the instrument ................................... 115
Safety information for instruments not manufactured by Thermo Fisher Scientic ..... 116
Instrument safety ............................................................. 116
General ................................................................. 116
Electrical safety .......................................................... 117
Cleaning and decontamination ............................................. 118
Safety and electromagnetic compatibility (EMC) standards ......................... 118
Safety ................................................................... 119
EMC .................................................................... 119
Environmental design ..................................................... 119
Chemical safety .............................................................. 120
Biological hazard safety ....................................................... 122
Contents
6QuantStudio™3D Digital PCR System User Guide

■Documentation and support ........................................... 123
Related documentation ........................................................ 123
Customer and technical support ................................................ 123
Limited product warranty ...................................................... 124
Contents
QuantStudio™3D Digital PCR System User Guide 7

Product information
About the QuantStudio™3D Digital PCR System
The QuantStudio™3D Digital PCR System provides quantitative and qualitative
detection of target nucleic acid sequences (targets) using post-PCR (endpoint)
analysis.
Use the QuantStudio™3D Digital PCR Instrument to perform imaging and preliminary
analysis of a QuantStudio™3D Digital PCR 20K Chip v2. The chip must have been
loaded with uorescent-labeled quantitative PCR reagents (TaqMan™probe-based
assays or SYBR™Green primer-based assays) and thermal cycled using a ProFlex™
2 × Flat PCR System (or Dual Flat Block GeneAmp™PCR System 9700). The
QuantStudio™3D AnalysisSuite™Software performs subsequent analysis and post-
processing to yield relative or absolute quantication results from the raw imaging
data.
1
4
3
6
7
8
59
10
212
11
Figure 1 Components of the QuantStudio™3D Digital PCR System
1QuantStudio™3D Digital PCR Thermal Pads
2QuantStudio™3D Digital PCR Chip Adapters
3ProFlex™2 × Flat PCR System (or Dual Flat Block GeneAmp™PCR System 9700)
4QuantStudio™3D Tilt Base
5QuantStudio™3D Digital PCR Instrument
6QuantStudio™3D Digital PCR Chip Lid v2
7QuantStudio™3D Digital PCR Sample Loading Blade
8QuantStudio™3D Digital PCR 20K Chip v2
9(Optional) QuantStudio™3D Digital PCR Chip Loader
10 Immersion Fluid syringe
11 QuantStudio™3D Digital PCR Master Mix v2
12 Fluorescent-labeled quantitative PCR reagents (TaqMan™Assays or SYBR™Green primers)
13 (Not shown) QuantStudio™3D AnalysisSuite™Software
1
8QuantStudio™3D Digital PCR System User Guide

Instruments, kits, consumables, and accessories
The following tables describe the products covered in this user guide.
Instrument system
Item Catalog No. Amount
QuantStudio™3D Digital PCR System package
with v2 chips and master mix, includes:
•QuantStudio™3D Digital PCR Instrument
•QuantStudio™3D Digital PCR Chip Loader
•QuantStudio™3D Digital PCR 20K Chips v2
•QuantStudio™3D Digital PCR Master Mix
v2
•ProFlex™2 × Flat PCR System
A29154 1 system
QuantStudio™3D Digital PCR Instrument with
power cord
4489084 1 instrument
QuantStudio™3D Digital PCR Tilt Base for
ProFlex™Thermal Cycler
A24898 1 base
QuantStudio™3D Digital PCR Tilt Base for
GeneAmp™PCR System 9700
4486414 1 base
QuantStudio™3D Digital PCR Chip Adapter Kit
for Flat Block Thermal Cycler
4485513 1 adapter
QuantStudio™3D Extended Arm WiFi Adapter A28598 1 wireless adapter
QuantStudio™3D Digital PCR 20K Chip Kit v2
and Master Mix v2, includes:
•8 × 12 packs of v2 chips, chip lids, and
QuantStudio™3D Digital PCR Sample
Loading Blades
•24 syringes of Immersion Fluid, plus tips
•1.5 mL of QuantStudio™3D Digital PCR
Master Mix v2
A26317 1 kit (96 chips)
QuantStudio™3D Digital PCR 20K Chip Kit v2,
includes:
•12 v2 chips, chip lids, and
QuantStudio™3D Digital PCR Sample
Loading Blades
•3 syringes of Immersion Fluid, plus tips
A26316 1 kit (12 chips)
QuantStudio™3D Digital PCR Immersion Fluid,
1.6 mL per syringe
A27322 3 syringes
Chapter 1 Product information
Instruments, kits, consumables, and accessories 1
QuantStudio™3D Digital PCR System User Guide 9

Instrument system
Item Catalog No. Amount
QuantStudio™3D Digital PCR Chip Loader 4482592 1 loader
QuantStudio™3D Digital PCR Chip Lids v2 and
QuantStudio™3D Digital PCR Sample Loading
Blades
A29247 12 each
QuantStudio™3D Digital PCR Master Mix v2 A26358
A26359
1.5 mL
5.0 mL
QuantStudio™3D Digital PCR Reagent Kit,
includes:
•Assays and reagents for system installation
and verication, or training of operators on
the use of the system
A26360 1 kit
QuantStudio™3D Digital PCR Starter Kit,
includes:
•QuantStudio™3D Digital PCR Reagent Kit
• QuantStudio™3D Digital PCR
20K Chip Kit v2 (12 chips)
A26361 1 kit
Required materials not supplied
This system uses common molecular biology equipment, supplies, and reagents.
Unless otherwise indicated, all materials are available through thermofisher.com.
"MLS" indicates that the material is available from fisherscientific.com or another
major laboratory supplier.
Item Source
Clean room-grade, low-lint polyester wipes Fisher Scientic
(Cat. No. NC0375992) or MLS
Gloves, powder-free, nitrile MLS
Microcentrifuge MLS
Pipette tips, 10 to 1000 μL MLS
Pipettes, P10 to P1000 MLS
Reaction tubes, DNase/RNase-free, non-stick or
low-binding: 0.5-mL or 1.5-mL
Fisher Scientic
(Cat. No. 13-864-253 or
13-864-254) or MLS
Vortexer MLS
Chapter 1 Product information
Required materials not supplied
1
10 QuantStudio™3D Digital PCR System User Guide