JUMP Cell Painting pilot dataset for perturbation conditions

Dataset Overview

Data Type

Fluorescence microscopy images

Citation

Publication: Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nature Methods (2024) https://doi.org/10.1038/s41592-024-02241-6; Cell Painting Gallery: an open resource for image-based profiling. Nature Methods (2024) https://doi.org/10.1038/s41592-024-02399-z

Dataset: cpg0000-jump-pilot on the Registry of Open Data on AWS (https://registry.opendata.aws/cellpainting-gallery/).

Dataset Card Authors

Chan Zuckerberg Initiative

Dataset Card Contact

Dataset source ID

cpg0000-jump-pilot or CPJUMP1

Uses

Primary Use Cases

• A pilot dataset to test different cell lines and perturbation conditions for JUMP Cell Painting datasets
• Investigate cellular responses to matching perturbations in small or large scale
• Train machine learning models
• Compare or benchmark performance of machine learning models

Out-of-Scope or Unauthorized Use Cases

Do not use the dataset for the following purposes:

• Usage not covered by the license.
• Any use that is not in accordance with the Acceptable Use Policy 

Dataset Structure

The images are organized into six folders, one for each batch of experiments. Each batch has multiple subfolders that each corresponds to one 384-well plate. Every well had nine (and sometimes 7, 8, or 16) sites imaged, each with five fluorescent channels and three brightfield images. The well position, site number and channels are indicated in the image filenames. More details see https://github.com/jump-cellpainting/2024_Chandrasekaran_NatureMethods

Personal and Sensitive Information

No personal and sensitive information is included.

Dataset Creation

Curation Rationale

The experiment was designed to have paired results from chemical perturbations and genetic perturbations. The Cell Painting assay was used to measure cell morphology comprehensively.

Data Collection and Processing

Experiments were carried out in 384-well plates where each plate has one cell line with one type of perturbation (small molecule, gene knockout by CRISPR-Cas9 or open reading frame overexpression) alongside corresponding negative controls. 160 genes or their protein products were each targeted with one or two small-molecule compounds (totaling 303 compounds), two CRISPR guides for gene knockout, and one overexpression. Images were taken at two time points post perturbation using Cell Painting assay v2.5 where six fluorescent dyes were used to visualize the following cellular structures: Hoechst for nucleus, SYTO 14 for nucleoli and cytoplasmic RNA, concanavalin A for endoplasmic reticulum, wheat germ agglutinin for Golgi and plasma membrane, MitoTracker for mitochondria, and phalloidin for the actin cytoskeleton. The images were acquired across five fluorescent channels plus three brightfield planes in widefield mode. More details see

Bias, Risks, and Limitations

• Some protein may remain at the time points when images were taken after the gene knockout.
• Small molecule compounds may have secondary or off-target effects on cell morphology.
• The experimental design and metadata is quite complex.
• Some plates were imaged multiple times.

More Information

Acknowledgements

See source reference: https://www.nature.com/articles/s41592-024-02241-6