=== YAML Fixing Applied ===
id: "doi:10.18130/V3/F3TD5R"
name: Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
title: Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
description: This dataset is 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 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).
doi: "doi:10.18130/V3/F3TD5R"
page: "https://doi.org/10.18130/V3/F3TD5R"
publisher: "https://dataverse.lib.virginia.edu"
issued: 2025-07-01
created_on: 2025-02-27
last_updated_on: 2025-10-22
version: "2.0"
license: CC 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
created_by:
  - CM4AI Consortium
  - University of Virginia Dataverse
purposes:
  - response: AI-ready datasets to support research in functional genomics
  - response: Enable AI model training on multi-modal cellular data
  - response: Support analysis of cellular processes and architecture under disease, treatment, and genetic perturbation conditions
tasks:
  - response: AI model training and benchmarking in functional genomics
  - response: Cellular process and architecture analysis
  - response: Multi-modal data integration (IF imaging, SEC-MS, perturb-seq)
addressing_gaps:
  - response: Provide interoperable, AI-ready multi-modal datasets from disease-relevant human cell lines to enable mapping of human cell architecture; predicted cell maps to be added in future releases.
creators:
  - name: CM4AI Consortium
    principal_investigator:
      name: Trey Ideker
      affiliation:
        - name: University of California San Diego
    affiliation:
      name: University of California San Diego
funders:
  - grantor:
      name: National Institutes of Health
    grant:
      name: Bridge2AI Functional Genomics Grand Challenge
      grant_number: 1OT2OD032742-01
instances:
  - representation: Multi-modal cellular datasets from human cell lines (KOLF2.1J iPSCs and derivatives; MDA-MB-468 breast cancer cells)
    instance_type: Immunofluorescence (IF) confocal images; size exclusion chromatography mass spectrometry (SEC-MS); CRISPRi perturb-seq scRNA-seq
    data_type: Imaging files (IF), proteomics (SEC-MS), and single-cell transcriptomics (perturb-seq/scRNA-seq); external raw data via SRA and MassIVE where applicable
    sampling_strategies:
      - is_sample:
          - yes
        source_data:
          - Commercially available de-identified human cell lines (e.g., KOLF2.1J iPSCs; MDA-MB-468)
        is_representative:
          - no
        why_not_representative:
          - Data derived from specific de-identified human cell lines and do not represent all biological variants in the population.
collection_mechanisms:
  - description:
      - IF imaging via immunofluorescence-based staining (ICC-IF) and confocal microscopy (Lundberg Lab, Stanford University)
      - Protein-protein interaction profiling via size exclusion chromatography mass spectrometry (SEC-MS)
      - CRISPRi-based perturb-seq single-cell RNA sequencing in undifferentiated KOLF2.1J iPSCs
data_collectors:
  - description:
      - CM4AI consortium across UC San Diego, UC San Francisco, Stanford University, and University of Virginia; IF imaging performed in the Lundberg Lab (Stanford).
collection_timeframes:
  - description:
      - Data creation date 2025-02-27; dataset release 2025-07-01 (Version 2.0).
ethical_reviews:
  - description:
      - Data Governance & Ethics oversight; Human Subjects: No; De-identified Samples: Yes; FDA Regulated: No.
      - Data Governance Committee contact: Jillian Parker (jillianparker@health.ucsd.edu).
      - Ethical review leads: Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Bélisle-Pipon (jean-christophe_belisle-pipon@sfu.ca).
is_deidentified:
  description:
    - Human subjects data are not included; samples are de-identified. Data derived from commercially available de-identified human cell lines.
external_resources:
  - external_resources:
      - Sequence Read Archive (SRA) Data via NCBI BioProject
    archival:
      - Hosted by NCBI SRA
    restrictions:
      - Some datasets may be under temporary pre-publication embargo.
  - external_resources:
      - Mass Spectrometry Data (Human iPSCs) via MassIVE Repository
    archival:
      - Hosted by MassIVE
    restrictions:
      - Some datasets may be under temporary pre-publication embargo.
  - external_resources:
      - Mass Spectrometry Data (Human Cancer Cells) via MassIVE Repository
    archival:
      - Hosted by MassIVE
    restrictions:
      - Some datasets may be under temporary pre-publication embargo.
preprocessing_strategies:
  - description:
      - Not explicitly detailed for this release; modality-specific pipelines implied (IF imaging processing; SEC-MS workflows; perturb-seq processing via scRNA-seq pipelines). See RO-Crate metadata for details.
raw_sources:
  - description:
      - Raw data and/or primary outputs are hosted in external repositories (SRA for sequencing; MassIVE for proteomics); IF image archives available as ZIPs in Dataverse.
future_use_impacts:
  - description:
      - Interim release; predicted cell maps not yet included.
