=== YAML Fixing Applied ===
id: "doi:10.18130/V3/B35XWX"
name: Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
title: Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
description: This dataset is the March 2025 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; 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. This data is Copyright (c) 2025 The Regents of the University of California except where otherwise noted. Spatial proteomics raw image data is copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University. Dataset licensed for reuse under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license. Attribution is required to the copyright holders and the authors. Any publications referencing this data or derived products should cite the related publications, as well as directly citing this data collection (2025-03-04). (2025-03-07)
language: en
page: "https://doi.org/10.18130/V3/B35XWX"
publisher: "https://dataverse.lib.virginia.edu/"
issued: "2025-03-03"
created_by:
  - CM4AI Consortium
created_on: "2025-02-27"
last_updated_on: "2025-03-07"
doi: "doi:10.18130/V3/B35XWX"
license: "https://creativecommons.org/licenses/by-nc-sa/4.0/"
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
version: "1.4"
purposes:
  - name: Primary purpose
    response: Release AI-ready, richly annotated functional genomics datasets (RO-Crate, FAIRSCAPE) from CM4AI for machine learning and AI research.
tasks:
  - name: Downstream tasks
    response: Multi-omics integration; protein localization analysis; protein-protein interaction inference; perturbation effect prediction; single-cell transcriptomics modeling.
addressing_gaps:
  - name: Gap addressed
    response: Provide standardized, provenance-rich, cross-modality datasets from disease-relevant human cell lines to accelerate AI method development and benchmarking in functional genomics.
creators:
  - name: CM4AI Consortium
    principal_investigator:
      name: Trey Ideker
      affiliation:
        - name: University of California San Diego
    affiliation:
      name: CM4AI (Cell Maps for Artificial Intelligence)
funders:
  - name: NIH Bridge2AI funding
    grantor:
      name: National Institutes of Health
    grant:
      name: 1OT2OD032742-01
      grant_number: 1OT2OD032742-01
instances:
  - name: Perturb-seq profiles
    representation: Single-cell transcriptomic profiles from CRISPRi perturbations in undifferentiated KOLF2.1J hiPSCs.
    instance_type: Cells and per-cell gene expression measurements.
    data_type: Raw and processed single-cell RNA-seq derived features/metadata described via RO-Crate.
  - name: Protein-protein interaction SEC-MS
    representation: Size exclusion chromatography–mass spectrometry profiles measuring protein complex co-elution.
    instance_type: Protein complex fraction/protein abundance features.
    data_type: Quantitative proteomics features and associated metadata described via RO-Crate.
  - name: Immunofluorescence images
    representation: Subcellular protein localization images in MDA-MB-468 cells under drug treatments and untreated.
    instance_type: Multichannel confocal microscopy images (DAPI, ER/calreticulin, tubulin, protein-of-interest).
    data_type: Image files packaged in ZIP archives with metadata.
external_resources:
  - name: External repositories
    external_resources:
      - PRIDE Archive (planned deposition for SEC-MS data)
      - CM4AI project website (https://cm4ai.org)
    future_guarantees:
      - Dataverse persistent DOI ensures landing page persistence.
    archival:
      - RO-Crate packaging with FAIRSCAPE provenance graphs.
    restrictions:
      - Dataset is under CC BY-NC-SA 4.0; additional third-party raw spatial proteomics images copyrighted by Stanford University as noted.
confidential_elements:
  - name: Confidentiality
    description:
      - Data are from established human cell lines; no patient-identifying content is included.
content_warnings:
  - name: Content notes
    warnings:
      - Microscopy images of cancer cell lines under chemotherapeutic treatment.
subpopulations:
  - name: Cell types and conditions
    identification:
      - KOLF2.1J human induced pluripotent stem cells (hiPSCs)
      - iPSC-derived NPCs, neurons, and cardiomyocytes (SEC-MS)
      - MDA-MB-468 breast cancer cells (IF images), untreated and treated with paclitaxel or vorinostat
deidentification:
  name: De-identification
  description:
    - No personally identifiable information; experiments on immortalized human cell lines.
sensitive_elements:
  - name: Sensitivity assessment
    description:
      - No direct human subject data; biomedical experimental data on cell lines and derived cells.
acquisition_methods:
  - name: Data acquisition summary
    description:
      - CRISPRi perturb-seq; SEC-MS proteomics; immunofluorescence confocal imaging.
    was_directly_observed: yes
    was_reported_by_subjects: no
    was_inferred_derived: yes
    was_validated_verified: yes
collection_mechanisms:
  - name: Experimental mechanisms
    description:
      - Genome-scale CRISPRi perturbation and single-cell RNA-seq (perturb-seq).
      - Size exclusion chromatography coupled to mass spectrometry (SEC-MS).
      - Immunofluorescence staining and confocal microscopy for protein localization.
data_collectors:
  - name: Contributing laboratories
    description:
      - Nevan Krogan Laboratory, UCSF (SEC-MS).
      - Lundberg Lab, Stanford University (immunofluorescence imaging).
