---
language:
- en
license_name: cc-by-with-restrictions
license_link: LICENSE.md
pretty_name: GDPx3
tags:
- biology
size_categories:
- 10K<n<100K
configs:
 - config_name: metadata
   data_files:
   - split: train
     path: metadata.csv
extra_gated_fields:
  First name: text
  Last name: text
  Company: text
  Work email: text
  I want to use this dataset for: text
---

# GDPx3

GDPx3 is a high-content imaging dataset (Cell Painting) generated by screening 40 compounds across four concentrations at two time points, plus controls. This data was collected in A549, dermal fibroblasts, aortic smooth muscle cells, and aortic endothelial cells. GDPx3 offers a wealth of phenotypic information ready for your AI models.

## Experimental Design

Experiments were performed in a 384-well format assay. Four cell lines – A549 (a human lung carcinoma epithelial cell line) plus aortic smooth muscle, dermal fibroblast, and aortic endothelial primary cells – were treated with 40 library compounds and tested at four concentrations (0.3, 1, 3 and 10 µM) using four replicates. DMSO was used as an inert control added using 10 replicates to different volumes (0.125%, 0.375%) to match the final DMSO concentrations found in compound-treated wells. Five additional controls were included using 8 replicates at one concentration each, apart from BrefeldinA which was included at two 0.3 and 1 µM. This generated 24 384-well plates that were fixed for imaging after 24 or 48 hours of exposure to the compounds or DMSO controls.

## Metadata - `metadata.csv`

File with sample-level annotations and sample-level quality control metrics. The metadata table has the following fields:

| Column                        | Type      | Example                   | Description                                                                                                 |
|:------------------------------|:----------|:--------------------------|:------------------------------------------------------------------------------------------------------------|
| `culture_id`                  | `int`     | 98835509                  | Unique ID of the sample (well) that experienced perturbation                                                |
| `container_id`                | `int`     | 1571275                   | Unique ID of the perturbation plate                                                                         |
| `column_id`                   | `int`     | 20                        | Column position in the plate                                                                                |
| `row_id`                      | `int`     | 15                        | Row position in the plate                                                                                   |
| `compound`                    | `string`  | Theobromine               | Name of compound used to perturb cells                                                                      |
| `compound_clean`              | `string`  | theobromine               | Normalized version of `compound` column                                                                     |
| `compound_concentration`      | `float`   | 100                       | Compound concentration                                                                                      |
| `compound_concentration_unit` | `string`  | uM                        | Compound concentration unit of measure                                                                      |
| `cell_line`                   | `string`  | A549                      | Cell line name                                                                                              |
| `timepoint`                   | `int`     | 24                        | Time between perturbation and lysis in hours                                                                |
| `condition`                   | `string`  | caffeine-100              | Combination of cell line, compound_clean, concentration, and timepoint, to help group replicates.           |
| `percent_volume_dmso`         | `float`   | 0.0625                    | Concentration of DMSO in perturbation sample, in percent volume. Compounds are dispensed dissolved in DMSO. |
| `sample_type`                 | `string`  | Ginkgo Neg Control - DMSO | Kind of sample, either "library" or the name of a control                                                   |
| `is_neg_control`              | `boolean` | False                     | Whether a sample is considered a negative control                                                           |
| `is_pos_control`              | `boolean` | True                      | Whether a sample is considered a positive control                                                           |
| `seeded_cell_count`           | `int`     | 3000                      | Count of cells seeded prior to perturbation                                                                 |

## Images - `images/c*/*.tiff`

The image data are 2200x2200 16-bit `tiff` files. The image paths, such as `images/c123456/9876543.s3_w2.tiff` can be read as:

* Container ID 123456
* Culture ID 9876543
* Site 3
* Channel 2

Four channels (w1–w4) are taken at each site, and four sites are imaged in each well. The four channels are referred to in order as Blue, Green, Red, and DeepRed. The physical resolution of the images is 0.27 micron/pixel.