Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
March 2025 Beta data release of Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org), a Functional Genomics Grand Challenge in the NIH Bridge2AI program. This release includes: - CRISPR perturb-seq in undifferentiated KOLF2.1J iPSCs - SEC-MS in undifferentiated KOLF2.1J iPSCs and iPSC-derived NPCs, neurons, and cardiomyocytes - Immunofluorescence (IF) subcellular images in MDA-MB-468 breast cancer cells under
untreated conditions and chemotherapy perturbations (vorinostat and paclitaxel)
Data are packaged as AI-ready RO-Crate datasets with provenance graphs and rich metadata using the FAIRSCAPE framework and will be augmented regularly through the end of the project. CM4AI is a collaboration among UCSD, UCSF, Stanford, UVA, Yale, University of Alabama at Birmingham, Simon Fraser University, and the Hastings Center.
Copyright (c) 2025 The Regents of the University of California except where otherwise noted. Spatial proteomics raw image data copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University. Licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International.
2025-03-03
2025-02-27
- 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
- Clark T (university Of Virginia) Orcid
- https://orcid.org/0000-0003-4060-7360
- Parker J (university Of California, San Diego) Orcid
- https://orcid.org/0000-0003-4535-3486
- Al Manir S (university Of Virginia) Orcid
- https://orcid.org/0000-0003-4647-3877
- Axelsson U (KTH Royal Institute of Technology,)
- Ballllosero Navarro F (stanford University) Orcid
- https://orcid.org/0000-0002-4180-422X
- Chinn B (University of California San Diego)
- Churas CP (University of California San Diego) https://orcid.org/0000-0001-9998-705X
- Dailamy A (university Of California, San Diego) Orcid
- https://orcid.org/0000-0002-6711-8260
- Doctor Y (university Of California, San Diego) Orcid
- https://orcid.org/0009-0009-0483-7506
- Fall J (KTH - Royal Institute of Technology)
- Forget A (university Of California San Francisco) Orcid
- https://orcid.org/0000-0003-0223-0312
- Gao J (university Of California San Diego) Orcid
- https://orcid.org/0000-0002-6311-3526
- Hansen Jn (stanford University) Orcid
- https://orcid.org/0000-0002-4650-9094
- Hu M (University of California San Diego) https://orcid.org/0000-0002-1571-8029
- Johannesson A (KTH - Royal Institute of Technology)
- Khaliq H (University of California San Diego)
- Lee Yh (university Of California San Diego) Orcid
- https://orcid.org/0000-0003-0917-355X
- Lenkiewicz J (University of California San Diego) https://orcid.org/0000-0001-7252-8638
- Levinson Ma (university Of Virginia) Orcid
- https://orcid.org/0000-0003-0384-8499
- Marquez C (university Of California San Diego) Orcid
- 0000-0003-3960-420X
- Metallo C (university Of California San Diego) Orcid
- https://orcid.org/0000-0003-2404-3040
- Muralidharan M (University of California San Francisco)
- Nourreddine S (University of California San Diego) https://orcid.org/0000-0003-3881-7588
- Niestroy J (university Of Virginia) Orcid
- https://orcid.org/0000-0002-1103-3882
- Obernier K (university Of California San Francisco) Orcid
- https://orcid.org/0000-0002-4025-1299
- Pan E (University of California San Diego)
- Polacco B (University of California San Francisco)
- Pratt D (university Of California San Diego) Orcid
- https://orcid.org/0000-0002-1471-9513
- Qian G (university Of California San Diego) Orcid
- https://orcid.org/0009-0005-4217-2745
- Schaffer L (university Of California San Diego) Orcid
- https://orcid.org/0000-0001-6339-9141
- Sigaeva A (kth Royal Institute Of Technology) Orcid
- https://orcid.org/0000-0003-3361-3797
- Thaker S (university Of Alabama At Birmingham) Orcid
- https://orcid.org/0000-0001-6730-2773
- Zhang Y (University of California San Diego)
- Bélisle Pipon Jc (simon Fraser University) Orcid
- https://orcid.org/0000-0002-8965-8153
- Brandt C (yale University) Orcid
- https://orcid.org/0000-0001-8179-1796
- Chen Jy (the University Of Alabama At Birmingham) Orcid
- https://orcid.org/0000-0002-6112-415X
- Ding Y (university Of Texas At Austin) Orcid
- https://orcid.org/0000-0003-2567-2009
- Fodeh S (yale University) Orcid
- https://orcid.org/0000-0003-4664-3143
- Krogan N (university Of California San Francisco) Orcid
- https://orcid.org/0000-0003-4902-337X
- Lundberg E (stanford University) Orcid
- https://orcid.org/0000-0001-7034-0850
- Mali P (University of California San Diego) https://orcid.org/0000-0002-3383-1287
- Payne Foster P (university Of Alabama) Orcid
- https://orcid.org/0000-0002-3508-3577
- Ratcliffe S (university Of Virginia) Orcid
- https://orcid.org/0000-0002-6644-8284
- Ravitsky V (university Of Montreal) Orcid
- https://orcid.org/0000-0002-7080-8801
- Sali A (university Of California San Diego) Orcid
- https://orcid.org/0000-0003-0435-6197
- Schulz W (yale University) Orcid
- https://orcid.org/0000-0002-2048-4028
- Ideker T (university Of California San Diego) Orcid
- https://orcid.org/0000-0002-1708-8454
| Role | Name | ORCID | Affiliation |
|---|---|---|---|
| Contributor | CM4AI March 2025 Release Overview | collection-overview | - |
| Contributor | ro-crate-metadata.json | CRISPR Perturbation Cell Atlas/ro-crate-metadata.json | - |
| Contributor | ro-crate-metadata.json | CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json | - |
| Contributor | cm4ai-v0.6-beta-if-images-untreated.zip | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip | - |
| Contributor | cm4ai-v0.6-beta-if-images-paclitaxel.zip | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip | - |
| Contributor | cm4ai-v0.6-beta-if-images-vorinostat.zip | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip | - |
| Contributor | ro-crate-metadata.json | Protein-protein Interaction SEC-MS/ro-crate-metadata.json | - |