=== 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-MB-468 breast cancer cells; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel).
language: en
publisher: "https://dataverse.lib.virginia.edu/"
issued: "2025-07-01"
page: "https://dataverse.lib.virginia.edu/dataset.xhtml?persistentId=doi:10.18130/V3/F3TD5R"
doi: "doi:10.18130/V3/F3TD5R"
license: "https://creativecommons.org/licenses/by-nc-sa/4.0/"
version: "2.0"
created_on: "2025-02-27"
last_updated_on: "2025-07-01"
keywords:
  - AI
  - artificial intelligence
  - Bridge2AI
  - CM4AI
  - machine learning
  - induced pluripotent stem cell
  - iPSC
  - KOLF2.1J
  - neural progenitor cell
  - NPC
  - neuron
  - cardiomyocyte
  - breast cancer
  - MDA-MB-468
  - paclitaxel
  - vorinostat
  - subcellular imaging
  - immunofluorescence
  - protein localization
  - protein-protein interaction
  - SEC-MS
  - size exclusion chromatography
  - mass spectroscopy
  - affinity purification
  - AP-MS
  - CRISPR/Cas9
  - perturb-seq
  - perturbation sequencing
  - single-cell RNA sequencing
  - scRNAseq
purposes:
  - name: Intended Use
    response: AI-ready datasets to support research in functional genomics; AI model training; cellular process analysis; analysis of cell architectural changes and interactions under disease, treatment, or genetic perturbation conditions.
tasks:
  - name: Downstream AI and bioinformatics tasks
    response: Training and evaluation of AI/ML models on functional genomics data; image-based protein localization analysis; proteomics-based interaction network inference; single-cell perturbation transcriptomics analysis.
addressing_gaps:
  - name: Interim data toward AI-ready cell maps
    response: Interim release providing multi-modal functional genomics data; predicted cell maps will be added in future releases.
creators:
  - name: Cell Maps for Artificial Intelligence (CM4AI) Consortium
    affiliation:
      name: University of California San Diego
  - name: Cell Maps for Artificial Intelligence (CM4AI) Consortium
    affiliation:
      name: University of California San Francisco
  - name: Cell Maps for Artificial Intelligence (CM4AI) Consortium
    affiliation:
      name: Stanford University
  - name: Cell Maps for Artificial Intelligence (CM4AI) Consortium
    affiliation:
      name: University of Virginia
funders:
  - name: NIH Bridge2AI Program Support
    grantor:
      name: National Institutes of Health
    grant:
      name: Bridge2AI CM4AI
      grant_number: 1OT2OD032742-01
subsets:
  - name: cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    description: Immunofluorescence confocal microscopy images displaying spatial localization of 464 proteins of interest in MDA-MB-468 breast cancer cells treated with paclitaxel. Channels include DAPI (nuclei, blue), calreticulin (ER, yellow), tubulin (microtubules, red), and protein of interest (green). Generated in the Lundberg Lab (Stanford) as part of CM4AI.
    media_type: application/zip
    compression: ZIP
    md5: 0d972b80744344ddeede516a0cf6e3d7
    issued: "2025-10-22"
    path: Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
  - name: cm4ai-ifimages-mda-mb-468-untreated.zip
    description: Immunofluorescence confocal microscopy images displaying spatial localization of 464 proteins of interest in untreated MDA-MB-468 breast cancer cells. Channels include DAPI (nuclei, blue), calreticulin (ER, yellow), tubulin (microtubules, red), and protein of interest (green). Generated in the Lundberg Lab (Stanford) as part of CM4AI.
    media_type: application/zip
    compression: ZIP
    md5: a98affcc05429650c6bb3906cd836d55
    issued: "2025-10-22"
    path: Images/cm4ai-ifimages-mda-mb-468-untreated.zip
  - name: cm4ai-ifimages-mda-mb-468-vorinostat.zip
    description: Immunofluorescence confocal microscopy images displaying spatial localization of 464 proteins of interest in MDA-MB-468 breast cancer cells treated with vorinostat. Channels include DAPI (nuclei, blue), calreticulin (ER, yellow), tubulin (microtubules, red), and protein of interest (green). Generated in the Lundberg Lab (Stanford) as part of CM4AI.
