=== 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). Some datasets are under temporary pre-publication embargo; the sets of proteins interrogated across modalities incompletely overlap; and computed cell maps are not included in this release.
language: English
page: "https://doi.org/10.18130/V3/F3TD5R"
doi: "doi:10.18130/V3/F3TD5R"
issued: 2025-07-01
created_on: 2025-02-27
version: "2.0"
created_by:
  - CM4AI Consortium
  - University of Virginia Dataverse
license: CC BY-NC-SA 4.0
keywords:
  - AI
  - artificial intelligence
  - machine learning
  - Bridge2AI
  - CM4AI
  - induced pluripotent stem cell
  - iPSC
  - KOLF2.1J
  - neural progenitor cell
  - NPC
  - neuron
  - cardiomyocyte
  - breast cancer
  - MDA-MB-468
  - perturb-seq
  - perturbation sequencing
  - single-cell RNA sequencing
  - scRNAseq
  - SEC-MS
  - size exclusion chromatography
  - mass spectrometry
  - protein-protein interaction
  - protein localization
  - subcellular imaging
  - affinity purification
  - AP-MS
  - paclitaxel
  - vorinostat
  - confocal microscopy
  - functional genomics
  - Medicine, Health and Life Sciences
status:
last_updated_on: 2025-07-01
purposes:
  - name: Intended Purpose
    response: AI-ready datasets to support research in functional genomics; enable AI model training; facilitate cellular process analysis and analysis of cell architectural changes and interactions under disease, treatment, or genetic perturbations.
tasks:
  - name: Primary Tasks
    response: Train and evaluate AI/ML models on multimodal cellular data (imaging, proteomics, single-cell transcriptomics); bioinformatics analysis of individual datasets.
addressing_gaps:
  - name: Gap Addressed
    response: Provide harmonized, AI-ready multimodal functional genomics data from disease-relevant human cell lines to accelerate building cell maps; interim release pending inclusion of predicted/computed cell maps in future versions.
creators:
  - name: Cell Maps for Artificial Intelligence (CM4AI) - UC San Diego Site
    principal_investigator:
      id: trey-ideker
      name: Trey Ideker
      affiliation:
        id: ucsd
        name: University of California San Diego
    affiliation:
      id: ucsd
      name: University of California San Diego
  - name: Cell Maps for Artificial Intelligence (CM4AI) - UCSF Site
    principal_investigator:
      id: nevan-krogan
      name: Nevan Krogan
      affiliation:
        id: ucsf
        name: University of California San Francisco
    affiliation:
      id: ucsf
      name: University of California San Francisco
  - name: Cell Maps for Artificial Intelligence (CM4AI) - Stanford Site
    principal_investigator:
      id: emma-lundberg
      name: Emma Lundberg
      affiliation:
        id: stanford
        name: Stanford University
    affiliation:
      id: stanford
      name: Stanford University
  - name: Cell Maps for Artificial Intelligence (CM4AI) - University of Virginia Site
    principal_investigator:
      id: tom-clark
      name: Thomas Clark
      affiliation:
        id: uva
        name: University of Virginia
    affiliation:
      id: uva
      name: University of Virginia
funders:
  - name: NIH Bridge2AI Program
    grantor:
      id: nih
      name: National Institutes of Health
    grant:
      id: 1OT2OD032742-01
      name: Bridge2AI Functional Genomics Grand Challenge
      grant_number: 1OT2OD032742-01
instances:
  - name: Immunofluorescence images (ICC-IF)
    representation: Confocal microscopy immunofluorescence images of MDA-MB-468 breast cancer cells under drug treatments (vorinostat, paclitaxel) and untreated.
    instance_type: "Image files (multichannel: DAPI, calreticulin/ER, tubulin/microtubules, protein-of-interest antibody)."
    data_type: Raw/confocal image data packaged as ZIP archives with associated provenance.
