=== 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: 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. Attribution is required to the copyright holders and the authors. Any publications referencing this data or derived products should cite the Related Publication, as well as directly cite this data collection (2025-03-04).
conforms_to: "https://w3id.org/ro/crate"
created_on: 2025-02-27
last_updated_on: 2025-03-07
doi: "doi:10.18130/V3/B35XWX"
issued: 2025-03-03
page: "https://doi.org/10.18130/V3/B35XWX"
license: "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#dist
    name: CM4AI March 2025 Data Release (distribution)
    description: Aggregated AI-ready distribution comprising perturb-seq in KOLF2.1J iPSCs, SEC-MS in KOLF2.1J iPSCs and iPSC-derived NPCs/neurons/cardiomyocytes, and ICC-IF confocal subcellular imaging in MDA-MB-468 cells ± chemotherapy (vorinostat, paclitaxel). Packaged with RO-Crate metadata and FAIRSCAPE provenance.
    page: "https://doi.org/10.18130/V3/B35XWX"
    issued: 2025-03-03
    license: "https://creativecommons.org/licenses/by-nc-sa/4.0/"
    is_tabular: "no"
    purposes:
      - name: Purpose
        response: Create AI-ready, FAIR, provenance-rich multimodal cellular datasets to enable machine learning and artificial intelligence research on human cell architecture and function.
    tasks:
      - name: Primary Task
        response: Train and evaluate machine learning and AI models on multimodal cellular data (perturb-seq, SEC-MS, subcellular imaging) for mapping human cell architecture.
    addressing_gaps:
      - name: Addressing Gap
        response: Provide standardized, FAIR, and provenance-tracked functional genomics data from disease-relevant human cell lines to accelerate AI-driven discovery in cell biology.
    creators:
      - name: CM4AI Consortium
        affiliation:
          id: CM4AI
          name: Cell Maps for Artificial Intelligence (CM4AI)
        principal_investigator:
          id: "https://orcid.org/0000-0002-1708-8454"
          name: Trey Ideker
          affiliation:
            id: UCSD
            name: University of California San Diego
      - name: Creator
        affiliation:
          id: UCSF
          name: University of California San Francisco
        principal_investigator:
          id: "https://orcid.org/0000-0003-4902-337X"
          name: Nevan Krogan
          affiliation:
            id: UCSF
            name: University of California San Francisco
      - name: Creator
        affiliation:
          id: Stanford
          name: Stanford University
        principal_investigator:
          id: "https://orcid.org/0000-0001-7034-0850"
          name: Emma Lundberg
          affiliation:
            id: Stanford
            name: Stanford University
      - name: Creator
        affiliation:
          id: UCSD
          name: University of California San Diego
        principal_investigator:
          id: "https://orcid.org/0000-0002-3383-1287"
          name: Prashant Mali
          affiliation:
            id: UCSD
            name: University of California San Diego
      - name: Creator
        affiliation:
          id: UCSF
          name: University of California San Francisco
        principal_investigator:
          id: "https://orcid.org/0000-0003-0435-6197"
          name: Andrej Sali
          affiliation:
            id: UCSF
            name: University of California San Francisco
    funders:
      - name: Funding
        grantor:
          id: NIH
          name: National Institutes of Health
        grant:
          id: NIH-1OT2OD032742-01
          name: NIH Bridge2AI (CM4AI)
          grant_number: 1OT2OD032742-01
    instances:
      - name: Perturb-seq modality
        representation: Single-cell transcriptomic profiles from CRISPRi perturbation in undifferentiated KOLF2.1J iPSCs
        data_type: Raw and processed scRNA-seq (perturb-seq) data with associated metadata and provenance
        label: None
      - name: Protein-protein interaction modality (SEC-MS)
        representation: Protein complex fractions and inferred interactions from size exclusion chromatography coupled to mass spectrometry (SEC-MS)
        data_type: Processed SEC-MS outputs with RO-Crate metadata; raw data to be deposited to PRIDE when available
        label: None
      - name: Subcellular imaging modality (ICC-IF confocal)
        representation: Multichannel immunofluorescence confocal images of MDA-MB-468 cells (nuclei, ER, microtubules, protein of interest) ± paclitaxel/vorinostat
        data_type: Image archives (ZIP) with RO-Crate metadata
        label: None
    external_resources:
      - name: SEC-MS raw data deposition
        external_resources:
          - PRIDE (planned deposition for SEC-MS raw data)
        future_guarantees:
          - Raw SEC-MS data will be uploaded to PRIDE when available
        archival:
          - RO-Crate metadata included with distributions
        restrictions:
          - Subject to PRIDE repository policies upon deposition
    is_deidentified:
      name: Deidentification
      description:
        - Dataset comprises data from established human cell lines and derived cell types; no personally identifiable information is included.
