=== 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).
doi: "doi:10.18130/V3/F3TD5R"
page: "https://doi.org/10.18130/V3/F3TD5R"
issued: "2025-07-01"
created_on: "2025-02-27"
last_updated_on: "2025-07-01"
publisher: "https://dataverse.lib.virginia.edu"
version: "2.0"
license: CC BY-NC-SA 4.0
language: en
keywords:
  - AI
  - artificial intelligence
  - Bridge2AI
  - CM4AI
  - functional genomics
  - machine learning
  - perturb-seq
  - perturbation sequencing
  - single-cell RNA sequencing
  - scRNAseq
  - CRISPR/Cas9
  - protein-protein interaction
  - SEC-MS
  - size exclusion chromatography
  - mass spectrometry
  - subcellular imaging
  - immunofluorescence
  - protein localization
  - breast cancer
  - MDA-MB-468
  - induced pluripotent stem cell
  - iPSC
  - KOLF2.1J
  - neural progenitor cell
  - NPC
  - neuron
  - cardiomyocyte
  - paclitaxel
  - vorinostat
  - Medicine, Health and Life Sciences
purposes:
  - response: AI-ready datasets to support research in functional genomics
  - response: AI model training
  - response: Cellular process analysis
  - response: Analysis of cell architectural changes and interactions under disease, treatment, or genetic perturbation conditions
tasks:
  - response: AI model training for functional genomics
  - response: Bioinformatics analysis of perturb-seq, SEC-MS, and IF imaging datasets
addressing_gaps: []
creators:
  - principal_investigator:
      name: Trey Ideker
      affiliation:
        name: University of California San Diego
    affiliation:
      name: University of California San Diego
  - principal_investigator:
      name: Nevan Krogan
      affiliation:
        name: University of California San Francisco
    affiliation:
      name: University of California San Francisco
  - principal_investigator:
      name: Emma Lundberg
      affiliation:
        name: Stanford University
    affiliation:
      name: Stanford University
funders:
  - grantor:
      name: National Institutes of Health
    grant:
      name: NIH OT2 award
      grant_number: 1OT2OD032742-01
instances:
  - representation: Single-cell transcriptomic profiles from CRISPRi perturb-seq experiments in undifferentiated KOLF2.1J iPSCs
    instance_type: scRNA-seq cell profiles and associated perturbation metadata
    data_type: Sequencing-derived count matrices/metadata (perturb-seq)
    label: Not specified
    sampling_strategies: []
    missing_information:
      - missing:
          - Computed cell maps not included in this release
        why_missing:
          - To be added in future releases
  - representation: Protein-protein interaction profiles using size exclusion chromatography mass spectrometry (SEC-MS)
    instance_type: Protein interaction/complex fractionation profiles across cell types and conditions
    data_type: Mass spectrometry-derived quantitative features
    label: Not specified
    sampling_strategies: []
    missing_information: []
  - representation: Immunofluorescence microscopy images showing protein localization in MDA-MB-468 cells under drug treatments and control
    instance_type: Multi-channel IF images (DAPI, ER, microtubules, protein of interest)
    data_type: Image data (confocal microscopy)
    label: Not specified
    sampling_strategies: []
    missing_information: []
sampling_strategies:
  - strategies:
      - Targeted selection of proteins/perturbations; interrogated protein sets incompletely overlap across modalities
    is_sample:
      - Yes
    is_random:
      - No
    is_representative:
      - No
    why_not_representative:
      - Data derived from specific de-identified human cell lines and targeted protein sets; not representative of all biological variation
missing_information: []
relationships:
  - description:
      - Protein-protein interactions (SEC-MS) provide explicit relationships among proteins/complexes
splits: []
anomalies: []
external_resources:
  - external_resources:
      - Sequence Read Archive (SRA) Data: NCBI BioProject
      - Mass Spectrometry Data (Human iPSCs): MassIVE Repository
      - Mass Spectrometry Data (Human Cancer Cells): MassIVE Repository
    future_guarantees:
      - Not specified
    archival:
      - Long-term preservation in the University of Virginia Dataverse
    restrictions:
      - External repositories may have their own access or reuse terms
confidential_elements:
  - description:
      - No human subjects; data from de-identified human cell lines
content_warnings: []