  - name: Size Exclusion Chromatography Mass Spectrometry (SEC-MS)
    representation: Protein-protein interaction profiles from SEC-MS across multiple human cell types (KOLF2.1J iPSCs, NPCs, neurons, cardiomyocytes, and MDA-MB-468 with/without treatment).
    instance_type: Proteomics fractions and quantitative profiles.
    data_type: Mass spectrometry-derived protein interaction/abundance measurements; RO-Crate metadata and provenance provided.
  - name: CRISPRi perturb-seq (scRNA-seq)
    representation: Single-cell transcriptomic responses to CRISPRi perturbations in undifferentiated KOLF2.1J iPSCs.
    instance_type: Single-cell RNA sequencing profiles per perturbation.
    data_type: scRNA-seq counts/metadata referenced via SRA BioProject.
sampling_strategies:
  - name: Representativeness
    is_sample:
      - Yes; datasets are derived from specific commercially available de-identified human cell lines.
    is_representative:
      - No
    why_not_representative:
      - Does not represent all biological variants seen in the broader human population.
relationships:
  - name: Molecular relationships captured
    description:
      - Protein-protein interactions (SEC-MS) and protein localization relationships from IF imaging; multi-omic alignment across modalities.
splits:
  - name: Data splits
    description:
      - No prescribed machine learning splits provided in this interim release.
anomalies:
  - name: Known limitations
    description:
      - Interim release; computed/predicted cell maps are not yet included; protein target sets incompletely overlap across modalities; some datasets under temporary pre-publication embargo.
external_resources:
  - name: External Data Repositories
    external_resources:
      - NCBI BioProject (Sequence Read Archive) for perturb-seq/scRNA-seq data
      - MassIVE repository for human iPSC SEC-MS data
      - MassIVE repository for human cancer cell SEC-MS data
    future_guarantees:
      - External repositories are operated by NCBI and MassIVE; persistence is governed by those repositories’ policies.
    archival:
      - Long-term preservation of this release in University of Virginia Dataverse.
    restrictions:
      - External repositories may have their own terms of use; see respective repository pages.
confidential_elements:
  - name: Confidentiality
    description:
      - No human subjects; data derived from de-identified, commercially available human cell lines; no non-public communications included.
content_warnings:
  - name: Prohibited uses
    warnings:
      - Not for clinical decision-making or any patient care context without appropriate regulatory oversight and approval.
subpopulations:
  - name: Cell types and conditions
    identification:
      - Subsets defined by cell line/type (KOLF2.1J iPSC, NPC, neuron, cardiomyocyte, MDA-MB-468) and treatment conditions (vorinostat, paclitaxel, untreated).
deidentification:
  - name: De-identification status
    description:
      - Human Subjects: No; De-identified Samples: Yes. Data are derived from de-identified human cell lines and do not enable identification of individuals.
sensitive_elements:
  - name: Sensitive data
    description:
      - No direct personal data; laboratory measurements on de-identified cell lines.
acquisition_methods:
  - name: Data acquisition overview
    description:
      - Direct observation via confocal microscopy for IF images; size exclusion chromatography coupled with mass spectrometry (SEC-MS) for protein interactions; single-cell RNA-seq (perturb-seq) for transcriptomics.
    was_directly_observed: Yes
    was_reported_by_subjects: No
    was_inferred_derived: Limited derived analyses; computed cell maps not included in this release.
    was_validated_verified: Not specified in this record.
collection_mechanisms:
  - name: Collection mechanisms
    description:
      - Hardware and laboratory protocols including confocal microscopes, immunofluorescence staining, size exclusion chromatography and mass spectrometry workflows, and CRISPRi perturbation with single-cell sequencing; provenance graphs and RO-Crate metadata provided for modalities.
data_collectors:
  - name: Contributing organizations
    description:
      - University of California San Diego; University of California San Francisco; Stanford University; University of Virginia.
