=== YAML Fixing Applied ===
id: "doi:10.18130/V3/B35XWX#collection"
name: Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
title: Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
description: "This dataset is the March 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 and iPSC-derived NPCs, neurons, and cardiomyocytes; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel). CM4AI output data are packaged with provenance graphs and rich metadata as AI-ready datasets in RO-Crate format using the FAIRSCAPE framework. Data presented here will be augmented regularly through the end of the project. CM4AI is a collaboration of UCSD, UCSF, Stanford, UVA, Yale, UA Birmingham, Simon Fraser University, and the Hastings Center. This data is Copyright (c) 2025 The Regents of the University of California except where otherwise noted. Spatial proteomics raw image data is copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University. Dataset licensed for reuse under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license (https://creativecommons.org/licenses/by-nc-sa/4.0/). Attribution is required to the copyright holders and the authors. Any publications referencing this data or derived products should cite the Related Publication below, as well as directly citing this data collection (2025-03-04). (2025-03-07)"
doi: "doi:10.18130/V3/B35XWX"
page: "https://doi.org/10.18130/V3/B35XWX"
issued: 2025-03-03
created_on: 2025-02-27
last_updated_on: 2025-03-07
license: "CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)"
version: "1.4"
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/B35XWX#dataset
    name: CM4AI March 2025 Data Release (Beta)
    title: Cell Maps for Artificial Intelligence - March 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 and iPSC-derived NPCs, neurons, and cardiomyocytes; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel). CM4AI output data are packaged with provenance graphs and rich metadata as AI-ready datasets in RO-Crate format using the FAIRSCAPE framework. Data will be augmented regularly through the end of the project.
    doi: "doi:10.18130/V3/B35XWX"
    page: "https://doi.org/10.18130/V3/B35XWX"
    issued: 2025-03-03
    created_on: 2025-02-27
    last_updated_on: 2025-03-07
    license: "CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)"
    version: "1.4"
    keywords:
      - AI
      - Bridge2AI
      - CM4AI
      - perturb-seq
      - SEC-MS
      - subcellular imaging
      - protein localization
      - protein-protein interaction
      - scRNAseq
      - iPSC
      - KOLF2.1J
      - MDA-MB-468
      - paclitaxel
      - vorinostat
      - neurons
      - cardiomyocytes
      - NPC
    purposes:
      - id: purpose-1
        name: CM4AI purpose
        description: Provide AI-ready, FAIR datasets with provenance for modeling human cell architecture and function across modalities.
        used_software: []
        response: Enable AI and machine learning analyses on standardized multi-modal functional genomics data with rich provenance (RO-Crate via FAIRSCAPE).
    tasks:
      - id: task-1
        name: AI model training and benchmarking
        response: Train and benchmark machine learning models for cell state, protein localization, and protein interaction inference.
      - id: task-2
        name: Mapping human cell architecture
        response: Build AI-ready maps of human cell architecture integrating perturb-seq, proteomics (SEC-MS), and imaging.
    addressing_gaps:
      - id: gap-1
        name: AI-ready multi-modal genomics gap
        response: Addresses the lack of standardized, provenance-rich, multi-modal functional genomics datasets suitable for AI/ML, spanning disease-relevant human cell lines.
    creators:
      - id: creator-ideker
        name: CM4AI Leadership
        principal_investigator:
          id: person-trey-ideker
          name: Trey Ideker
          description: Point of contact listed on the dataset record.
          affiliation:
            - id: org-ucsd
              name: University of California San Diego
        affiliation:
          id: org-ucsd
          name: University of California San Diego
      - id: creator-ucsf
        name: CM4AI Partner - UCSF
        affiliation:
          id: org-ucsf
          name: University of California San Francisco
      - id: creator-stanford
        name: CM4AI Partner - Stanford University
        affiliation:
          id: org-stanford
          name: Stanford University
      - id: creator-uva
        name: CM4AI Partner - University of Virginia
        affiliation:
          id: org-uva
          name: University of Virginia
      - id: creator-yale
        name: CM4AI Partner - Yale University
        affiliation:
          id: org-yale
          name: Yale University
      - id: creator-uab
        name: CM4AI Partner - University of Alabama at Birmingham
        affiliation:
          id: org-uab
          name: University of Alabama at Birmingham
      - id: creator-sfu
        name: CM4AI Partner - Simon Fraser University
        affiliation:
          id: org-sfu
          name: Simon Fraser University
      - id: creator-hastings
        name: CM4AI Partner - The Hastings Center
        affiliation:
          id: org-hastings
          name: The Hastings Center
    funders:
      - id: funder-nih-ot2
        name: NIH Bridge2AI award
        grantor:
          id: org-nih
          name: National Institutes of Health
        grant:
          id: grant-1OT2OD032742-01
          name: NIH OT2 Award
          grant_number: 1OT2OD032742-01
    instances:
      - id: inst-perturbseq
        name: Perturb-seq scRNA-seq
        representation: Single-cell RNA sequencing (perturb-seq) and fitness phenotypes from CRISPRi perturbations in undifferentiated KOLF2.1J hiPSCs.
        instance_type: Cells and transcriptomes
        data_type: Raw and processed sequencing-derived features (gene expression matrices, phenotypic readouts).
