=== YAML Fixing Applied ===
id: "doi:10.18130/V3/B35XWX"
name: Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
title: Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
description: >-
  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 immunofluorescence (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. 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 (https://creativecommons.org/licenses/by-nc-sa/4.0/).
language: en
publisher: "https://dataverse.lib.virginia.edu/"
issued: 2025-03-03
page: "https://doi.org/10.18130/V3/B35XWX"
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
created_by:
  - Cell Maps for Artificial Intelligence (CM4AI) Consortium
  - University of California San Diego
  - University of California San Francisco
  - Stanford University
  - University of Virginia
  - Yale University
  - University of Alabama at Birmingham
  - Simon Fraser University
  - The Hastings Center
created_on: 2025-02-27
version: "1.4"
license: "https://creativecommons.org/licenses/by-nc-sa/4.0/"
resources:
  - title: CRISPR Perturbation Cell Atlas (RO-Crate metadata)
    description: >-
      Expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated
      KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes associated with
      11,739 targeted genes. Findings validated via phenotypic, protein-interaction,
      and metabolic tracing assays.
    format: JSON-LD
    media_type: application/json
    path: ro-crate-metadata.json
    md5: cbdb263b1c099396d75e16f00a79a818
    instances:
      - representation: Single-cell transcriptomic and fitness phenotype readouts from genome-scale CRISPRi perturbations in KOLF2.1J hiPSCs
        data_type: RO-Crate metadata (JSON-LD) describing AI-ready dataset packaging and provenance
    collection_mechanisms:
      - description:
          - CRISPR interference (CRISPRi) perturbation-seq (single-cell RNA-seq)
    acquisition_methods:
      - description:
          - Single-cell RNA sequencing of CRISPRi-perturbed hiPSCs (KOLF2.1J)
        was_directly_observed: yes
        was_inferred_derived: yes
        was_validated_verified: yes
    funders:
      - grantor:
          name: National Institutes of Health
        grant:
          name: Bridge2AI Functional Genomics Grand Challenge (CM4AI)
          grant_number: 1OT2OD032742-01
    distribution_formats:
      - description:
          - RO-Crate (JSON-LD)
    distribution_dates:
      - description:
          - 2025-03-03
    license_and_use_terms:
      description:
        - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
    maintainers:
      - description:
          - Hosted on University of Virginia Dataverse; Point of Contact: Trey Ideker (UC San Diego)
    is_deidentified:
      description:
        - Dataset contains cell line data; no personally identifiable information.
  - title: CRISPR Perturbation RNA Sequences - Raw Sequences (RO-Crate metadata)
    description: >-
      Raw sequence data from the expressed genome-scale CRISPRi Perturbation Cell
      Atlas in KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes
      associated with 11,739 targeted genes.
    format: JSON-LD
    media_type: application/json
    path: ro-crate-metadata.json
    md5: 1cafefa32a897998e3e2ba0a29a3ef5c
    instances:
      - representation: Raw RNA sequencing reads associated with CRISPRi perturb-seq in KOLF2.1J hiPSCs
        data_type: RO-Crate metadata (JSON-LD) describing raw sequence data packaging and provenance
    collection_mechanisms:
      - description:
          - CRISPRi perturb-seq (single-cell RNA sequencing)
    acquisition_methods:
      - description:
          - RNA sequencing of CRISPRi-perturbed hiPSCs (KOLF2.1J)
        was_directly_observed: yes
        was_inferred_derived: no
    funders:
      - grantor:
          name: National Institutes of Health
        grant:
          name: Bridge2AI Functional Genomics Grand Challenge (CM4AI)
          grant_number: 1OT2OD032742-01
    distribution_formats:
      - description:
          - RO-Crate (JSON-LD)
    distribution_dates:
      - description:
          - 2025-03-03
    license_and_use_terms:
      description:
        - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
    maintainers:
      - description:
          - Hosted on University of Virginia Dataverse; Point of Contact: Trey Ideker (UC San Diego)
    is_deidentified:
      description:
        - Dataset contains cell line data; no personally identifiable information.
  - title: Protein Localization Subcellular Images (MDA-MB-468)
    description: >-
      Immunofluorescence-based subcellular localization images of 563 proteins in
      MDA-MB-468 breast cancer cells under untreated conditions and after treatment
      with paclitaxel or vorinostat. Imaging performed in the Lundberg Lab
      (Stanford University) using ICC-IF and confocal microscopy. Channels: nuclei
      (DAPI, blue), endoplasmic reticulum (calreticulin antibody, yellow),
      microtubules (tubulin antibody, red), protein of interest (green).
