We’re happy to share that researchers from Ardigen co-authored a study just published in Nature Methods. This work, developed as part of theJUMP Cell Painting Consortium, presents the most extensive open dataset to date exploring how gene activity affects human cell morphology.
What’s the study about?
The team applied the Cell Painting assay – a high-throughput imaging method – to observe the effects of changing gene expression on the structure of human cells. In total:
- 12,609 genes were overexpressed using ORF transfection
- 7,975 genes were knocked out with CRISPR-Cas9
- Millions of cell images were collected
- Each perturbation was analyzed to create a detailed morphological profile
To ensure reliable data, the team carefully addressed technical variability and ran multiple rounds of quality control.
Why it matters
The resulting dataset offers a solid foundation for:
- Understanding gene function and cellular behavior
- Identifying new links between genes and disease processes
- Supporting AI model training in biological research
- Advancing drug discovery and biomarker work
Ardigen’s contribution
We’re proud to acknowledge our colleagues who played key roles in this work:
Tomasz Jetka, Krzysztof Rataj, Adriana Borowa, Agata Zaremba, Magdalena Otrocka, Michał Warchoł, and Tomasz Krawiec – contributing across methodology, analysis, software, supervision, and writing.
In addition to the deep learning and bioinformatics expertise we provided to support this study, Ardigen developed JUMP-CP DataExplorer . phenAID JUMP CP Data Explorer is a free web based application, that enables viewing images and metadata corresponding to each genetic perturbation and searching for and downloading up to 100 nearest neighbors . The tool visualizes ORF and CRISPR profiles, representing them as a UMAP projection color-coded by morphological clusters (see the Genetic Perturbation tab).
Author list
Corresponding author:
Dr. Anne E. Carpenter – Broad Institute of MIT and Harvard
Full list of contributing authors (in publication order):
Srinivas Niranj Chandrasekaran, Shantanu Singh, John Arevalo, Erin Weisbart, Marzieh Haghighi, Zitong Chen, Jessica Ewald, Alexandr Kalinin, Alan Munoz, Yu Han, Nikita Moshkov, Rebecca Senft, Beth Cimini, John Doench, Briana Fritchman, Desiree Hernandez, David Root, Brittany Marion, Maria Kost-Alimova, Amy Goodale, Lisa Miller, Patrick Byrne, Andrei Zinovyev, Holger Hennig, Arne Monsees, Rahul Valiya Veettil, William Charles, Tim James, Zahra Hanifehlou, Christina Jacob, Arnaud Ogier, Amelie Weiss, Peter Sommer, Amandine Thibaudeau, Tomasz Jetka, Krzysztof Rataj, Adriana Borowa, Agata Zaremba, Magdalena Otrocka, Michał Warchoł, Tomasz Krawiec, William Van Trump, Michael Wiest, Francesco Rubbo, Sarah Trisorus, Colin Fuller, Ben Komalo, Sui Wang, Boxiong Deng, Douglas Selinger, Jedidiah Gaetz, Eric Alix, Simon Scrace, Nicola McCarthy, Glynn Martin.