      - Modalities interrogate overlapping but not identical protein sets across assays.
      - Domain expertise recommended for meaningful analysis.
      - Data derived from specific de-identified human cell lines and do not represent all biological variants.
discouraged_uses:
  - description:
      - Not for clinical decision-making or any context involving patient care without appropriate regulatory oversight and approval.
distribution_formats:
  - description:
      - Dataverse-hosted files (HTML datasheet; RO-Crate JSON metadata; modality-specific provenance HTML)
  - description:
      - ZIP archives for IF images (application/zip)
  - description:
      - External repositories (SRA, MassIVE) for raw/primary modality data
distribution_dates:
  - description:
      - 2025-07-01 (initial public release, Version 2.0)
  - description:
      - 2025-10-22 (IF image ZIP archives published)
license_and_use_terms:
  description:
    - CC BY-NC-SA 4.0; community norms expect proper citation using the dataset citation on the page.
maintainers:
  - description:
      - Long-term preservation and hosting in the University of Virginia Dataverse (supported by committed institutional funds). Contact University of Virginia Dataverse Support.
updates:
  description:
    - Dataset will be regularly updated and augmented through November 2026; updates on a quarterly basis.
subsets:
  - name: release-ro-crate-datasheet.html
    description: HTML datasheet summarizing key release information.
    path: release-ro-crate-datasheet.html
    media_type: text/html
    md5: 599c9ece9b88b3ce797b82463b4a1eb4
    issued: 2025-07-01
  - name: release-ro-crate-metadata.json
    description: Release RO-Crate with pointers to sub ro-crates.
    path: release-ro-crate-metadata.json
    media_type: application/json
    md5: 99f9e00053bff3020fd9832a3a518bbb
    issued: 2025-07-01
  - name: cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    description: IF imaging of 464 proteins in MDA-MB-468 cells treated with paclitaxel (ICC-IF confocal microscopy; DAPI, calreticulin, tubulin, POI channels).
    path: Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    media_type: application/zip
    md5: 0d972b80744344ddeede516a0cf6e3d7
    issued: 2025-10-22
  - name: cm4ai-ifimages-mda-mb-468-untreated.zip
    description: IF imaging of 464 proteins in untreated MDA-MB-468 cells (ICC-IF confocal microscopy; DAPI, calreticulin, tubulin, POI channels).
    path: Images/cm4ai-ifimages-mda-mb-468-untreated.zip
    media_type: application/zip
    md5: a98affcc05429650c6bb3906cd836d55
    issued: 2025-10-22
  - name: cm4ai-ifimages-mda-mb-468-vorinostat.zip
    description: IF imaging of 464 proteins in MDA-MB-468 cells treated with vorinostat (ICC-IF confocal microscopy; DAPI, calreticulin, tubulin, POI channels).
    path: Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip
    media_type: application/zip
    md5: ad4e68ccc14b0f3349dad3321e7b81b2
    issued: 2025-10-22
  - name: Images-paclitaxel-provenance-graph.html
    description: IF imaging provenance graph (paclitaxel condition); download to view properly.
    path: Images/paclitaxel/Images-paclitaxel-provenance-graph.html
    media_type: text/html
    md5: e38e63e4c8dfc5808a5ffa2d7829fc38
    issued: 2025-07-01
  - name: Images-untreated-provenance-graph.html
    description: IF imaging provenance graph (untreated condition); download to view properly.
    path: Images/untreated/Images-untreated-provenance-graph.html
    media_type: text/html
    md5: 1a3b510f74d3f8647e07c6559ce64ee8
    issued: 2025-07-01
  - name: Images-vorinostat-provenance-graph.html
    description: IF imaging provenance graph (vorinostat condition); download to view properly.
    path: Images/vorinostat/Images-vorinostat-provenance-graph.html
    media_type: text/html
    md5: 58935fe4e254b31d33fed019f24c7668
    issued: 2025-07-01
  - name: mass-spec-cancer-cells-provenance-graph.html
    description: SEC-MS provenance graph for human cancer cells; download to view properly.
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-provenance-graph.html
    media_type: text/html
    md5: 931ad9b552562024cb84ebe62d1f1838
    issued: 2025-07-01
  - name: mass-spec-cancer-cells-ro-crate-metadata.json
    description: RO-Crate metadata for SEC-MS cancer cell data.
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json
    media_type: application/json
    md5: 3a7063bb391ea5e05a32ba5da5f4b2f8
    issued: 2025-07-01