DOI: 10.18130/v3/f3td5r
title: Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)

description: &lt;h3&gt;Description&lt;/h3&gt;
&lt;p&gt;This dataset is a revision of the June 2025 Data Release of Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org), the Functional Genomics Grand Challenge in the NIH Bridge2AI program. This revision includes adding RGB immunofluorescent images, corrections to ro-crate metadata, and changes to naming conventions. 
&lt;/p&gt;
&lt;p&gt;
This Beta release includes perturb-seq data in undifferentiated KOLF2.1J iPSCs; SEC-MS data in undifferentiated KOLF2.1J iPSCs, iPSC-derived NPCs, neurons, cardiomyocytes, and treated and untreated MDA-MB468 breast cancer cells; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel).&lt;/p&gt;

&lt;h3&gt;External Data Links&lt;/h3&gt;
&lt;p&gt;Access external data resources related to this dataset:&lt;/p&gt;
&lt;ul&gt;
 &lt;li&gt;&lt;strong&gt;Sequence Read Archive (SRA) Data: &lt;/strong&gt; Embargoed&lt;/li&gt;
 &lt;li&gt;&lt;strong&gt;Mass Spectrometry Data (Human iPSCs):&lt;/strong&gt; &lt;a href="https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=de876e1d228c4f7ab02f84027894bed7" target="_blank"&gt;MassIVE Repository&lt;/a&gt;&lt;/li&gt;
 &lt;li&gt;&lt;strong&gt;Mass Spectrometry Data (Human Cancer Cells):&lt;/strong&gt; &lt;a href="https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=ad8b8084f5b14af5bafac70fdd42a577" target="_blank"&gt;MassIVE Repository&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;
&lt;hr&gt;&lt;/hr&gt;

&lt;h3&gt;Data Governance & Ethics&lt;/h3&gt;
&lt;ul&gt;
 &lt;li&gt;&lt;strong&gt;Human Subjects:&lt;/strong&gt; No&lt;/li&gt;
 &lt;li&gt;&lt;strong&gt;De-identified Samples:&lt;/strong&gt; Yes&lt;/li&gt;
 &lt;li&gt;&lt;strong&gt;FDA Regulated:&lt;/strong&gt; No&lt;/li&gt;
 &lt;li&gt;&lt;strong&gt;Data Governance Committee:&lt;/strong&gt; Jillian Parker (jillianparker@health.ucsd.edu)&lt;/li&gt;
 &lt;li&gt;&lt;strong&gt;Ethical Review:&lt;/strong&gt; Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca)&lt;/li&gt;
&lt;/ul&gt;

&lt;h3&gt;Completeness&lt;/h3&gt;
&lt;p&gt;These data are not yet in completed final form:&lt;/p&gt;
&lt;ul&gt;
 &lt;li&gt;Some datasets are under temporary pre-publication embargo&lt;/li&gt;
 &lt;li&gt;Protein-protein interaction (SEC-MS), protein localization (IF imaging), and CRISPRi perturbSeq data interrogate sets of proteins which incompletely overlap&lt;/li&gt;
 &lt;li&gt;Computed cell maps not included in this release&lt;/li&gt;
&lt;/ul&gt;

&lt;h3&gt;Maintenance Plan&lt;/h3&gt;
&lt;ul&gt;
 &lt;li&gt;Dataset will be regularly updated and augmented through the end of the project in November 2026&lt;/li&gt;
 &lt;li&gt;Updates on a quarterly basis&lt;/li&gt;
 &lt;li&gt;Long term preservation in the University of Virginia Dataverse, supported by committed institutional funds&lt;/li&gt;
&lt;/ul&gt;

&lt;h3&gt;Intended Use&lt;/h3&gt;
&lt;p&gt;This dataset is intended for:&lt;/p&gt;
&lt;ul&gt;
 &lt;li&gt;AI-ready datasets to support research in functional genomics&lt;/li&gt;
 &lt;li&gt;AI model training&lt;/li&gt;
 &lt;li&gt;Cellular process analysis&lt;/li&gt;
 &lt;li&gt;Cell architectural changes and interactions in presence of specific disease processes, treatment conditions, or genetic perturbations&lt;/li&gt;
&lt;/ul&gt;

&lt;h3&gt;Limitations&lt;/h3&gt;
&lt;p&gt;&lt;strong&gt;Researchers should be aware of inherent limitations:&lt;/strong&gt;&lt;/p&gt;
&lt;ul&gt;
 &lt;li&gt;This is an interim release&lt;/li&gt;
 &lt;li&gt;Does not contain predicted cell maps, which will be added in future releases&lt;/li&gt;
 &lt;li&gt;The current release is most suitable for bioinformatics analysis of the individual datasets&lt;/li&gt;
 &lt;li&gt;Requires domain expertise for meaningful analysis&lt;/li&gt;
&lt;/ul&gt;

&lt;h3&gt;Prohibited Uses&lt;/h3&gt;
&lt;ul&gt;
 &lt;li&gt;&lt;strong&gt;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&lt;/strong&gt;&lt;/li&gt;
&lt;/ul&gt;

&lt;h3&gt;Potential Sources of Bias&lt;/h3&gt;
&lt;p&gt;Users should be aware of potential biases:&lt;/p&gt;
&lt;ul&gt;
 &lt;li&gt;Data in this release was derived from commercially available de-identified human cell lines&lt;/li&gt;
 &lt;li&gt;Does not represent all biological variants which may be seen in the population at large&lt;/li&gt;
&lt;/ul&gt;