# === YAML Fixing Applied ===
id: "doi:10.18130/V3/B35XWX"
name: CM4AI 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"
publisher: "https://dataverse.lib.virginia.edu"
license: "https://creativecommons.org/licenses/by-nc-sa/4.0/"
version: "1.4"
conforms_to: "https://www.researchobject.org/ro-crate/"
keywords:
  - AI
  - artificial intelligence
  - Bridge2AI
  - CM4AI
  - perturb-seq
  - CRISPR/Cas9
  - single-cell RNA sequencing
  - scRNAseq
  - protein-protein interaction
  - SEC-MS
  - size exclusion chromatography
  - mass spectroscopy
  - protein localization
  - subcellular imaging
  - immunofluorescence
  - MDA-MB-468
  - KOLF2.1J
  - induced pluripotent stem cell
  - iPSC
  - neural progenitor cell
  - NPC
  - neuron
  - cardiomyocyte
  - paclitaxel
  - vorinostat
  - affinity purification
  - AP-MS
  - machine learning
  - breast cancer
purposes:
  - id: purpose-1
    name: CM4AI functional genomics Grand Challenge
    response: >
      Provide AI-ready, richly documented and provenance-tracked multimodal
      functional genomics datasets (perturb-seq, SEC-MS, IF imaging) to enable
      artificial intelligence and machine learning approaches to map human cell
      architecture and function from disease-relevant cell lines.
tasks:
  - id: task-1
    name: AI/ML on multimodal cellular data
    response: >
      Train and evaluate AI/ML models for single-cell transcriptomics (perturb-seq),
      protein complex inference (SEC-MS), and protein localization and morphology
      analysis (immunofluorescence imaging) in disease-relevant cell lines.
creators:
  - id: creator-ideker
    name: CM4AI UCSD Lead
    principal_investigator:
      id: person-ideker
      name: Ideker T
      affiliation:
        - id: org-ucsd
          name: University of California San Diego
    affiliation:
      id: org-ucsd
      name: University of California San Diego
  - id: creator-krogan
    name: CM4AI UCSF Lead
    principal_investigator:
      id: person-krogan
      name: Krogan N
      affiliation:
        - id: org-ucsf
          name: University of California San Francisco
    affiliation:
      id: org-ucsf
      name: University of California San Francisco
  - id: creator-lundberg
    name: CM4AI Stanford Lead
    principal_investigator:
      id: person-lundberg
      name: Lundberg E
      affiliation:
        - id: org-stanford
          name: Stanford University
    affiliation:
      id: org-stanford
      name: Stanford University
  - id: creator-clark
    name: CM4AI UVA Lead
    principal_investigator:
      id: person-clark
      name: Clark T
      affiliation:
        - id: org-uva
          name: University of Virginia
    affiliation:
      id: org-uva
      name: University of Virginia
funders:
  - id: funding-nih-ot2
    name: National Institutes of Health Bridge2AI
    grantor:
      id: org-nih
      name: National Institutes of Health
    grant:
      id: grant-1OT2OD032742-01
      name: 1OT2OD032742-01
      grant_number: 1OT2OD032742-01
instances:
  - id: inst-perturb-seq
    name: Perturb-seq in KOLF2.1J iPSCs
    representation: Single-cell transcriptomes and fitness phenotypes from CRISPRi perturbations in undifferentiated KOLF2.1J hiPSCs.
    instance_type: scRNA-seq profiles and perturbation-associated phenotypes.
    data_type: Raw sequence data and processed transcriptomic features; provenance and metadata in RO-Crate.
  - id: inst-sec-ms
    name: Protein-protein interaction SEC-MS
    representation: Protein complex and interaction evidence from size exclusion chromatography-mass spectrometry.
    instance_type: Fractionation profiles and mass spectrometry measurements from KOLF2.1J hiPSCs and iPSC-derived NPCs, neurons, and cardiomyocytes.
    data_type: Mass spectrometry data (with upload to PRIDE when available); provenance and metadata in RO-Crate.
  - id: inst-if-imaging
    name: Immunofluorescence imaging (protein localization)
    representation: Confocal IF images of protein localization in MDA-MB-468 cells under untreated and chemotherapeutic conditions.
    instance_type: Multichannel microscopy images (DAPI, calreticulin/ER, tubulin/microtubules, antibody to protein of interest).
    data_type: Image files packaged in ZIP archives; provenance and metadata in RO-Crate.
collection_mechanisms:
  - id: mech-1
    description:
      - CRISPRi-based perturb-seq in KOLF2.1J hiPSCs.
      - Size exclusion chromatography coupled to mass spectrometry (SEC-MS).
      - Immunofluorescence staining and confocal microscopy (ICC-IF) for protein localization.
data_collectors:
  - id: collectors-1
    description:
      - Perturb-seq: CM4AI consortium (multiple institutions).
      - SEC-MS: Nevan Krogan laboratory, University of California San Francisco.
      - IF imaging: Lundberg Lab, Stanford University.
collection_timeframes:
  - id: timeframe-1
    description:
      - Data creation date: 2025-02-27.
