Cell Maps for Artificial Intelligence - June 2026 Data Release (Beta)

<h3>Description</h3> <p>This dataset is the June 2026 Data Release of Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org), the Functional Genomics Grand Challenge in the NIH Bridge2AI program. CM4AI is generating multi-modal data including protein-protein interaction (PPI), spatial localization, and genetic perturbation data in MDA-MB-468 breast cancer cells (+/- paclitaxel or vorinostat) and iPSCs (+/- differentiation). This Beta release includes:</p> <ul> <li>Perturb-seq data for MDA-MB-468 breast cancer cells +/- treatment and undifferentiated (parental) KOLF2.1J iPSCs</li> <li>SEC-MS data for MDA-MB-468 breast cancer cells +/- treatment, undifferentiated KOLF2.1J iPSCs, and iPSC-derived neuron progenitor cells (NPCs), neurons, and cardiomyocytes</li> <li>AP-MS data for MDA-MB-468 breast cancer cells + treatment</li> <li>IF images in MDA-MB-468 breast cancer cells +/- treatment</li> </ul> <h3>External Data Links</h3> <p>Access external data resources related to this dataset:</p> <ul> <li><strong>Perturb-seq data in KOLF2.1J iPSCs (undifferentiated): </strong>Embargoed</li> <li><strong>Perturb-seq data in MDA-MB-468 breast cancer cells (+/- treatment): </strong>Embargoed</li> <li><strong>CRISPRi Perturbation Atlas of iPSCs: </strong><a href="https://figshare.com/s/ee85bb1880921326249b" target="_blank">Figshare</a></li> <li><strong>SEC-MS data in KOLF2.1J iPSCs (undifferentiated, NPC, neuron, and cardiomyocyte):</strong> <a href="https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=de876e1d228c4f7ab02f84027894bed7" target="_blank">MassIVE Repository</a></li> <li><strong>SEC-MS data in MDA-MB-468 breast cancer cells (+/- treatment):</strong> <a href="https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=ad8b8084f5b14af5bafac70fdd42a577" target="_blank">MassIVE Repository</a></li> <li><strong>AP-MS data in MDA-MB-468 breast cancer cells (treated with paclitaxel):</strong> <a href="https://doi.org/doi:10.25345/C5KH0FC9M" target="_blank">MassIVE Repository</a></li> <li><strong>AP-MS data in MDA-MB-468 breast cancer cells (treated with vorinostat):</strong> <a href="https://doi.org/doi:10.25345/C59Z90S2N" target="_blank">MassIVE Repository</a></li> </ul> <hr></hr> <h3>Data Governance & Ethics</h3> <ul> <li><strong>Human Subjects:</strong> No</li> <li><strong>De-identified Samples:</strong> Yes</li> <li><strong>FDA Regulated:</strong> No</li> <li><strong>Data Governance Committee:</strong> Jillian Parker (jillianparker@health.ucsd.edu)</li> <li><strong>Ethical Review:</strong> Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca)</li> </ul> <h3>Completeness</h3> <p>These data are not yet in completed final form:</p> <ul> <li>Some datasets are under temporary pre-publication embargo</li> <li>Protein-protein interaction (SEC-MS), protein localization (IF imaging), and CRISPRi perturbSeq data interrogate sets of proteins which incompletely overlap</li> <li>Computed cell maps not included in this release</li> </ul> <h3>Maintenance Plan</h3> <ul> <li>Dataset will be regularly updated and augmented through the end of the project in November 2026</li> <li>Updates on a quarterly basis</li> <li>Long term preservation in the University of Virginia Dataverse, supported by committed institutional funds</li> </ul> <h3>Intended Use</h3> <p>This dataset is intended for:</p> <ul> <li>AI-ready datasets to support research in functional genomics</li> <li>AI model training</li> <li>Cellular process analysis</li> <li>Cell architectural changes and interactions in presence of specific disease processes, treatment conditions, or genetic perturbations</li> </ul> <h3>Limitations</h3> <p><strong>Researchers should be aware of inherent limitations:</strong></p> <ul> <li>This is an interim release</li> <li>Does not contain predicted cell maps, which will be added in future releases</li> <li>The current release is most suitable for bioinformatics analysis of the individual datasets</li> <li>Requires domain expertise for meaningful analysis</li> </ul> <h3>Prohibited Uses</h3> <ul> <li><strong>These laboratory data are not to be used in clinical decision-making or in any context involving patient care without appropriate regulatory oversight and approval</strong></li> </ul> <h3>Potential Sources of Bias</h3> <p>Users should be aware of potential biases:</p> <ul> <li>Data in this release was derived from commercially available de-identified human cell lines</li> <li>Does not represent all biological variants which may be seen in the population at large</li> </ul>

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