    media_type: application/zip
    compression: ZIP
    md5: ad4e68ccc14b0f3349dad3321e7b81b2
    issued: "2025-10-22"
    path: Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip
  - name: release-ro-crate-datasheet.html
    description: HTML datasheet summarizing key release information.
    media_type: text/html
    md5: 599c9ece9b88b3ce797b82463b4a1eb4
    issued: "2025-07-01"
    path: release-ro-crate-datasheet.html
  - name: release-ro-crate-metadata.json
    description: RO-Crate metadata with pointers to sub RO-Crates for this release.
    format: JSON
    media_type: application/json
    md5: 99f9e00053bff3020fd9832a3a518bbb
    issued: "2025-07-01"
    path: release-ro-crate-metadata.json
  - name: mass-spec-cancer-cells-ro-crate-metadata.json
    description: RO-Crate metadata for mass spectrometry data (human cancer cells).
    format: JSON
    media_type: application/json
    md5: 3a7063bb391ea5e05a32ba5da5f4b2f8
    issued: "2025-07-01"
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json
  - name: Images-paclitaxel-provenance-graph.html
    description: HTML provenance graph for paclitaxel-treated image dataset (download to view correctly).
    media_type: text/html
    md5: e38e63e4c8dfc5808a5ffa2d7829fc38
    issued: "2025-07-01"
    path: Images/paclitaxel/Images-paclitaxel-provenance-graph.html
  - name: Images-untreated-provenance-graph.html
    description: HTML provenance graph for untreated image dataset (download to view correctly).
    media_type: text/html
    md5: 1a3b510f74d3f8647e07c6559ce64ee8
    issued: "2025-07-01"
    path: Images/untreated/Images-untreated-provenance-graph.html
  - name: Images-vorinostat-provenance-graph.html
    description: HTML provenance graph for vorinostat-treated image dataset (download to view correctly).
    media_type: text/html
    md5: 58935fe4e254b31d33fed019f24c7668
    issued: "2025-07-01"
    path: Images/vorinostat/Images-vorinostat-provenance-graph.html
instances:
  - name: Immunofluorescence microscopy images (MDA-MB-468)
    representation: Images of subcellular protein localization across 464 proteins under untreated, paclitaxel-treated, and vorinostat-treated conditions in MDA-MB-468 cells.
    data_type: Raw/confocal microscopy image data in ZIP archives; multichannel ICC-IF (DAPI, calreticulin, tubulin, protein-of-interest).
    label: Protein-of-interest channel with cellular markers; experimental condition (treated vs untreated).
  - name: SEC-MS proteomics (iPSCs, NPCs, neurons, cardiomyocytes, cancer cells)
    representation: Size exclusion chromatography mass spectrometry (SEC-MS) protein-protein interaction measurements across multiple human cell types.
    data_type: Proteomics data (linked via MassIVE repositories); release contains RO-Crate metadata and provenance.
  - name: CRISPRi perturb-seq (KOLF2.1J iPSCs)
    representation: Single-cell RNA-seq under CRISPR interference perturbations in undifferentiated KOLF2.1J induced pluripotent stem cells.
    data_type: scRNA-seq read data (linked via NCBI SRA BioProject).
external_resources:
  - name: Linked external repositories
    external_resources:
      - Sequence Read Archive (SRA) Data via NCBI BioProject (perturb-seq, KOLF2.1J iPSCs)
      - Mass Spectrometry Data (Human iPSCs) via MassIVE repository
      - Mass Spectrometry Data (Human Cancer Cells) via MassIVE repository
    archival:
      - Primary raw read and proteomics data are hosted by respective domain repositories; RO-Crate metadata included in this Dataverse release.
    restrictions:
      - Refer to external repository terms; this Dataverse release is CC BY-NC-SA 4.0.
confidential_elements:
  - name: Confidentiality assessment
    description:
      - No human subjects. Data derived from commercially available de-identified human cell lines.
content_warnings:
  - name: Prohibited uses notice
    warnings:
      - Laboratory research data only; do not use for clinical decision-making or any patient care context without appropriate regulatory oversight and approval.
subpopulations:
  - name: Cell line and cell type coverage
    identification:
      - Human cell lines and derived cell types: KOLF2.1J iPSCs; iPSC-derived NPCs, neurons, cardiomyocytes; MDA-MB-468 breast cancer cells (treated/untreated).
    distribution:
      - Modalities cover overlapping but not identical protein sets across assays; see Completeness notes.
sensitive_elements:
  - name: Sensitivity assessment
    description:
      - No PII/PHI; de-identified cell lines; no FDA-regulated clinical data.
is_deidentified:
  name: De-identification
  description:
    - Human Subjects: No
    - De-identified Samples: Yes (commercially available human cell lines)
acquisition_methods:
  - name: Data acquisition modalities
    description:
      - Direct observation via confocal microscopy (ICC-IF).
