QuantStudio™ 3D Digital PCR System

for use with:

QuantStudio™ 3D Digital PCR Instrument

Dual Flat Block GeneAmp® PCR System 9700

QuantStudio™ 3D Digital PCR Master Mix

QuantStudio™ 3D Digital PCR 20K Chip

QuantStudio™ 3D Digital PCR Chip Loader

Catalog Number 4482593 and 4481097

Publication Number MAN0007720

Revision A.0

QUANT STUDIO 3D QuanStudio 3D

For Research Use Only. Not for use in diagnostic procedures.

The information in this guide is subject to change without notice.

DISCLAIMER

LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. TO THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF.

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

The trademarks mentioned herein are the property of Life Technologies Corporation and/or its affiliate(s) or their respective owners. Microsoft and Windows are registered trademarks of Microsoft Corporation. Macintosh is a registered trademark of Apple, Inc. TaqMan is a registered trademark of Roche Molecular Systems, Inc., used under permission and license.

© 2013 Life Technologies Corporation. All rights reserved.

About This Guide ..... 7
Revision history ..... 7
Purpose ..... 7
Prerequisites ..... 7
Instrument hardware ..... 8
Instrument software ..... 8
Computer requirements ..... 8
Instrument consumables ..... 9
About the Digital PCR 20K Chip ..... 9
CHAPTER 1 Getting Started ..... 10
About the QuantStudio™ 3D Digital PCR System ..... 10
Data collection ..... 11
Instrument filters and supported dyes ..... 11
Operating the instrument ..... 12
Compatible reagent kits and consumables ..... 12
Operational workflow ..... 12
Prepare the QuantStudio™ 3D Digital PCR System for use ..... 13
About the installation ..... 13
Materials required ..... 13
Before you begin ..... 13
Plan the laboratory layout ..... 13
Choose additional protective devices ..... 15
Install the QuantStudio™ 3D Digital PCR System ..... 15
Configure the GeneAmp® PCR System 9700 settings ..... 25
Connect the QuantStudio™ 3D Instrument to a network ..... 27
Connect the QuantStudio™ 3D AnalysisSuite™ Software ..... 27
CHAPTER 2 Prepare Samples and Load Reactions ..... 28
Prepare the DNA samples ..... 28
Quality of DNA ..... 28
Quantity of DNA ..... 28
Sample dilution ..... 29
Determine the optimal dilution when the target is known ..... 29

Determine the optimal dilution when the target is unknown ..... 30
Prepare the digital PCR reactions ..... 30
Required materials ..... 30
Guidelines for PCR sample preparation ..... 30
Prepare the reaction mix and samples ..... 31
Load the Digital PCR 20K Chips ..... 32
Guidelines for loading and sealing Digital PCR 20K Chips ..... 32
Load the chips using the Chip Loader ..... 33
Load chips manually ..... 41
CHAPTER 3 Perform the PCR ..... 49
Choosing a thermal cycler ..... 49
About the Dual Flat Block GeneAmp® PCR System 9700 ..... 49
Prepare the GeneAmp® PCR System 9700 ..... 50
Thermal cycle the Digital PCR 20K Chips ..... 52
Materials required ..... 52
Guidelines for handling Chip Cases ..... 52
Perform the PCR ..... 53
Unload the thermal cycler ..... 55
CHAPTER 4 Analyze the Prepared Chips ..... 57
Using the QuantStudio™ 3D Digital PCR Instrument ..... 57
About imaging and primary analysis ..... 57
Analysis workflow ..... 58
About the instrument interface ..... 59
Analyze the chips ..... 60
Materials required ..... 60
Guidelines for high-throughput analysis ..... 60
Image the Digital PCR 20K Chips ..... 60
Analyzing the data ..... 63
About the analysis ..... 63
About the results screen ..... 64
About data quality flags ..... 65
About the data files ..... 65
Transfer the results ..... 66
Using the QuantStudio™ 3D Analysis Suite™ Software ..... 67
Computer requirements ..... 67
Access the software from a cloud account ..... 68
Obtaining information from the Help system ..... 68
CHAPTER 5 Troubleshooting ..... 69
Troubleshooting chip images using the Chip View ..... 69

APPENDIX A Maintenance ..... 72
Cleaning the chip tray and sample block ..... 72
Materials required ..... 72
Clean the chip tray or sample block ..... 73
Configure the instrument settings ..... 73
Set the instrument name ..... 73
Set the date and time ..... 74
Returning your QuantStudio™ 3D Instrument for service ..... 75
Replace the instrument fuses ..... 75
Materials required ..... 75
Replace the fuses ..... 76
Update the instrument firmware ..... 76
Update the firmware ..... 77
View the instrument log ..... 77
View the log ..... 78
APPENDIX B Networking ..... 79
Networking overview ..... 79
About the network port and wireless adapter ..... 79
Networking guidelines and best practices ..... 80
Connect the instrument to the network ..... 80