=== 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"
issued: "2025-07-01"
created_on: "2025-02-27"
page: "https://doi.org/10.18130/V3/F3TD5R"
license: CC BY-NC-SA 4.0
version: "2.0"
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
resources:
  - id: doi:10.18130/V3/F3TD5R#release
    name: CM4AI June 2025 Data Release (Beta)
    title: Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
    description: 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"
    issued: "2025-07-01"
    created_on: "2025-02-27"
    page: "https://doi.org/10.18130/V3/F3TD5R"
    license: CC BY-NC-SA 4.0
    version: "2.0"
    created_by:
      - Clark T (University of Virginia) - ORCID: https://orcid.org/0000-0003-4060-7360
      - Parker J (University of California, San Diego) - ORCID: https://orcid.org/0000-0003-4535-3486
      - Al Manir S (University of Virginia) - ORCID: https://orcid.org/0000-0003-4647-3877
      - Axelsson U (KTH Royal Institute of Technology)
      - Ballllosero Navarro F (Stanford University) - ORCID: https://orcid.org/0000-0002-4180-422X
      - Chinn B (University of California San Diego)
      - Churas CP (University of California San Diego) - ORCID: https://orcid.org/0000-0001-9998-705X
      - Dailamy A (University of California, San Diego) - ORCID: https://orcid.org/0000-0002-6711-8260
      - Doctor Y (University of California, San Diego) - ORCID: https://orcid.org/0009-0009-0483-7506
      - Fall J (KTH - Royal Institute of Technology)
      - Forget A (University of California San Francisco) - ORCID: https://orcid.org/0000-0003-0223-0312
      - Gao J (University of California San Diego) - ORCID: https://orcid.org/0000-0002-6311-3526
      - Hansen JN (Stanford University) - ORCID: https://orcid.org/0000-0002-4650-9094
      - Hu M (University of California San Diego) - ORCID: https://orcid.org/0000-0002-1571-8029
      - Johannesson A (KTH - Royal Institute of Technology)
      - Khaliq H (University of California San Diego)
      - Lee YH (University of California San Diego) - ORCID: https://orcid.org/0000-0003-0917-355X
      - Lenkiewicz J (University of California San Diego) - ORCID: https://orcid.org/0000-0001-7252-8638
      - Levinson MA (University of Virginia) - ORCID: https://orcid.org/0000-0003-0384-8499
      - Marquez C (University of California San Diego) - ORCID: 0000-0003-3960-420X
      - Metallo C (University of California San Diego) - ORCID: https://orcid.org/0000-0003-2404-3040
      - Muralidharan M (University of California San Francisco)
      - Nourreddine S (University of California San Diego) - ORCID: https://orcid.org/0000-0003-3881-7588
      - Niestroy J (University of Virginia) - ORCID: https://orcid.org/0000-0002-1103-3882
      - Obernier K (University of California San Francisco) - ORCID: https://orcid.org/0000-0002-4025-1299
      - Pan E (University of California San Diego)
      - Polacco B (University of California San Francisco)
      - Pratt D (University of California San Diego) - ORCID: https://orcid.org/0000-0002-1471-9513
      - Qian G (University of California San Diego) - ORCID: https://orcid.org/0009-0005-4217-2745
      - Schaffer L (University of California San Diego) - ORCID: https://orcid.org/0000-0001-6339-9141
      - Sigaeva A (KTH Royal Institute of Technology) - ORCID: https://orcid.org/0000-0003-3361-3797
      - Thaker S (University of Alabama at Birmingham) - ORCID: https://orcid.org/0000-0001-6730-2773
      - Zhang Y (University of California San Diego)
      - Bélisle-Pipon JC (Simon Fraser University) - ORCID: https://orcid.org/0000-0002-8965-8153
      - Brandt C (Yale University) - ORCID: https://orcid.org/0000-0001-8179-1796
      - Chen JY (The University of Alabama at Birmingham) - ORCID: https://orcid.org/0000-0002-6112-415X
      - Ding Y (University of Texas at Austin) - ORCID: https://orcid.org/0000-0003-2567-2009
      - Fodeh S (Yale University) - ORCID: https://orcid.org/0000-0003-4664-3143
      - Krogan N (University of California San Francisco) - ORCID: https://orcid.org/0000-0003-4902-337X
      - Lundberg E (Stanford University) - ORCID: https://orcid.org/0000-0001-7034-0850
      - Mali P (University of California San Diego) - ORCID: https://orcid.org/0000-0002-3383-1287
      - Payne-Foster P (University of Alabama) - ORCID: https://orcid.org/0000-0002-3508-3577
      - Ratcliffe S (University of Virginia) - ORCID: https://orcid.org/0000-0002-6644-8284
      - Ravitsky V (University of Montreal) - ORCID: https://orcid.org/0000-0002-7080-8801
      - Sali A (University of California San Diego) - ORCID: https://orcid.org/0000-0003-0435-6197
      - Schulz W (Yale University) - ORCID: https://orcid.org/0000-0002-2048-4028
      - Ideker T (University of California San Diego) - ORCID: https://orcid.org/0000-0002-1708-8454
    funders:
      - grantor:
          name: National Institutes of Health
        grant:
          name: NIH Bridge2AI Program
          grant_number: 1OT2OD032742-01
    purposes:
      - response: AI-ready datasets to support research in functional genomics within the NIH Bridge2AI CM4AI project.