      - Direct measurement via size exclusion chromatography-coupled mass spectrometry (SEC-MS).
      - Direct sequencing via single-cell RNA-seq under CRISPRi perturbations (perturb-seq).
    was_directly_observed: yes
    was_reported_by_subjects: no
    was_inferred_derived: no
collection_mechanisms:
  - name: Collection procedures
    description:
      - ICC-IF staining with antibodies (DAPI, calreticulin, tubulin, protein-of-interest) and confocal imaging (Lundberg Lab).
      - SEC-MS workflows for protein-protein interaction profiling.
      - CRISPRi perturbation and scRNA-seq (perturb-seq) in KOLF2.1J iPSCs.
data_collectors:
  - name: Contributing laboratories and institutions
    description:
      - Stanford University (Lundberg Lab; ICC-IF imaging)
      - University of California San Diego
      - University of California San Francisco
      - University of Virginia
collection_timeframes:
  - name: Release timeline
    description:
      - Data creation date: 2025-02-27; publication date: 2025-07-01. Some image ZIP subsets published 2025-10-22.
ethical_reviews:
  - name: Data Governance & Ethics
    description:
      - Data Governance Committee: Jillian Parker (jillianparker@health.ucsd.edu)
      - Ethical Review: Vardit Ravitsky (ravitskyv@thehastingscenter.org), Jean-Christophe Bélisle-Pipon (jean-christophe_belisle-pipon@sfu.ca)
preprocessing_strategies:
  - name: ICC-IF staining and imaging
    description:
      - Multichannel antibody staining (DAPI, calreticulin, tubulin, protein-of-interest) followed by confocal microscopy.
cleaning_strategies:
  - name: Release completeness notes
    description:
      - Interim beta release; computed cell maps not included; some datasets under temporary pre-publication embargo.
raw_sources:
  - name: Raw data availability
    description:
      - Raw scRNA-seq reads available via NCBI SRA BioProject; proteomics data via MassIVE; raw/confocal image data provided in ZIP archives in this release.
existing_uses:
  - name: Related publications
    description:
      - Clark T et al. 2024. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. doi: http://doi.org/10.1101/2024.05.21.589311
      - Nourreddine S et al. 2024. A Perturbation Cell Atlas of Human Induced Pluripotent Stem Cells. bioRxiv 2024.11.03.621734. https://doi.org/10.1101/2024.11.03.621734
future_use_impacts:
  - name: Potential sources of bias and limitations
    description:
      - Data derived from commercially available de-identified human cell lines; may not represent all biological variants in the broader population.
      - Interim release; predicted cell maps not yet included; modalities interrogate overlapping but incomplete protein sets.
discouraged_uses:
  - name: Prohibited uses
    description:
      - Do not use for clinical decision-making or any patient care context without appropriate regulatory oversight and approval.
distribution_formats:
  - name: Distribution
    description:
      - Public access via University of Virginia Dataverse landing page and Data Access API.
      - RO-Crate metadata (JSON) and HTML datasheets/provenance graphs.
      - ZIP archives for large image datasets.
distribution_dates:
  - name: Release dates
    description:
      - Main dataset publication: 2025-07-01
      - IF image ZIP subsets publication: 2025-10-22
license_and_use_terms:
  name: License
  description:
    - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
maintainers:
  - name: Dataset maintainers
    description:
      - University of Virginia Dataverse (hosting/preservation)
      - Point of Contact: Trey Ideker (University of California San Diego)
updates:
  name: Maintenance plan
  description:
    - Dataset will be regularly updated and augmented through November 2026.
    - Updates on a quarterly basis.
    - Long-term preservation in the University of Virginia Dataverse, supported by institutional funds.