subpopulations:
  - identification:
      - Undifferentiated KOLF2.1J iPSCs; iPSC-derived NPCs, neurons, cardiomyocytes; MDA-MB-468 breast cancer cells (treated and untreated)
    distribution:
      - Not specified
sensitive_elements:
  - description:
      - Data derived from human cell lines; no personally identifiable information; no PHI
acquisition_methods:
  - description:
      - Data are directly observed via sequencing (perturb-seq), mass spectrometry (SEC-MS), and immunofluorescence confocal microscopy (IF)
    was_directly_observed: Yes
    was_reported_by_subjects: No
    was_inferred_derived: Some analyses may derive features, but computed cell maps are not included in this release
    was_validated_verified: Not specified
collection_mechanisms:
  - description:
      - Immunofluorescence-based staining (ICC-IF) and confocal microscopy (Lundberg Lab at Stanford)
  - description:
      - Size exclusion chromatography mass spectrometry (SEC-MS)
  - description:
      - CRISPRi perturb-seq (single-cell RNA sequencing)
data_collectors:
  - description:
      - Lundberg Lab (Stanford University) generated IF imaging data
  - description:
      - CM4AI consortium labs generated perturb-seq and SEC-MS data (UC San Diego, UC San Francisco, Stanford University, University of Virginia)
collection_timeframes:
  - description:
      - Data creation date 2025-02-27; dataset published 2025-07-01 (V2.0). Additional image ZIPs published 2025-10-22.
ethical_reviews:
  - description:
      - Ethical review/oversight by Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca). Human Subjects: No. De-identified Samples: Yes. FDA Regulated: No. Data Governance Committee: Jillian Parker (jillianparker@health.ucsd.edu).
data_protection_impacts: []
preprocessing_strategies: []
cleaning_strategies: []
labeling_strategies: []
raw_sources:
  - description:
      - Raw/primary data accessible via external repositories (SRA BioProject, MassIVE) as linked from the dataset landing page
existing_uses:
  - description:
      - Related publications include CM4AI preprints/articles (e.g., bioRxiv 2024.05.21.589311; 2024.11.03.621734)
use_repository: []
other_tasks:
  - description:
      - Development and benchmarking of AI methods for multimodal cell mapping
future_use_impacts:
  - description:
      - Potential biases due to use of specific de-identified human cell lines and targeted protein sets; not representative of all biological variants
discouraged_uses:
  - description:
      - Not for clinical decision-making or any patient-care context without appropriate regulatory oversight and approval
distribution_formats:
  - description:
      - ZIP archives (images)
  - description:
      - JSON (RO-Crate metadata)
  - description:
      - HTML (datasheets/provenance graph visualizations)
distribution_dates:
  - description:
      - 2025-07-01 (V2.0 release)
  - description:
      - 2025-10-22 (additional IF image ZIPs)
license_and_use_terms:
  description:
    - CC BY-NC-SA 4.0. Community norms expect proper citation. Laboratory data are not to be used for clinical decision-making or patient care without appropriate regulatory oversight and approval.
ip_restrictions:
  description:
    - None indicated
regulatory_restrictions:
  description:
    - Not FDA regulated (per dataset description)
maintainers:
  - description:
      - Long-term preservation and hosting by the University of Virginia Dataverse
  - description:
      - Data Governance Committee contact: Jillian Parker (jillianparker@health.ucsd.edu)
  - description:
      - Point of contact: Trey Ideker (University of California San Diego)
errata: []
updates:
  description:
    - Dataset will be regularly updated and augmented through the end of the project in November 2026; updates on a quarterly basis
retention_limit:
  description:
    - Not specified
version_access:
  description:
    - Versions maintained by University of Virginia Dataverse (current version V2.0)
extension_mechanism:
  description:
    - RO-Crate packaging used with pointers to sub RO-Crates; contributions via CM4AI project data releases
is_deidentified:
  description:
    - Data derived from commercially available de-identified human cell lines; no human subjects
is_tabular: Mixed modalities (images, mass spectrometry, single-cell RNA-seq)
subsets:
  - name: release-ro-crate-datasheet.html
    title: Release RO-Crate datasheet
    description: HTML datasheet summarizing key release information.