    tasks:
      - response: AI model training
      - response: Cellular process analysis
      - response: Analysis of cell architectural changes and interactions under disease, treatment, or genetic perturbations
    addressing_gaps:
      - response: Interim AI-ready multi-omic and imaging data release; computed cell maps are not yet included and will be added in future releases.
    instances:
      - representation: perturb-seq single-cell RNA sequencing in undifferentiated KOLF2.1J iPSCs
        data_type: scRNA-seq counts/metadata from CRISPRi perturb-seq experiments
      - representation: SEC-MS protein-protein interaction profiles in iPSCs, NPCs, neurons, cardiomyocytes, and MDA-MB-468 cells (treated/untreated)
        data_type: Size exclusion chromatography followed by mass spectrometry (fractionation-based protein complex profiles)
      - representation: Immunofluorescence confocal images of MDA-MB-468 cells under treatment conditions
        data_type: Multichannel confocal microscopy images (DAPI, ER/calreticulin, microtubules/tubulin, protein-of-interest antibody)
    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
    confidential_elements: []
    content_warnings: []
    subpopulations:
      - identification:
          - Cell line and treatment condition (MDA-MB-468; untreated, vorinostat, paclitaxel)
        distribution:
          - Imaging subsets stratified by treatment; mass spectrometry and perturb-seq stratified by cell type/state
    sensitive_elements: []
    acquisition_methods:
      - description:
          - Data were directly measured via confocal microscopy (IF imaging), mass spectrometry (SEC-MS), and single-cell sequencing (perturb-seq).
        was_directly_observed: yes
        was_reported_by_subjects: no
        was_inferred_derived: partial (protein complex inferences from SEC-MS elution profiles)
        was_validated_verified: not specified
    collection_mechanisms:
      - description:
          - Confocal microscopy (IF/ICC-IF staining)
          - Size exclusion chromatography followed by mass spectrometry (SEC-MS)
          - CRISPRi perturb-seq single-cell RNA sequencing
    data_collectors:
      - description:
          - Lundberg Lab (Stanford University) for IF imaging
          - University of California San Diego, University of California San Francisco, University of Virginia (multi-site generation)
    collection_timeframes:
      - description:
          - Data creation date 2025-02-27; initial public release 2025-07-01; additional imaging archives published 2025-10-22.
    ethical_reviews:
      - description:
          - Human Subjects: No; De-identified Samples: Yes; FDA Regulated: No.
          - Data Governance Committee: Jillian Parker (jillianparker@health.ucsd.edu).
          - Ethical Review: Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca).
    preprocessing_strategies: []
    cleaning_strategies: []
    labeling_strategies: []
    raw_sources:
      - description:
          - Raw and primary data accessible via external repositories (NCBI SRA BioProject and MassIVE) as linked from the Dataverse dataset page.
    existing_uses:
      - 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
      - description:
          - 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
    other_tasks:
      - description:
          - Bioinformatics analysis of individual modalities (imaging, SEC-MS, perturb-seq) prior to integrated map release
    future_use_impacts:
      - description:
          - Interim release; computed cell maps not included yet.
          - Modalities cover overlapping but not identical protein sets across experiments.
          - Domain expertise recommended for meaningful analysis.
          - Data derived from commercially available de-identified human cell lines and may not represent all biological variants in the broader population.
    discouraged_uses:
      - description:
          - Not for clinical decision-making or any context involving patient care without appropriate regulatory oversight and approval.
    distribution_formats:
      - description:
          - Dataverse web UI file access
          - Dataverse Data Access API
          - ZIP archives (images)
          - RO-Crate metadata (JSON, HTML)
    distribution_dates:
      - description:
          - 2025-07-01 (dataset publication)
      - description:
          - 2025-10-22 (additional image ZIP archives)
    license_and_use_terms:
      description:
        - CC BY-NC-SA 4.0; proper citation of the dataset is required as per Dataverse norms.
    ip_restrictions:
      description:
        - No third-party IP restrictions noted beyond dataset license; some datasets may be under temporary pre-publication embargo.