collection_timeframes:
  - name: Timeframe
    description:
      - Data creation date: 2025-02-27; dataset publication date (Version 2.0): 2025-07-01. Additional IF image ZIP archives published 2025-10-22.
ethical_reviews:
  - name: Data Governance & Ethics
    description:
      - Human Subjects: No; De-identified Samples: Yes; FDA Regulated: No. Data Governance Committee contact: Jillian Parker (jillianparker@health.ucsd.edu). Ethical review by Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca).
data_protection_impacts:
  - name: Data protection assessment
    description:
      - No human subjects and de-identified samples reduce privacy risk; users should consider potential biases from use of specific cell lines.
preprocessing_strategies:
  - name: Laboratory processing
    description:
      - ICC-IF staining channels: nuclei (DAPI), endoplasmic reticulum (calreticulin antibody), microtubules (tubulin antibody), and protein-of-interest antibody; SEC fractionation prior to MS; CRISPRi perturbation prior to scRNA-seq.
raw_sources:
  - name: Raw data availability
    description:
      - Raw and primary data for sequencing and proteomics are accessible via external repositories (NCBI SRA BioProject and MassIVE) referenced from this Dataverse record.
existing_uses:
  - name: Related publications
    description:
      - Clark T, Parker J, Schaffer L, Obernier K, 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, Doctor Y, Dailamy A, Forget A, 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
other_tasks:
  - name: Additional potential uses
    description:
      - Cell architectural analysis; cross-modal integration; benchmarking AI models on multimodal cell data; method development for protein interaction inference and localization prediction.
future_use_impacts:
  - name: Risks and mitigations
    description:
      - Data derived from specific de-identified cell lines may introduce biases and may not generalize to all biological contexts; requires domain expertise for meaningful analysis; not suitable for clinical use. Users should avoid interpretations that could lead to unfair treatment or clinical actions without validation.
discouraged_uses:
  - name: Prohibited uses
    description:
      - Clinical decision-making or any context involving patient care without appropriate regulatory oversight and approval.
distribution_formats:
  - name: Distribution
    description:
      - Dataverse-hosted files including ZIP archives (images), HTML summaries/provenance, and JSON RO-Crate metadata; external links to SRA and MassIVE.
distribution_dates:
  - name: Distribution timeline
    description:
      - 2025-07-01 (Dataset Version 2.0 publication); 2025-10-22 (IF image ZIP archives published).
license_and_use_terms:
  name: License and terms
  description:
    - CC BY-NC-SA 4.0; Community norms expect proper citation using the dataset citation provided on the landing page.
ip_restrictions:
  name: IP restrictions
  description:
    - No additional IP-based restrictions specified; external repositories may have their own terms.
regulatory_restrictions:
  name: Export/regulatory restrictions
  description:
    - None stated.
maintainers:
  - name: Hosting and contacts
    description:
      - University of Virginia Dataverse (long-term preservation and hosting).
      - CM4AI Data Governance Committee: Jillian Parker (jillianparker@health.ucsd.edu).
      - Point of Contact: Trey Ideker (University of California San Diego).
updates:
  name: Update plan
  description:
    - Dataset will be regularly updated and augmented through November 2026, with updates on a quarterly basis; long-term preservation in the University of Virginia Dataverse supported by committed institutional funds.
version_access:
  name: Version access and persistence
  description:
    - Versions are maintained within University of Virginia Dataverse; older versions remain accessible per Dataverse versioning.
retention_limit:
  name: Retention
  description:
    - Not specified beyond long-term preservation commitment in Dataverse.
is_deidentified:
  - name: De-identified
    description:
      - Yes; derived from de-identified, commercially available human cell lines.
is_tabular: "no"
subsets:
  - id: release-ro-crate-datasheet.html
    name: release-ro-crate-datasheet.html
    title: Release RO-Crate Datasheet (HTML)
    description: HTML datasheet summarizing key release information.
