ThermoFisher Scientific QuantStudio Series User Manual

For Research Use Only. Not for use in diagnostic procedures.
QuantStudio
™
Design and Analysis v2
USER GUIDE
for use with:
QuantStudio
™
7 Pro Real-Time PCR System
QuantStudio
™
6 Pro Real-Time PCR System
QuantStudio
™
5 Real-Time PCR System
QuantStudio
™
3 Real-Time PCR System
QuantStudio
™
1 Real-Time PCR System
Publication Number MAN0018202
Revision F.0

ThermoFisher Scientific QuantStudio Series Specifications

General

Brand	ThermoFisher Scientific
Model	QuantStudio Series
Category	Laboratory Equipment
Language	English

Summary

CHAPTER 1 About the software

Compatible instruments

Lists instruments the software is compatible with for setting up runs.

Compatible data files

CHAPTER 3 Set up a plate file

Select a system template or existing plate file

Guide to choosing a template or file for a new plate setup.

Confirm or edit run method

Details on modifying run method elements like stages, steps, and cycles.

Select plate wells

Add samples and assign to plate wells

Methods for importing or manually adding samples to wells.

Add targets or SNP assays and assign to plate wells

Assigning targets or SNP assays to wells.

Set up the standard curve

Process for setting up standard curves for analysis.

CHAPTER 4 Review and analyze data

Workflow: General procedures to review the primary analysis results

Open a data file

Review results in the Amplification Plot

Examining amplification curves and settings.

Review the amplification status for each well

Review or edit threshold settings in the Amplification Plot

Adjusting amplification curve threshold values.

Review or edit baseline settings in the Amplification Plot

Modifying baseline start and end cycles.

Identify and omit outliers from analysis

Removing wells with outlier Cq values to improve precision.

Review results the Melt Curve Plot

Review QC alerts in the Well Table

Checking Curve Quality and Result Quality Issues.

Edit primary analysis settings

Modifying Cq, Melt, and QC settings.

Override the calibration data

Perform additional analysis

CHAPTER 5 Export results

Export the Well Table

Export data in the QuantStudio™ file format

Export data in the RDML format

Generate a report

CHAPTER 8 Manage analysis modules

About analysis modules

Select an analysis module

Choosing an analysis module for data analysis.

CHAPTER 10 About data analysis

About the quantification cycle (Cq)

Explanation of Cq calculation and its importance.

About melt curve analysis

Understanding melt curve analysis for Tm determination.

Primary analysis settings overview

Cq settings overview

Guidelines for manual threshold and baseline settings for Cq analysis

Recommendations for manual Cq analysis settings.

Melt analysis settings overview

Amplification Plot overview

Melt Curve Plot overview

APPENDIX A Troubleshooting

High fluorescence signal

Diagnosing and resolving high fluorescence signal issues.

Inconsistent communication between instrument and computer or instrument and Connect

Troubleshooting communication problems.