    media_type: application/zip
    compression: ZIP
    instances:
      - representation: Immunofluorescence confocal microscopy images of MDA-MB-468 cells
        data_type: Multi-channel TIFF images packaged in ZIP archives
    subsets:
      - title: Untreated images
        name: cm4ai-v0.6-beta-if-images-untreated.zip
        path: cm4ai-v0.6-beta-if-images-untreated.zip
        media_type: application/zip
        compression: ZIP
        md5: 0b4d129f5fbc3bb7f7ea564cd032cef7
        is_data_split: no
        is_subpopulation: no
      - title: Vorinostat-treated images
        name: cm4ai-v0.6-beta-if-images-vorinostat.zip
        path: cm4ai-v0.6-beta-if-images-vorinostat.zip
        media_type: application/zip
        compression: ZIP
        md5: ac577109a41a9806978461157b777d52
        is_data_split: no
        is_subpopulation: no
      - title: Paclitaxel-treated images
        name: cm4ai-v0.6-beta-if-images-paclitaxel.zip
        path: cm4ai-v0.6-beta-if-images-paclitaxel.zip
        media_type: application/zip
        compression: ZIP
        md5: 9422486c80bc9e1d35b2fbbc72a5f043
        is_data_split: no
        is_subpopulation: no
    collection_mechanisms:
      - description:
          - Immunofluorescence staining (ICC-IF) and confocal microscopy
    acquisition_methods:
      - description:
          - Direct imaging of stained cells (MDA-MB-468) across multiple channels
        was_directly_observed: yes
        was_inferred_derived: no
        was_validated_verified: yes
    data_collectors:
      - description:
          - Lundberg Lab, Stanford University
    funders:
      - grantor:
          name: National Institutes of Health
        grant:
          name: Bridge2AI Functional Genomics Grand Challenge (CM4AI)
          grant_number: 1OT2OD032742-01
    distribution_formats:
      - description:
          - ZIP archives
    distribution_dates:
      - description:
          - 2025-03-03
    license_and_use_terms:
      description:
        - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
    is_deidentified:
      description:
        - Dataset contains cell line images; no personally identifiable information.
  - title: Protein-protein Interaction SEC-MS (RO-Crate metadata)
    description: >-
      Size exclusion chromatography–mass spectrometry (SEC-MS) in undifferentiated
      KOLF2.1J hiPSCs, generated in the Nevan Krogan laboratory at UCSF. Data will
      be uploaded to PRIDE when available.
    format: JSON-LD
    media_type: application/json
    path: ro-crate-metadata.json
    md5: cb67e7749b15ce87b9042a9feba9d032
    instances:
      - representation: Protein complex size fractionation profiles with mass spectra (SEC-MS) from KOLF2.1J hiPSCs and iPSC-derived lineages
        data_type: RO-Crate metadata (JSON-LD) describing SEC-MS dataset packaging and provenance
    collection_mechanisms:
      - description:
          - Size exclusion chromatography coupled to mass spectrometry (SEC-MS)
    data_collectors:
      - description:
          - Nevan Krogan Lab, University of California San Francisco
    external_resources:
      - external_resources:
          - Planned deposition to PRIDE repository
        future_guarantees:
          - PRIDE archival upon availability (as stated)
    funders:
      - grantor:
          name: National Institutes of Health
        grant:
          name: Bridge2AI Functional Genomics Grand Challenge (CM4AI)
          grant_number: 1OT2OD032742-01
    distribution_formats:
      - description:
          - RO-Crate (JSON-LD)
    distribution_dates:
      - description:
          - 2025-03-03
    license_and_use_terms:
      description:
        - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
    is_deidentified:
      description:
        - Dataset contains cell line proteomics data; no personally identifiable information.
purposes:
  - response: >-
      Create AI-ready, richly annotated functional genomics datasets to map human
      cell architecture from disease-relevant cell lines (CM4AI, NIH Bridge2AI).
tasks:
  - response: >-
      Enable machine learning and AI analyses across perturb-seq, proteomics (SEC-MS),
      and subcellular imaging modalities.
funders:
  - grantor:
      name: National Institutes of Health
    grant:
      name: Bridge2AI Functional Genomics Grand Challenge (CM4AI)
      grant_number: 1OT2OD032742-01
collection_timeframes:
  - description:
      - Data creation date: 2025-02-27; Publication date: 2025-03-03
distribution_formats:
  - description:
      - RO-Crate (JSON-LD)
      - ZIP archives
      - Dataverse distribution
distribution_dates:
  - description:
      - 2025-03-03
license_and_use_terms:
  description:
    - Dataset licensed under CC BY-NC-SA 4.0. Attribution to copyright holders and authors is required.
    - Cite the related publications and this dataset collection (2025-03-04, noted by authors).
maintainers:
  - description:
      - University of Virginia Dataverse (host)
      - Point of Contact: Trey Ideker (University of California San Diego)
existing_uses:
  - description:
      - Related publications include:
      - 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
      - Nourreddine S. et al. "A Perturbation Cell Atlas of Human Induced Pluripotent Stem Cells." bioRxiv. 2024. doi: https://doi.org/10.1101/2024.11.03.621734
is_deidentified:
  description:
    - Dataset comprises experiments on established cell lines and derived cells; no personal or patient-identifying data are included.