      - Dataset publication date: 2025-03-03.
preprocessing_strategies:
  - id: prep-1
    description:
      - Packaging with provenance graphs and rich metadata as AI-ready datasets in RO-Crate format using the FAIRSCAPE framework.
labeling_strategies:
  - id: label-if
    description:
      - IF image channels: nuclei (DAPI, blue), endoplasmic reticulum (calreticulin antibody, yellow), microtubules (tubulin antibody, red), protein of interest (green).
external_resources:
  - id: ext-1
    external_resources:
      - PRIDE repository (planned upload for SEC-MS data when available).
    future_guarantees:
      - Not specified.
    archival:
      - RO-Crate packaging provides embedded metadata and provenance.
    restrictions:
      - CC BY-NC-SA 4.0 license applies to dataset reuse.
existing_uses:
  - id: use-1
    description:
      - Clark T, Parker J, Schaffer L, Obernier K, Al Manir S, 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"
  - id: use-2
    description:
      - Nourreddine S, Doctor Y, Dailamy A, Forget A, Lee YH, 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"
distribution_formats:
  - id: distfmt-1
    description:
      - JSON (RO-Crate metadata files), ZIP archives (image datasets)
distribution_dates:
  - id: distdate-1
    description:
      - Published 2025-03-03
license_and_use_terms:
  id: license-terms
  description:
    - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0): "https://creativecommons.org/licenses/by-nc-sa/4.0/"
    - Attribution required to the copyright holders and the authors.
    - Cite the related publication(s) and this data collection in any derived works.
ip_restrictions:
  id: ip-1
  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-1
    description:
      - Hosted and maintained via University of Virginia Dataverse repository. Point of contact listed on dataset page (e.g., Ideker T, UC San Diego).
updates:
  id: updates-1
  description:
    - Data will be augmented regularly through the end of the project.
is_tabular: "no"
subsets:
  - id: subset-crispri-atlas-rocrate
    name: ro-crate-metadata.json
    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; validated via phenotypic, protein-interaction,
      and metabolic tracing assays.
    path: CRISPR Perturbation Cell Atlas/ro-crate-metadata.json
    format: JSON
    media_type: application/json
    md5: cbdb263b1c099396d75e16f00a79a818
    distribution_dates:
      - id: subset-crispri-atlas-date
        description:
          - Published Mar 3, 2025
  - id: subset-crispri-rawseq-rocrate
    name: ro-crate-metadata.json
    title: CRISPR Perturbation RNA Sequences - Raw Sequences RO-Crate metadata
    description: >
      Raw sequence data from an expressed genome-scale CRISPRi Perturbation Cell
      Atlas in KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes
      associated with 11,739 targeted genes.
    path: CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json
    format: JSON
    media_type: application/json
    md5: 1cafefa32a897998e3e2ba0a29a3ef5c
    distribution_dates:
      - id: subset-crispri-rawseq-date
        description:
          - Published Mar 3, 2025
  - id: subset-sec-ms-rocrate
    name: ro-crate-metadata.json
    title: Protein-protein Interaction SEC-MS RO-Crate metadata
    description: >
      SEC-MS dataset on undifferentiated KOLF2.1J hiPSCs (with extension to
      iPSC-derived NPCs, neurons, and cardiomyocytes) generated in the Nevan
      Krogan laboratory at UCSF; data to be uploaded to PRIDE when available.
    path: Protein-protein Interaction SEC-MS/ro-crate-metadata.json
    format: JSON
    media_type: application/json
    md5: cb67e7749b15ce87b9042a9feba9d032
    distribution_dates:
      - id: subset-secms-date
        description:
          - Published Mar 3, 2025
  - id: subset-if-paclitaxel
    name: cm4ai-v0.6-beta-if-images-paclitaxel.zip
    title: Protein Localization Subcellular Images - Paclitaxel
    description: >
      Spatial localization of 563 proteins in MDA-MB-468 breast cancer cells
      treated with paclitaxel, imaged by ICC-IF and confocal microscopy in the
      Lundberg Lab at Stanford University. Channels: nuclei (DAPI, blue), ER
      (calreticulin, yellow), microtubules (tubulin, red), protein of interest
      (green).
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip
    compression: ZIP
    media_type: application/zip
    md5: 9422486c80bc9e1d35b2fbbc72a5f043
    distribution_dates:
      - id: subset-if-pac-date
        description:
          - Published Mar 3, 2025
  - id: subset-if-untreated
    name: cm4ai-v0.6-beta-if-images-untreated.zip
    title: Protein Localization Subcellular Images - Untreated
    description: >
      Spatial localization of 563 proteins in untreated MDA-MB-468 breast cancer
      cells, imaged by ICC-IF and confocal microscopy in the Lundberg Lab at
      Stanford University. Channels: nuclei (DAPI, blue), ER (calreticulin,
      yellow), microtubules (tubulin, red), protein of interest (green).
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip
    compression: ZIP
    media_type: application/zip
    md5: 0b4d129f5fbc3bb7f7ea564cd032cef7
    distribution_dates:
      - id: subset-if-untreated-date
        description:
          - Published Mar 3, 2025
  - id: subset-if-vorinostat
    name: cm4ai-v0.6-beta-if-images-vorinostat.zip
    title: Protein Localization Subcellular Images - Vorinostat
    description: >
      Spatial localization of 563 proteins in MDA-MB-468 breast cancer cells
      treated with vorinostat, imaged by ICC-IF and confocal microscopy in the
      Lundberg Lab at Stanford University. Channels: nuclei (DAPI, blue), ER
      (calreticulin, yellow), microtubules (tubulin, red), protein of interest
      (green).
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip
    compression: ZIP
    media_type: application/zip
    md5: ac577109a41a9806978461157b777d52
    distribution_dates:
      - id: subset-if-vori-date
        description:
          - Published Mar 3, 2025