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.