AriaMx Real-Time PCR Software - Agilent

1 Agilent TechnologiesAriaMx Real-Time PCR SoftwareUser manual For Research Use Only. Not for use in diagnostic AriaMx Real-Time PCR ProgramNotices Agilent Technologies, Inc. 2014 2016No part of this manual may be reproduced in any form or by any means (including elec-tronic storage and retrieval or translation into a foreign language) without prior agree-ment and written consent from Agilent Technologies, Inc. as governed by United States and international copyright Part NumberG8830-90000 EditionRevision C0, February 2016 Agilent Technologies, Inc. 5301 Stevens Creek Blvd.

2 Santa Clara, CA 95051 WarrantyThe material contained in this docu-ment is provided as is, and is sub-ject to being changed, without notice, in future editions. Further, to the max-imum extent permitted by applicable law, Agilent disclaims all warranties, either express or implied, with regard to this manual and any information contained herein, including but not limited to the implied warranties of merchantability and fitness for a par-ticular purpose. Agilent shall not be liable for errors or for incidental or consequential damages in connec-tion with the furnishing, use, or per-formance of this document or of any information contained herein.

3 Should Agilent and the user have a separate written agreement with warranty terms covering the material in this document that conflict with these terms, the warranty terms in the sep-arate agreement shall Licenses The hardware and/or Software described in this document are furnished under a license and may be used or copied only in accor-dance with the terms of such Rights Government Restricted Rights. Soft-ware and technical data rights granted to the federal government include only those rights customarily provided to end user cus-tomers. Agilent provides this customary commercial license in Software and techni-cal data pursuant to FAR (Technical Data) and (Computer Software ) and, for the Department of Defense, DFARS (Technical Data - Commercial Items) and DFARS (Rights in Commercial Computer Software or Com-puter Software Documentation).

4 Safety NoticesCAUTIONA CAUTION notice denotes a haz-ard. It calls attention to an operat-ing procedure, practice, or the like that, if not correctly performed or adhered to, could result in damage to the product or loss of important data. Do not proceed beyond a CAUTION notice until the indicated conditions are fully understood and met. WARNINGA WARNING notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that, if not correctly per-formed or adhered to, could result in personal injury or death. Do not proceed beyond a WARNING notice until the indicated condi-tions are fully understood and AriaMx Real-Time PCR Program31 Getting Started with the AriaMx Program 15 The AriaMx program 16 Getting Started with the AriaMx Software 17 Introduction to the AriaMx Software 17 Overview of the user interface 19 Home screen 19 Menu toolbar 19 Tabs 19 Left and right panels 19 Home/Notifications/Help icons 20 Getting Started screen 20 Experiment Notes / Project Notes 20 Help access for the AriaMx Software 21

5 Help system 21 Video tutorials 22 Sample experiments 222 Specifying Instrument and Program Settings 23 Update instrument optics 24 Change the default crosstalk correction settings 26 Set program preferences 293 Performing Hardware and Software Tests and HRM Calibrations 31 Run an instrument qualification test 32 Run the test 32 About the Qualification Test graphical data 33 Perform an Installation Qualification test 35 Run an HRM calibration plate (HCP) 37 Prepare the plate 37 Run an HCP 384 Agilent AriaMx Real-Time PCR ProgramIf the HCP fails 394 Creating/Opening an Experiment 41 Overview of the Getting Started screen 42 Tools available on the Getting Started screen 43 About the AriaMx file types 44 Quick Start Protocol 45 How to create, set up, run, analyze.

6 And generate reports for an experiment 45 Create a new experiment 48 Create an experiment based on experiment type 48 Create an experiment from a template 49 Open an existing experiment 50 Save a copy of an existing experiment 51 Create a template from an existing experiment 52 Convert an experiment to a new experiment type 535 Selecting an Experiment Type 55 Overview of Experiment Types 56 Quantitative PCR 56 Comparative Quantitation 56 Allele Discrimination - Fluorescence Probes 57 Allele Discrimination - DNA Binding Dye with High-Resolution Melt 57 user Defined 57 The Quantitative PCR Experiment Type 58 Multiplexing quantitative PCR experiments 58 Well types for Quantitative PCR experiments 59 The Comparative Quantitation Experiment Type 60 Normalizing chance variations in target levels 60 Determining amplification efficiencies for the targets of interest and normalizer targets 61 Agilent AriaMx Real-Time PCR Program5 Including biological replicates in comparative quantitation 62 Well types for Comparative Quantitation experiments

7 63 The Allele Discrimination - DNA Binding Dye Experiment Type 64 About HRM calibration plates 64 Well types for Allele Discrimination - DNA Binding Dye experiments 65 The Allele Discrimination - Fluorescence Probe Experiment Type 66 Well types for Allele Discrimination - Fluorescence Probe experiments 67 The user Defined Experiment Type 686 Setting Up the Plate 69 Overview of the Plate Setup screen 70 The plate map 71 Well type 71 Well name / Sample name 71 Target information 72 Replicate number 72 Reference dye 72 The Properties panel 73 Additional tools for setting up a plate 73 Import a plate setup 75 Select and view wells in the plate map 76 Select wells in the plate map 76 Unselect wells in the plate map 77 View details of a well or wells 77 Export the plate map image 82 Assign plate properties for a Quantitative PCR DNA Binding Dye experiment 83 Assign well types 83 Assign well names 83 Assign dyes/targets 84 Select a reference dye 856 Agilent AriaMx Real-Time PCR ProgramAssign replicates

8 86 Assign quantities to Standard wells 88 Assign plate properties for a Quantitative PCR Fluorescence Probe experiment 90 Assign well types 90 Assign well names 90 Assign dyes/targets 91 Select a reference dye 92 Assign replicates 93 Assign quantities to Standard wells 95 Assign plate properties for a Comparative Quantitation experiment 97 Assign well types 97 Assign well names 98 Assign sample names and biological replicates 98 Assign dyes/targets 100 Select a reference dye 101 Designate the normalizer 101 Assign replicates 102 Assign quantities to Standard wells 104 Assign plate properties for an Allele Discrimination DNA Binding Dye experiment 106 Assign well types 106 Assign well names 107 Assign sample names 107 Assign dyes/targets 108 Select a reference dye 109 Assign replicates 110 Assign plate properties for an Allele Discrimination Fluorescence Probe experiment 113 Assign well types 113 Assign well names 114 Assign sample names 114 Assign dyes/targets 115 Select a reference dye 116 Agilent

9 AriaMx Real-Time PCR Program7 Assign Alleles 117 Assign replicates 117 Assign plate properties for a user Defined experiment 120 Assign well types 120 Assign well names 120 Assign sample names and biological replicates 121 Assign dyes/targets 123 Select a reference dye 124 Designate the normalizer 124 Assign Alleles 125 Assign replicates 125 Assign quantities to Standard wells 1287 Setting Up the Thermal Profile 129 Set up the thermal profile 130 Elements of a Thermal Profile 131 Edit the thermal profile 133 Export the thermal profile image 1428 Running and Monitoring Experiments 143 Overview of the Instrument Explorer dialog box 144 Add instruments to your network 145 Add a new instrument based on its IP address 145 Add a new instrument based on its port number 146 View information about an instrument 146 Start, stop, or pause a run 148 Start a run 148 Cancel a run 149 Pause a run 150 Monitor a run 151 Connect to the running instrument 1518 Agilent AriaMx real -Tim