---
title: "Primary Screening (Execution Mode)"
slug: "primary-screening-execution-mode"
updated: 2026-09-09T13:57:29Z
published: 2026-09-09T13:57:29Z
canonical: "docs.discngine.com/primary-screening-execution-mode"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://docs.discngine.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Primary Screening (Execution Mode)

## Scientific Background

Compound cytotoxicity is an important parameter to measure when developing potential human therapeutics.

Jurkat clone E6.1 was screened against a diverse collection of 3,520 compounds. All compounds were tested once at a 1 μM final concentration.

A luciferase-based cell proliferation/viability assay endpoint kit was used as the readout. The kit measures the amount of ATP present in the microtiter plate well. If ATP is not present, the catalytic conversion of luciferin into oxyluciferin is not possible, and no luminescence results. Since metabolically active cells produce ATP, the absence of ATP correlates with the presence of non-viable cells.

This campaign used doxorubicin, an antibiotic used as an anti-cancer drug, as the positive control. The assay was conducted in 384-well format.

To select a practical number of compounds that exhibited high activity in the primary screen for follow-up assays, a cutoff value of the primary %Inhibition was applied. The cutoff value was calculated as the sum of the average percent inhibition of all compounds tested and three times their standard deviation (= HITS).

![Primary Screening Analysis with ASSAY](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-well-validation-tsw-2-2-3.png?sv=2026-02-06&spr=https&st=2026-11-10T22%3A18%3A26Z&se=2026-11-10T23%3A18%3A26Z&sr=c&sp=r&sig=zbD7v91GXWxzdXFEE89YrCJ9QMWjb%2B%2B6YE%2FJy6jC%2FMw%3D)

## Prerequisites

- An existing run template, created using `Design Mode`, following the tutorial in [Primary Screening Tutorial](/public/docs/primary-screening-design-modes).

Files to use:

- [01-Primary_Screening_10p384raw_data](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/discngine-assay-01-primary-screening-10p384raw-data.txt?sv=2026-02-06&spr=https&st=2026-11-10T22%3A18%3A26Z&se=2026-11-10T23%3A18%3A26Z&sr=c&sp=r&sig=zbD7v91GXWxzdXFEE89YrCJ9QMWjb%2B%2B6YE%2FJy6jC%2FMw%3D)
- [01_Sample_Mapping_Primary_Screening](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/discngine-assay-01-sample-mapping-primary-screening.txt?sv=2026-02-06&spr=https&st=2026-11-10T22%3A18%3A26Z&se=2026-11-10T23%3A18%3A26Z&sr=c&sp=r&sig=zbD7v91GXWxzdXFEE89YrCJ9QMWjb%2B%2B6YE%2FJy6jC%2FMw%3D)

## Run Creation

- Click the `New Run` button to create a new run.
- Select `Execution Mode` as the mode.
- Select the appropriate `Run Template` (the one saved in the Publisher Step of `Design Mode`).
- Enter a `Run Name`.
- Go to the `File Reading` step.

## File Reading

- The reader named `Analyst GT (TAB)` is already fixed.
- Upload the file `01-Primary_Screening_10p384raw_data`.
- Go to the `Raw Data File` step.

## Raw Data File

- Number of measurements per plate is already mapped: `1`.
- The `Readout Alias` is fixed to `READOUT1` and cannot be modified.
- Go to the `Plate Mapping` step.

## Plate Mapping

The Control Layout named **Primary_Screening** is already applied to all plates.

- Go to the `Well Validation` step.

## Well Validation

The visualization template selected in Design Mode is already applied. You can change this template.

For **QC Validation**, select aberrant wells in the visualization and click on the ![Well Validation step: Invalidation button](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-runs-invalidation-button-2-3-4-5-6.png?sv=2026-02-06&spr=https&st=2026-11-10T22%3A18%3A26Z&se=2026-11-10T23%3A18%3A26Z&sr=c&sp=r&sig=zbD7v91GXWxzdXFEE89YrCJ9QMWjb%2B%2B6YE%2FJy6jC%2FMw%3D) button. Multiple selection is allowed by holding the Ctrl key.

              
              

Plate_ZSCORE_READOUT1 < -2 or Plate_ZSCORE_READOUT1 > 2.

- Go to the `Sample Mapping` step.

## Sample Mapping

- Click on the **Edit Sample Information** button.
- Select filling mode **File** and tick **Sample** and **Dose** for content.
- Choose file `01_Sample_Mapping_Primary_Screening`.
- Click on the **Apply** button.

Samples and doses are filled in.

- Click on the **Continue** button. Samples and doses are mapped for all plates.
- Click on the **Sample Analysis Settings** button.

## Sample Analysis Settings

- Groups are automatically created (3,520 groups).
- Basic Statistics analysis is already applied.
- Go to `Sample Analysis`.

## Sample Analysis

The template specified in Design mode is applied.

- For **Hits Selection**, select points (“hits”) in visualization and add them to a list (click on the **Add Hits** button). This selection can be exported in CSV format (export button).
- **Lock** your Analysis (**Lock Run** button).

## Publish Data

Depends on the Publisher defined in the run template.