      - CM4AI consortium groups across UCSD, UCSF, Stanford, UVA, Yale, UAB, Simon Fraser University, and the Hastings Center.
collection_timeframes:
  - name: Collection/production dates
    description:
      - Data creation date 2025-02-27; dataset published 2025-03-03.
preprocessing_strategies:
  - name: Packaging and provenance
    description:
      - Data packaged as RO-Crate with FAIRSCAPE provenance graphs; AI-ready formatting and rich metadata.
existing_uses:
  - name: Related publications
    description:
      - Clark T et al. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. 2024. doi: http://doi.org/10.1101/2024.05.21.589311
      - Nourreddine S et al. A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS. bioRxiv. 2024 Nov 4;2024.11.03.621734. PMCID: PMC11580897 doi: https://doi.org/10.1101/2024.11.03.621734
future_use_impacts:
  - name: Considerations
    description:
      - Cross-modality integration and differences in cell types, treatments, and experimental modalities should be considered to avoid biased models; adhere to license terms for non-commercial use and share-alike.
discouraged_uses:
  - name: Usage cautions
    description:
      - Do not use in applications requiring identifiable human subject data; non-compliant uses with CC BY-NC-SA 4.0 (e.g., commercial use) are discouraged.
distribution_formats:
  - name: Distribution channels and formats
    description:
      - Dataverse dataset with per-file downloads and Data Access API.
      - RO-Crate JSON metadata files.
      - ZIP archives for image datasets.
distribution_dates:
  - name: Publication date
    description:
      - 2025-03-03
license_and_use_terms:
  name: License and terms
  description:
    - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). Attribution required to copyright holders and authors; cite dataset and related publications.
ip_restrictions:
  name: IP and copyrights
  description:
    - Copyright (c) 2025 The Regents of the University of California except where noted; spatial proteomics raw image data copyright (c) 2025 Stanford University Board of Trustees.
maintainers:
  - name: Dataset maintainers
    description:
      - University of Virginia Dataverse (repository); point of contact: Trey Ideker via Dataverse contact link.
updates:
  name: Update plan
  description:
    - Data will be augmented regularly through the end of the project; subsequent versions will be released via Dataverse.
version_access:
  name: Versioning
  description:
    - Current dataset version is 1.4; older versions accessible via Dataverse version history when available.
is_tabular: "false"
subsets:
  - name: CRISPR Perturbation Cell Atlas RO-Crate metadata
    title: ro-crate-metadata.json (CRISPR Perturbation Cell Atlas)
    description: RO-Crate metadata describing an expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes for 11,739 targeted genes.
    format: JSON
    media_type: application/json
    path: CRISPR Perturbation Cell Atlas/ro-crate-metadata.json
    md5: cbdb263b1c099396d75e16f00a79a818
    issued: "2025-03-03"
  - name: CRISPR Perturbation RNA Sequences RO-Crate metadata
    title: ro-crate-metadata.json (CRISPR Perturbation RNA Sequences - Raw Sequences)
    description: RO-Crate metadata for raw sequence data from a genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs.
    format: JSON
    media_type: application/json
    path: CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json
    md5: 1cafefa32a897998e3e2ba0a29a3ef5c
    issued: "2025-03-03"
  - name: IF images - paclitaxel
    title: cm4ai-v0.6-beta-if-images-paclitaxel.zip
    description: "Immunofluorescence images showing spatial localization of 563 proteins in MDA-MB-468 cells treated with paclitaxel; channels: DAPI (blue), ER/calreticulin (yellow), tubulin (red), protein-of-interest (green)."
    compression: ZIP
    media_type: application/zip
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip
    md5: 9422486c80bc9e1d35b2fbbc72a5f043
    issued: "2025-03-03"
  - name: IF images - untreated
    title: cm4ai-v0.6-beta-if-images-untreated.zip
    description: "Immunofluorescence images showing spatial localization of 563 proteins in untreated MDA-MB-468 cells; channels: DAPI (blue), ER/calreticulin (yellow), tubulin (red), protein-of-interest (green)."
    compression: ZIP
    media_type: application/zip
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip
    md5: 0b4d129f5fbc3bb7f7ea564cd032cef7
    issued: "2025-03-03"
  - name: IF images - vorinostat
    title: cm4ai-v0.6-beta-if-images-vorinostat.zip
    description: "Immunofluorescence images showing spatial localization of 563 proteins in MDA-MB-468 cells treated with vorinostat; channels: DAPI (blue), ER/calreticulin (yellow), tubulin (red), protein-of-interest (green)."
    compression: ZIP
    media_type: application/zip
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip
    md5: ac577109a41a9806978461157b777d52
    issued: "2025-03-03"
  - name: Protein-protein Interaction SEC-MS RO-Crate metadata
    title: ro-crate-metadata.json (Protein-protein Interaction SEC-MS)
    description: RO-Crate metadata for SEC-MS dataset generated on undifferentiated KOLF2.1J hiPSCs in the Nevan Krogan laboratory at UCSF; deposition to PRIDE planned.
    format: JSON
    media_type: application/json
    path: Protein-protein Interaction SEC-MS/ro-crate-metadata.json
    md5: cb67e7749b15ce87b9042a9feba9d032
    issued: "2025-03-03"