    path: release-ro-crate-datasheet.html
    media_type: text/html
    md5: 599c9ece9b88b3ce797b82463b4a1eb4
  - id: release-ro-crate-metadata.json
    name: release-ro-crate-metadata.json
    title: Release RO-Crate Metadata (JSON)
    description: RO-Crate metadata with pointers to sub RO-Crates.
    path: release-ro-crate-metadata.json
    media_type: application/json
    format: JSON
    md5: 99f9e00053bff3020fd9832a3a518bbb
  - id: Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    name: cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    title: IF Images - MDA-MB-468 treated with paclitaxel (ZIP)
    description: "Spatial localization of 464 proteins in MDA-MB-468 cells treated with paclitaxel; ICC-IF and confocal microscopy (channels: DAPI/ER/tubulin/POI)."
    path: Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    media_type: application/zip
    md5: 0d972b80744344ddeede516a0cf6e3d7
    is_data_split: "no"
  - id: Images/cm4ai-ifimages-mda-mb-468-untreated.zip
    name: cm4ai-ifimages-mda-mb-468-untreated.zip
    title: IF Images - MDA-MB-468 untreated (ZIP)
    description: "Spatial localization of 464 proteins in untreated MDA-MB-468 cells; ICC-IF and confocal microscopy (channels: DAPI/ER/tubulin/POI)."
    path: Images/cm4ai-ifimages-mda-mb-468-untreated.zip
    media_type: application/zip
    md5: a98affcc05429650c6bb3906cd836d55
    is_data_split: "no"
  - id: Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip
    name: cm4ai-ifimages-mda-mb-468-vorinostat.zip
    title: IF Images - MDA-MB-468 treated with vorinostat (ZIP)
    description: "Spatial localization of 464 proteins in MDA-MB-468 cells treated with vorinostat; ICC-IF and confocal microscopy (channels: DAPI/ER/tubulin/POI)."
    path: Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip
    media_type: application/zip
    md5: ad4e68ccc14b0f3349dad3321e7b81b2
    is_data_split: "no"
  - id: Images/paclitaxel/Images-paclitaxel-provenance-graph.html
    name: Images-paclitaxel-provenance-graph.html
    title: IF Images (paclitaxel) provenance graph (HTML)
    description: Provenance graph for paclitaxel-treated IF images (download to view properly).
    path: Images/paclitaxel/Images-paclitaxel-provenance-graph.html
    media_type: text/html
    md5: e38e63e4c8dfc5808a5ffa2d7829fc38
  - id: Images/untreated/Images-untreated-provenance-graph.html
    name: Images-untreated-provenance-graph.html
    title: IF Images (untreated) provenance graph (HTML)
    description: Provenance graph for untreated IF images (download to view properly).
    path: Images/untreated/Images-untreated-provenance-graph.html
    media_type: text/html
    md5: 1a3b510f74d3f8647e07c6559ce64ee8
  - id: Images/vorinostat/Images-vorinostat-provenance-graph.html
    name: Images-vorinostat-provenance-graph.html
    title: IF Images (vorinostat) provenance graph (HTML)
    description: Provenance graph for vorinostat-treated IF images (download to view properly).
    path: Images/vorinostat/Images-vorinostat-provenance-graph.html
    media_type: text/html
    md5: 58935fe4e254b31d33fed019f24c7668
  - id: mass-spec/cancer-cells/mass-spec-cancer-cells-provenance-graph.html
    name: mass-spec-cancer-cells-provenance-graph.html
    title: Mass spectrometry (cancer cells) provenance graph (HTML)
    description: Provenance graph for SEC-MS data in 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
  - id: mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json
    name: mass-spec-cancer-cells-ro-crate-metadata.json
    title: Mass spectrometry (cancer cells) RO-Crate metadata (JSON)
    description: RO-Crate metadata describing SEC-MS data for human cancer cells.
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json
    media_type: application/json
    format: JSON
    md5: 3a7063bb391ea5e05a32ba5da5f4b2f8