ThermoFisher Applied BioSystems, QuantStudio Design & Analysis Configuration Guide

Purpose

To provide details about the necessary steps to implement the Applied BioSystems QuantStudio Design & Analysis Connector for use with the Benchling Connect platform.

Introduction

The ThermoFisher QuantStudio Design & Analysis Connector is a component used in the context of the Benchling Connect platform to parse data from QuantStudio Design & Analysis software to an Allotrope Simple Model (ASM) and make those data available within the Benchling UI in the context of a Run. The QuantStudio Design & Analysis software is used in conjunction with the QuantStudio 1, 3, 5, 6/7 Flex, 12K, and 6/7 Pro Real-Time PCR systems.

The Benchling Connect - QuantStudio Design & Analysis Connector is a ‘file-based’ based connector, meaning that it processes Excel file (.xlsx) exports generated by the QuantStudio Design & Analysis software. The data within the file export (.xlsx) is then accessed by Benchling Connect through the use of a ‘watched’ file directory on the local computer hosting a Benchling Gateway, which has been configured via a Connection from within Benchling.

In order to successfully implement the QuantStudio Design & Analysis Connector for use with the Benchling platform, there are specific steps that need to be followed across the QuantStudio Design & Analysis software.

This guide details the steps to be taken in the QuantStudio Design & Analysis software for manual export of the results file in order to configure the integration. 

Steps within QuantStudio Design & Analysis software

The following steps should be performed by the user within QuantStudio Design & Analysis.

Prior to performing experiment:

- Updating Sample Names (optional)

- Updating the Plate Identifier (recommended)

At conclusion of experiment

- Generate the .XLSX export of the experiment data

- Ensure the .XLSX file is placed within the watched directory configured via the Benchling Connection

Supported Experiment Formats

The QuantStudio Design & Analysis software supports qPCR experiments performed in 96-well, 384-well, and an Open Array format - which is used exclusively with the QuantStudio 12K platform. The Benchling Connect - QuantStudio Design & Analysis Connect currently does not support processing data from Open Array experiments.

Updating Sample Names within QuantStudio Design & Analysis

For tracking experimental results, it is always recommended that the user provide at the point of data collection sample identifiers that correspond to entities and are either previously registered within Benchling or they wish to register upon processing of results. The user may do this by manually entering Sample Names or Importing a Sample Definition File (see p.21 QuantStudio™ Design & Analysis Software v2 User Guide).

Updating Plate Identifier within QuantStudio Design & Analysis

In all cases, it is strongly recommended that the user provide a plate identifier which corresponds to a plate currently (or to be) registered within Benchling. This is true regardless of whether the user has opted to enter sample names in the previous step.

The a plate identifier can be entered within the Plate Information view, which can be accessed under the Actions menu. Alternatively, the Barcode can be included within the Sample Definition File described in the previous step.

Generating XLSX export of experimental data

The user is expected to generate a .xlsx export from the Export window within the QuantStudio UI. 

To navigate to the Export window, the user should navigate to Actions -> Export

The user should select .xlsx as the file format. Processing of the .csv, .txt, and .xls formats are not currently supported by the Connector.

The user should select that all export tables be combined into one file.

The user should set the Destination to be the target directory specified during Connection configuration.

Steps within Benchling

From within Benchling, a user must:

1. Enable the QuantStudio Design & Analysis Connector on the tenant [internal admin console]
2. Configure a QuantStudio Design & Analysis Connection
3. Create a Result schema to structure the data to be recorded
4. Configure a Run schema to accept data from QuantStudio Design & Analysis and records Results

For steps 1 - 4, please reference the Benchling Connect Installation Guide for details related to creating and installing a Gateway and configuring a Connection.

Create Result Schema for QuantStudio Design & Analysis data

The Benchling Connect - QuantStudio Design & Analysis Connector uses the Allotrope Simple Model (ASM) to structure the information parsed from the ThermoFisher QuantStudio Design & Analysis file export (.xlsx). The data is processed in a two step process; step one from QuantStudio Design & Analysis export to the .json to (3) .csv files available for ingest to Benchling - the well file in which each each row corresponds to a well in the PCR plate, the measurement file in which each row corresponds to each measurement taken, and the group file in which each row corresponds to a ‘group’ with results aggregated across sample identifier and target DNA. 

Details about the qPCR ASM schema can be found here:

https://github.com/Benchling-Open-Source/allotropy/tree/main/src/allotropy/allotrope/schemas 

• The well file can contain the following columns (if available within the data):
• device identifier
• model number
• device serial number
• data system instance identifier
  - this represents the computer from which the data was retrieved
• file name
• UNC path - this corresponds to the complete file path of data file 
• software name
• software version
• ASM converter
• ASM converter version
• experimental data identifier - this corresponds to the “Experiment Name” in QuantStudio
• experiment type
• container type
• plate well count
• measurement identifier <reporter dye>
• measurement time
• target DNA description <reporter dye>
• sample identifier
• sample role type <reporter dye>
• well location identifier
• well plate identifier
• device type
• measurement method identifier
• total cycle number setting
• pcr detection chemistry
• reporter dye setting <reporter dye>
• quencher dye setting <reporter dye>
• passive reference dye setting
• automatic cycle threshold enabled setting
• cycle threshold value setting <reporter dye>
• automatic baseline determination enabled setting
• baseline determination start cycle setting <reporter dye>
• baseline determination end cycle setting <reporter dye>
• genotyping determination method
• genotyping determination method setting <reporter dye>
• cycle threshold result <reporter dye>
• normalized reporter result <reporter dye>
• baseline corrected reporter result <reporter dye>
• genotyping determination result <reporter dye>

Those parameters whose values may differ between channels in a multiplexed assay are appended with the <reporter dye> (e.g. VIC, FAM).

The measurement file can contain the following columns (if available within the data):

• device identifier
• model number
• device serial number
• brand name
• product manufacturer
• data system instance identifier
• file name
• UNC path 
• software name
• software version
• ASM converter
• ASM converter version
• experimental data identifier
• measurement identifier
• experiment type
• container type
• plate well count
• measurement time
• sample identifier
• reporter dye setting
• target DNA description
• well plate identifier
• device type
• sample role type
• omit
• pcr detection chemistry
• measurement method identifier
• sample color
• target color
• quencher dye setting
• passive reference dye setting
• automatic cycle threshold enabled setting
• cycle threshold value setting
• automatic baseline determination enabled setting
• baseline determination start cycle setting
• baseline determination end cycle setting
• genotyping determination method
• genotyping determination method setting
• cycle threshold result
• normalized reporter result
• baseline corrected reporter result
• genotyping determination result

The group file can contain the following columns (if available within the data):

• device identifier
• model number
• device serial number
• data system instance identifier
• file name
• UNC path 
• software name
• software version
• ASM converter
• ASM converter version
• target DNA description <reporter dye>
• sample identifier
• sample role type <reporter dye>
• Quantity
• Quantity Mean
• Quantity SD
• Ct Mean
• Ct SD
• Delta Ct Mean
• Delta Ct SE
• Delta Delta Ct
• RQ
• RQ min
• RQ max
• Rn Mean
• Rn SD
• Y-Intercept
• Rsquared
• Slope
• Efficiency

Sample files can be found here.

Applied Bio QuantStudio Design & Analysis Connector Requirements

* This is the version of QuantStudio Design & Analysis with which the connector has been developed and tested. The connector may work with other versions of QuantStudio Design & Analysis, but that must be verified by the user.

Revision History

2024/03/27

Initial Version

2024/09/18

Added Github testdata link

2024/09/27

Added description of measurement data file .CSV including expected column headers (if available within the data)