      - id: inst-sec-ms
        name: SEC-MS proteomics
        representation: Size exclusion chromatography–mass spectrometry (SEC-MS) profiling of protein complexes in KOLF2.1J hiPSCs and iPSC-derived cell types.
        instance_type: Proteins and protein complexes
        data_type: Mass spectrometry-derived protein/complex abundance features.
      - id: inst-if-images
        name: Immunofluorescence imaging
        representation: Confocal immunofluorescence images of MDA-MB-468 cells with and without chemotherapy (vorinostat, paclitaxel) showing protein subcellular localization.
        instance_type: Images and image-derived features
        data_type: Multichannel confocal microscopy images (DAPI, calreticulin, tubulin, protein-of-interest).
    subpopulations:
      - id: subpop-ipsc
        name: KOLF2.1J hiPSCs
        identification:
          - Undifferentiated KOLF2.1J human induced pluripotent stem cells
      - id: subpop-derived
        name: iPSC-derived cell types
        identification:
          - Neural progenitor cells (NPCs)
          - Neurons
          - Cardiomyocytes
      - id: subpop-mdamb468
        name: MDA-MB-468 breast cancer cell line
        identification:
          - MDA-MB-468 cells (untreated; treated with paclitaxel or vorinostat)
    acquisition_methods:
      - id: acq-1
        name: Multi-modal acquisition
        description:
          - CRISPRi-based perturb-seq assays for single-cell transcriptomes and fitness phenotypes.
          - Size exclusion chromatography–mass spectrometry (SEC-MS) for protein complex profiling.
          - Confocal immunofluorescence imaging for subcellular protein localization.
        was_directly_observed: yes (imaging)
        was_reported_by_subjects: no
        was_inferred_derived: yes (derived features from sequencing/proteomics and image processing)
        was_validated_verified: Not specified in repository record
    collection_mechanisms:
      - id: mech-1
        name: Experimental instrumentation and pipelines
        description:
          - Confocal microscopy with ICC-IF staining (DAPI, calreticulin, tubulin, protein-of-interest antibodies).
          - SEC-MS proteomics workflow (size exclusion chromatography followed by mass spectrometry).
          - CRISPRi perturbation and single-cell RNA-seq (perturb-seq).
    collection_timeframes:
      - id: timeframe-1
        name: Initial release timeframe
        description:
          - Data creation date: 2025-02-27.
          - First published: 2025-03-03.
          - Data will be augmented regularly through the end of the project.
    external_resources:
      - id: ext-pride
        name: PRIDE (planned)
        external_resources:
          - PRIDE Proteomics Repository (planned upload for SEC-MS dataset)
        future_guarantees:
          - Not specified
        archival:
          - RO-Crate packaging with provenance graphs via FAIRSCAPE
        restrictions:
          - Subject to CC BY-NC-SA 4.0 license and any PRIDE repository terms when applicable
    preprocessing_strategies:
      - id: prep-roc
        name: RO-Crate provenance packaging
        description:
          - AI-ready datasets packaged with provenance graphs and rich metadata in RO-Crate format using the FAIRSCAPE framework.
    raw_sources:
      - id: raw-perturbseq
        name: Raw perturb-seq sequences
        description:
          - Raw sequence data for the CRISPR perturbation cell atlas are included in the release (see "CRISPR Perturbation RNA Sequences - Raw Sequences").
    existing_uses:
      - id: use-relpub-1
        name: Related publication (conceptual use)
        description:
          - 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
      - id: use-relpub-2
        name: Related publication (perturbation atlas)
        description:
          - A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS. bioRxiv. 2024 Nov 4;2024.11.03.621734. https://doi.org/10.1101/2024.11.03.621734
    future_use_impacts:
      - id: fut-1
        name: Ongoing updates
        description:
          - Ongoing augmentation through the project may affect reproducibility; users should note dataset version and release date when conducting analyses.
    distribution_formats:
      - id: dist-1
        name: RO-Crate JSON metadata
        description:
          - RO-Crate metadata (JSON) describing datasets, provenance, and context.
      - id: dist-2
        name: ZIP Archives (imaging datasets)
        description:
          - Large image bundles provided as ZIP archives via Dataverse.
      - id: dist-3
        name: Dataverse access
        description:
          - Files accessible via University of Virginia Dataverse web interface and Data Access API.
    distribution_dates:
      - id: dist-date-1
        name: Initial public release
        description:
          - 2025-03-03
    license_and_use_terms:
      id: terms-1
      name: CC BY-NC-SA 4.0 with attribution
      description:
        - Licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (https://creativecommons.org/licenses/by-nc-sa/4.0/).
        - Attribution is required to the copyright holders and the authors; cite this data collection and the related publications.
    ip_restrictions:
      id: ipr-1
      name: Copyright notices
      description:
        - Copyright (c) 2025 The Regents of the University of California except where otherwise noted.
