Work with Low-Throughput NAb Data: /Documentation/Archive/23.11

Work with Low-Throughput NAb Data

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The NAb Assay Tutorial covers the process of working with NAb data using a high-throughput assay and uploading data and metadata from files. This topic covers importing data from a low-throughput NAb assay. This process requires more data entry of specific metadata, and gives you the option to see the use of multiple data identifiers in action.

Create a New NAb Assay Design
Import Data
NAb Dashboard

Create a New NAb Assay Design

Select (Admin) > Manage Assays.
Click Configure Plate Templates.
Select new 96 well (8x12) NAb single-plate template from the dropdown.
Click Create to open the editor.

Specify the following in the plate template editor:

Provide a Template Name, for example: "NAb Plate 1"
Leave all other settings at their default values (in order to create the default NAb plate).
Click Save & Close.

Select (Admin) > Manage Assays.
Click New Assay Design.

Click the Specialty Assays tab.
Under Use Instrument Specific Data Format, select TZM-bl Neutralization (NAb).
As the Assay Location, select "Current Folder (NAb Assay Tutorial)" (your folder name may vary).
Click Choose TZM-bl Neutralization (NAb) Assay.

Specify the following in the assay designer:

Name: "NAbAssayDesign"
Plate Template: NAb Plate 1
Metadata Input Format: Confirm Manual is selected for this tutorial.
Leave all other fields at their default values.
Click Save.

Import Data

When importing runs for this tutorial, you provide metadata, in this case sample information, manually through the UI. If instead you had a file containing that sample information, you could upload it using the File Upload option for Metadata Input Format. See NAb Assay Reference for more information.

Select (Admin) > Manage Assays.
On the Assay List, click NAbAssayDesign, then Import Data.
For Participant/Visit, select Specimen/sample id. Do not check the box to also provide participant/visit information.
Click Next and enter experiment data as follows:

Property	Value
Assay Id	Leave blank. This field defaults to the name of the data file import.
Cutoff Percentage (1)	50
Cutoff Percentage (2)	80
Host Cell	T
Experiment Performer	<your name>
Experiment ID	NAb32
Incubation Time	30
Plate Number	1
Curve Fit Method	Five parameter
Virus Name	HIV-1
Virus ID	P392
Run Data	Browse to the file: [LabKeyDemoFiles]\Assays\NAb\NAbresults1.xls
Specimen IDs	Enter the following (in the row of fields below the run data file):
Specimen 1	526455390.2504.346
Specimen 2	249325717.2404.493
Specimen 3	249320619.2604.640
Specimen 4	249328595.2604.530
Specimen 5	526455350.4404.456
Initial Dilution	Place a checkmark and enter 20
Dilution Factor	Place a checkmark and enter 3
Method	Place a checkmark and select Dilution

Click Save and Finish.

NAb Dashboard

When the import is complete, you can view detailed information about any given run right away, giving quick confirmation of a good set of data or identifying any potential issues. The run summary dashboard looks something like this:

The percent coefficient of variation (%CV) is shown on the neutralization curve charts as vertical lines from each data point. Additional quality control, including excluding particular wells from calculations is available for NAb assays. See NAb Assay QC for details.

As with high-throughput NAb data you can customize graphs and views before integrating or sharing your results. Once a good set of data is confirmed, it could be linked to a study or data repository for further analysis and integration.

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