    subpopulations:
      - name: Cell types and lines
        identification:
          - Undifferentiated KOLF2.1J human induced pluripotent stem cells (hiPSCs)
          - iPSC-derived neural progenitor cells (NPCs), neurons, cardiomyocytes
          - MDA-MB-468 breast cancer cell line ± chemotherapy (paclitaxel, vorinostat)
        distribution:
          - Modalities cover specified cell types/conditions as described per subset files
    acquisition_methods:
      - name: Acquisition
        description:
          - Direct experimental observation via high-throughput sequencing (perturb-seq), mass spectrometry (SEC-MS), and confocal microscopy (ICC-IF)
        was_directly_observed: yes
        was_reported_by_subjects: no
        was_inferred_derived: some derivative features may be computed from raw data; provenance captured in RO-Crate
        was_validated_verified: yes
    collection_mechanisms:
      - name: Mechanisms
        description:
          - CRISPRi perturbation sequencing (perturb-seq)
          - Size exclusion chromatography coupled to mass spectrometry (SEC-MS)
          - Immunocytochemistry-based immunofluorescence (ICC-IF) and confocal microscopy
    data_collectors:
      - name: Contributors and labs
        description:
          - SEC-MS generated in the Nevan Krogan laboratory (UCSF)
          - ICC-IF confocal imaging generated in the Lundberg Lab (Stanford University)
          - Perturb-seq produced by CM4AI consortium investigators (UCSD, UCSF, and partners)
    collection_timeframes:
      - name: Release timeline
        description:
          - Data creation date 2025-02-27; publication date 2025-03-03 (March 2025 Beta release)
    preprocessing_strategies:
      - name: Packaging and provenance
        description:
          - AI-ready packaging with RO-Crate metadata and FAIRSCAPE provenance graphs
    raw_sources:
      - name: Raw data availability
        description:
          - Raw perturb-seq sequence data are included in the release
          - SEC-MS raw data will be uploaded to PRIDE when available
    existing_uses:
      - name: Related publications
        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
          - 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
    distribution_formats:
      - name: Distribution formats
        description:
          - RO-Crate JSON metadata (application/json)
          - ZIP archives containing imaging data (application/zip)
    distribution_dates:
      - name: Initial release
        description:
          - 2025-03-03
    license_and_use_terms:
      name: License and terms
      description:
        - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
        - Attribution required to copyright holders and authors; non-commercial reuse; share-alike
    maintainers:
      - name: Maintainer
        description:
          - University of Virginia Dataverse (repository host)
          - Point of contact listed on dataset page: Trey Ideker (UC San Diego)
    updates:
      name: Update plan
      description:
        - Data will be augmented regularly through the end of the project; subsequent versions will appear on the Dataverse record
    subsets:
      - id: doi:10.18130/V3/B35XWX#perturbseq-rocrate
        name: ro-crate-metadata.json (CRISPR Perturbation Cell Atlas)
        description: RO-Crate metadata for the expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes for 11,739 targeted genes.
        path: CRISPR Perturbation Cell Atlas/ro-crate-metadata.json
        format: JSON
        media_type: application/json
        md5: cbdb263b1c099396d75e16f00a79a818
        issued: 2025-03-03
      - id: doi:10.18130/V3/B35XWX#perturbseq-rawseq-rocrate
        name: ro-crate-metadata.json (CRISPR Perturbation RNA Sequences - Raw Sequences)
        description: RO-Crate metadata for raw sequence data from the CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs.
        path: CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json
        format: JSON
        media_type: application/json
        md5: 1cafefa32a897998e3e2ba0a29a3ef5c
        issued: 2025-03-03
      - id: doi:10.18130/V3/B35XWX#secms-rocrate
        name: ro-crate-metadata.json (Protein-protein Interaction SEC-MS)
        description: RO-Crate metadata for SEC-MS data generated in undifferentiated KOLF2.1J hiPSCs; raw SEC-MS data will be uploaded to PRIDE when available.
        path: Protein-protein Interaction SEC-MS/ro-crate-metadata.json
        format: JSON
        media_type: application/json
        md5: cb67e7749b15ce87b9042a9feba9d032
        issued: 2025-03-03
      - id: doi:10.18130/V3/B35XWX#if-untreated
        name: cm4ai-v0.6-beta-if-images-untreated.zip
        description: Subcellular immunofluorescence confocal images displaying spatial localization of 563 proteins in untreated MDA-MB-468 cells (nuclei DAPI, ER calreticulin, microtubules tubulin, protein-of-interest).
        path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip
        compression: ZIP
        media_type: application/zip
        md5: 0b4d129f5fbc3bb7f7ea564cd032cef7
        issued: 2025-03-03
      - id: doi:10.18130/V3/B35XWX#if-paclitaxel
        name: cm4ai-v0.6-beta-if-images-paclitaxel.zip
        description: Subcellular immunofluorescence confocal images displaying spatial localization of 563 proteins in MDA-MB-468 cells treated with paclitaxel.
        path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip
        compression: ZIP
        media_type: application/zip
        md5: 9422486c80bc9e1d35b2fbbc72a5f043
        issued: 2025-03-03
      - id: doi:10.18130/V3/B35XWX#if-vorinostat
        name: cm4ai-v0.6-beta-if-images-vorinostat.zip
        description: Subcellular immunofluorescence confocal images displaying spatial localization of 563 proteins in MDA-MB-468 cells treated with vorinostat.
        path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip
        compression: ZIP
        media_type: application/zip
        md5: ac577109a41a9806978461157b777d52
        issued: 2025-03-03