Release Overview
Description
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. This Beta release includes perturb-seq data in undifferentiated KOLF2.1J iPSCs; SEC-MS data in undifferentiated KOLF2.1J iPSCs and iPSC-derived NPCs, neurons, and cardiomyocytes; AP-MS data in MDA-MB-468 breast cancer cells in the presence of chemotherapy (vorinostat and paclitaxel); and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel). CM4AI output data are packaged with provenance graphs and rich metadata as AI-ready datasets in RO-Crate format using the FAIRSCAPE framework. Data presented here will be augmented regularly through the end of the project. CM4AI is a collaboration of UCSD, UCSF, Stanford, UVA, Yale, UA Birmingham, Simon Fraser University, and the Hastings Center.
Authors
Clark, T, Parker, J, Al Manir, S, Axelsson, U, Ballllosero Navarro, F, Chinn, B, Churas, CP, Dailamy, A, Doctor, Y, Fall, J, Forget, A, Gao, J, Hansen, JN, Hu, M, Johannesson, A, Khaliq, H, Lee, YH, Lenkiewicz, J, Levinson, MA, Marquez, C, Metallo, C, Muralidharan, M, Nourreddine, S, Niestroy, J, Obernier, K, Pan, E, Polacco, B, Pratt, D, Qian, G, Schaffer, L, Sigaeva, A, Thaker, S, Zhang, Y, Bélisle-Pipon, JC, Brandt, C, Chen, JY, Ding, Y, Fodeh, S, Krogan, N, Lundberg, E, Mali, P, Payne-Foster, P, Ratcliffe, S, Ravitsky, V, Sali, A, Schulz, W, Ideker, T
Publisher
https://dataverse.lib.virginia.edu/
Principal Investigator
Trey Ideker
Data Governance Committee
Jilian Parker
Ethical Review
Vardit Ravistky ravitskyv@thehastingscenter.org and Jean-Christophe Belisle-Pipon jean-christophe_belisle-pipon@sfu.ca.
Copyright
Copyright (c) 2026 The Regents of the University of California except where otherwise noted. Spatial proteomics raw image data is copyright (c) 2026 The Board of Trustees of the Leland Stanford Junior University.
Terms of Use
Attribution is required to the copyright holders and the authors. Any publications referencing this data or derived data products should cite the Related Publications below, as well as directly citing this data collection.
HL7 Confidentiality Level
Unrestricted
Keywords
AI,
affinity purification,
AP-MS,
artificial intelligence,
breast cancer,
Bridge2AI,
cardiomyocyte,
CM4AI,
CRISPR/Cas9,
induced pluripotent stem cell,
iPSC,
KOLF2.1J,
machine learning,
mass spectroscopy,
MDA-MB-468,
neural progenitor cell,
NPC,
neuron,
paclitaxel,
perturb-seq,
perturbation sequencing,
protein-protein interaction,
protein localization,
single-cell RNA sequencing,
scRNAseq,
SEC-MS,
size exclusion chromatography,
subcellular imaging,
vorinostat,
Artificial intelligence,
Breast cancer,
CRISPR perturbation,
Cell maps,
IPSC,
Machine learning,
Mass spectroscopy,
Perturb-seq,
Protein-protein interaction,
cell maps
Cite As
Clark T; Parker J; Al Manir S; Axelsson U; Ballllosero Navarro F; Chinn B; Churas CP; Dailamy A; Doctor Y; Fall J; Forget A; Gao J; Hansen JN; Hu M; Johannesson A; Khaliq H; Lee YH; Lenkiewicz J; Levinson MA; Metallo C; Muralidharan M; Nourreddine S; Niestroy J; Obernier K; Pan E; Park, S; Polacco B; Pratt D; Qian G; Schaffer, LV; Sigaeva A; Thaker S; Zhang Y; Zhao, X; Bélisle-Pipon JC; Brandt C; Chen JY; Ding Y; Fodeh S; Krogan N; Lundberg E; Mali P; Payne-Foster P; Ratcliffe S; Ravitsky V; Sali A; Schulz W; Ideker T, 2025, "Cell Maps for Artificial Intelligence - June 2026 Data Release (Beta)", https://doi.org/10.18130/V3/HIGT4C , https://dataverse.lib.virginia.edu/, V1
Funding
National Institutes of Health: 1OT2OD032742-01, R01HG012351, R01NS131560, U54CA274502, #S10 OD026929. Department of Defense: W81XWH-22-1-0401. CIRM training: EDUC4-12804. Dutch Research Council: NWO, 019.231EN.013. National Cancer Institute: P30CA023100
Completeness
These data are not yet in completed final form, and some datasets are under temporary pre-publication embargo. Protein-protein interaction (SEC-MS), protein localization (IF imaging), and CRISPRi perturbSeq data interrogate sets of proteins which incompletely overlap. Computed cell maps not included in this release.
Human Subjects & Regulatory
Human Subjects Research: None - data collected from commercially available cell lines
De-identified Samples: Yes
FDA Regulated: No
IRB Protocol ID: N/A
Institutional Review Board:
N/A
Human Subjects Exemptions:
Exempt — research with commercially available de-identified human cell lines does not constitute human subjects research.