        - Spatial proteomics raw image data copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University.
    maintainers:
      - id: maint-uva-dv
        name: Repository hosting
        description:
          - University of Virginia Dataverse (hosting and distribution)
      - id: maint-cm4ai
        name: Project team
        description:
          - CM4AI project team (data producers)
    updates:
      id: update-plan-1
      name: Regular augmentation
      description:
        - Dataset will be augmented regularly through the end of the project; new files and versions published via Dataverse.
    version_access:
      id: version-access-1
      name: Dataverse versioning
      description:
        - Dataset versions managed and hosted in Dataverse; users should reference the persistent identifier and version when citing.
    is_deidentified:
      id: deid-1
      name: Deidentification status
      description:
        - Data are derived from human cell lines and iPSC-derived cells; no direct personal identifiers are included in the described datasets.
    subsets:
      - id: subset-crispr-cell-atlas
        name: CRISPR Perturbation Cell Atlas
        title: CRISPR Perturbation Cell Atlas
        description:
          - Expressed genome-scale CRISPRi perturbation cell atlas in undifferentiated KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes associated with 11,739 targeted genes.
        format: JSON
        media_type: application/json
        md5: cbdb263b1c099396d75e16f00a79a818
        distribution_formats:
          - id: df-cca-1
            name: RO-Crate JSON
            description:
              - ro-crate-metadata.json describing the atlas and provenance
        instances:
          - id: inst-cca-1
            name: Perturb-seq instances
            representation: Single-cell RNA sequencing and fitness phenotypes under CRISPRi perturbations.
            data_type: Sequencing-derived features and associated metadata.
      - id: subset-crispr-raw
        name: CRISPR Perturbation RNA Sequences - Raw Sequences
        title: CRISPR Perturbation RNA Sequences - Raw Sequences
        description:
          - Raw sequence data from the CRISPRi perturbation cell atlas in KOLF2.1J hiPSCs.
        format: JSON
        media_type: application/json
        md5: 1cafefa32a897998e3e2ba0a29a3ef5c
        distribution_formats:
          - id: df-crs-1
            name: RO-Crate JSON
            description:
              - ro-crate-metadata.json referencing raw sequence data
      - id: subset-if-untreated
        name: Protein Localization Subcellular Images - untreated
        title: Protein Localization Subcellular Images (untreated)
        description:
          - Spatial localization of 563 proteins in untreated MDA-MB-468 cells imaged by ICC-IF and confocal microscopy in the Lundberg Lab at Stanford University.
        compression: ZIP
        media_type: application/zip
        md5: 0b4d129f5fbc3bb7f7ea564cd032cef7
        instances:
          - id: inst-img-unt
            name: IF images (untreated)
            representation: Multichannel confocal images (DAPI, calreticulin, tubulin, protein-of-interest).
            data_type: Image files packaged in ZIP archive.
      - id: subset-if-paclitaxel
        name: Protein Localization Subcellular Images - paclitaxel
        title: Protein Localization Subcellular Images (paclitaxel treated)
        description:
          - Spatial localization of 563 proteins in MDA-MB-468 cells treated with paclitaxel, imaged by ICC-IF and confocal microscopy in the Lundberg Lab at Stanford University.
        compression: ZIP
        media_type: application/zip
        md5: 9422486c80bc9e1d35b2fbbc72a5f043
        instances:
          - id: inst-img-pac
            name: IF images (paclitaxel)
            representation: Multichannel confocal images with paclitaxel treatment.
            data_type: Image files packaged in ZIP archive.
      - id: subset-if-vorinostat
        name: Protein Localization Subcellular Images - vorinostat
        title: Protein Localization Subcellular Images (vorinostat treated)
        description:
          - Spatial localization of 563 proteins in MDA-MB-468 cells treated with vorinostat, imaged by ICC-IF and confocal microscopy in the Lundberg Lab at Stanford University.
        compression: ZIP
        media_type: application/zip
        md5: ac577109a41a9806978461157b777d52
        instances:
          - id: inst-img-vor
            name: IF images (vorinostat)
            representation: Multichannel confocal images with vorinostat treatment.
            data_type: Image files packaged in ZIP archive.
      - id: subset-sec-ms
        name: Protein-protein Interaction SEC-MS
        title: Protein-protein Interaction SEC-MS
        description:
          - SEC-MS dataset generated on undifferentiated KOLF2.1J hiPSCs in the Nevan Krogan laboratory at UCSF. The data will be uploaded to PRIDE when available.
        format: JSON
        media_type: application/json
        md5: cb67e7749b15ce87b9042a9feba9d032
        external_resources:
          - id: ext-sec-pride
            name: PRIDE (planned)
            external_resources:
              - PRIDE Proteomics Repository (planned upload)
            future_guarantees:
              - Not specified
            archival:
              - RO-Crate metadata present; full dataset to be deposited to PRIDE
            restrictions:
              - Subject to CC BY-NC-SA 4.0 license and PRIDE terms upon deposition
        instances:
          - id: inst-sec-1
            name: SEC-MS instances
            representation: Size exclusion chromatography–mass spectrometry fractions and protein complex profiles.
            data_type: Proteomics features derived from mass spectrometry.