    regulatory_restrictions: {}
    maintainers:
      - description:
          - University of Virginia Dataverse (hosting and long-term preservation)
          - Data Governance Committee contact: Jillian Parker (jillianparker@health.ucsd.edu)
          - Point of Contact (Dataverse entry): 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, with quarterly updates; long-term preservation in the University of Virginia Dataverse with committed institutional funds.
    retention_limit: {}
    extension_mechanism: {}
    is_deidentified:
      description:
        - Human Subjects: No; De-identified Samples: Yes; data derived from commercially available de-identified human cell lines.
    is_tabular: "no"
  - id: file: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
    issued: "2025-07-01"
  - id: file:release-ro-crate-metadata.json
    name: release-ro-crate-metadata.json
    title: Release RO-Crate Metadata (JSON)
    description: Release RO-Crate with pointers to sub ro-crates.
    path: release-ro-crate-metadata.json
    format: JSON
    media_type: application/json
    md5: 99f9e00053bff3020fd9832a3a518bbb
    issued: "2025-07-01"
  - id: file: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: This data set displays the spatial localization of 464 proteins of interest in cells of the breast cancer cell line MDA-MB-468 treated with paclitaxel as imaged by immunofluorescence-based staining (ICC-IF) and confocal microscopy in the Lundberg Lab at Stanford University, as part of the CM4AI project.
    path: Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    media_type: application/zip
    md5: 0d972b80744344ddeede516a0cf6e3d7
    issued: "2025-10-22"
  - id: file: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: This data set displays the spatial localization of 464 proteins of interest in cells of the breast cancer cell line MDA-MB-468 as imaged by immunofluorescence-based staining (ICC-IF) and confocal microscopy in the Lundberg Lab at Stanford University, as part of the CM4AI project.
    path: Images/cm4ai-ifimages-mda-mb-468-untreated.zip
    media_type: application/zip
    md5: a98affcc05429650c6bb3906cd836d55
    issued: "2025-10-22"
  - id: file: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: This data set displays the spatial localization of 464 proteins of interest in cells of the breast cancer cell line MDA-MB-468 treated with vorinostat as imaged by immunofluorescence-based staining (ICC-IF) and confocal microscopy in the Lundberg Lab at Stanford University, as part of the CM4AI project.
    path: Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip
    media_type: application/zip
    md5: ad4e68ccc14b0f3349dad3321e7b81b2
    issued: "2025-10-22"
  - id: file:Images/paclitaxel/Images-paclitaxel-provenance-graph.html
    name: Images-paclitaxel-provenance-graph.html
    title: IF Images Paclitaxel Provenance Graph (HTML)
    description: HTML provenance graph for paclitaxel imaging subset. Requires download to view properly; Dataverse preview will not display.
    path: Images/paclitaxel/Images-paclitaxel-provenance-graph.html
    media_type: text/html
    md5: e38e63e4c8dfc5808a5ffa2d7829fc38
    issued: "2025-07-01"
  - id: file:Images/untreated/Images-untreated-provenance-graph.html
    name: Images-untreated-provenance-graph.html
    title: IF Images Untreated Provenance Graph (HTML)
    description: HTML provenance graph for untreated imaging subset. Requires download to view properly; Dataverse preview will not display.
    path: Images/untreated/Images-untreated-provenance-graph.html
    media_type: text/html
    md5: 1a3b510f74d3f8647e07c6559ce64ee8
    issued: "2025-07-01"
  - id: file:Images/vorinostat/Images-vorinostat-provenance-graph.html
    name: Images-vorinostat-provenance-graph.html
    title: IF Images Vorinostat Provenance Graph (HTML)
    description: HTML provenance graph for vorinostat imaging subset. Requires download to view properly; Dataverse preview will not display.
    path: Images/vorinostat/Images-vorinostat-provenance-graph.html
    media_type: text/html
    md5: 58935fe4e254b31d33fed019f24c7668
    issued: "2025-07-01"
  - id: file:mass-spec/cancer-cells/mass-spec-cancer-cells-provenance-graph.html
    name: mass-spec-cancer-cells-provenance-graph.html
    title: Mass Spec Cancer Cells Provenance Graph (HTML)
    description: HTML provenance graph for cancer cell mass spectrometry subset. Requires download to view properly; Dataverse preview will not display.
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-provenance-graph.html
    media_type: text/html
    md5: 931ad9b552562024cb84ebe62d1f1838
    issued: "2025-07-01"
  - id: file:mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json
    name: mass-spec-cancer-cells-ro-crate-metadata.json
    title: Mass Spec Cancer Cells RO-Crate Metadata (JSON)
    description: RO-Crate metadata for cancer cell mass spectrometry subset.
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json
    format: JSON
    media_type: application/json
    md5: 3a7063bb391ea5e05a32ba5da5f4b2f8
    issued: "2025-07-01"
__class__: DatasetCollection