    path: release-ro-crate-datasheet.html
    media_type: text/html
    md5: 599c9ece9b88b3ce797b82463b4a1eb4
    issued: "2025-07-01"
    license: CC BY-NC-SA 4.0
  - name: release-ro-crate-metadata.json
    title: Release RO-Crate metadata
    description: Release RO-Crate with pointers to sub RO-Crates.
    path: release-ro-crate-metadata.json
    media_type: application/json
    format: JSON
    md5: 99f9e00053bff3020fd9832a3a518bbb
    issued: "2025-07-01"
    license: CC BY-NC-SA 4.0
  - name: cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    title: IF images - MDA-MB-468 treated with paclitaxel
    description: Spatial localization of 464 proteins in MDA-MB-468 cells treated with paclitaxel; ICC-IF confocal microscopy (Lundberg Lab).
    path: Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    media_type: application/zip
    md5: 0d972b80744344ddeede516a0cf6e3d7
    issued: "2025-10-22"
    license: CC BY-NC-SA 4.0
  - name: cm4ai-ifimages-mda-mb-468-untreated.zip
    title: IF images - MDA-MB-468 untreated
    description: Spatial localization of 464 proteins in untreated MDA-MB-468 cells; ICC-IF confocal microscopy (Lundberg Lab).
    path: Images/cm4ai-ifimages-mda-mb-468-untreated.zip
    media_type: application/zip
    md5: a98affcc05429650c6bb3906cd836d55
    issued: "2025-10-22"
    license: CC BY-NC-SA 4.0
  - name: cm4ai-ifimages-mda-mb-468-vorinostat.zip
    title: IF images - MDA-MB-468 treated with vorinostat
    description: Spatial localization of 464 proteins in MDA-MB-468 cells treated with vorinostat; ICC-IF confocal microscopy (Lundberg Lab).
    path: Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip
    media_type: application/zip
    md5: ad4e68ccc14b0f3349dad3321e7b81b2
    issued: "2025-10-22"
    license: CC BY-NC-SA 4.0
  - name: Images-paclitaxel-provenance-graph.html
    title: IF images (paclitaxel) provenance graph
    description: HTML provenance graph (download to view correctly).
    path: Images/paclitaxel/Images-paclitaxel-provenance-graph.html
    media_type: text/html
    md5: e38e63e4c8dfc5808a5ffa2d7829fc38
    issued: "2025-07-01"
    license: CC BY-NC-SA 4.0
  - name: Images-untreated-provenance-graph.html
    title: IF images (untreated) provenance graph
    description: HTML provenance graph (download to view correctly).
    path: Images/untreated/Images-untreated-provenance-graph.html
    media_type: text/html
    md5: 1a3b510f74d3f8647e07c6559ce64ee8
    issued: "2025-07-01"
    license: CC BY-NC-SA 4.0
  - name: Images-vorinostat-provenance-graph.html
    title: IF images (vorinostat) provenance graph
    description: HTML provenance graph (download to view correctly).
    path: Images/vorinostat/Images-vorinostat-provenance-graph.html
    media_type: text/html
    md5: 58935fe4e254b31d33fed019f24c7668
    issued: "2025-07-01"
    license: CC BY-NC-SA 4.0
  - name: mass-spec-cancer-cells-provenance-graph.html
    title: Mass spec (cancer cells) provenance graph
    description: HTML provenance graph for mass spectrometry data (download to view correctly).
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-provenance-graph.html
    media_type: text/html
    md5: 931ad9b552562024cb84ebe62d1f1838
    issued: "2025-07-01"
    license: CC BY-NC-SA 4.0
  - name: mass-spec-cancer-cells-ro-crate-metadata.json
    title: Mass spec (cancer cells) RO-Crate metadata
    description: RO-Crate metadata for mass spectrometry cancer cell data.
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json
    media_type: application/json
    format: JSON
    md5: 3a7063bb391ea5e05a32ba5da5f4b2f8
    issued: "2025-07-01"
    license: CC BY-NC-SA 4.0
creators:
  - principal_investigator:
      name: Trey Ideker
      affiliation:
        name: University of California San Diego
    affiliation:
      name: University of California San Diego
  - principal_investigator:
      name: Nevan Krogan
      affiliation:
        name: University of California San Francisco
    affiliation:
      name: University of California San Francisco
  - principal_investigator:
      name: Emma Lundberg
      affiliation:
        name: Stanford University
    affiliation:
      name: Stanford University