=== 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. Attribution is required to the copyright holders and the authors. Any publications referencing this data or derived products should cite the related publications and directly cite this data collection.
language: English
publisher: University of Virginia Dataverse
issued: 2025-03-03
created_on: 2025-02-27
page: "https://doi.org/10.18130/V3/B35XWX"
doi: "doi:10.18130/V3/B35XWX"
version: "1.4"
license: "https://creativecommons.org/licenses/by-nc-sa/4.0/"
conforms_to: "https://w3id.org/ro/crate"
keywords:
  - AI
  - artificial intelligence
  - machine learning
  - Bridge2AI
  - CM4AI
  - KOLF2.1J
  - induced pluripotent stem cell
  - iPSC
  - CRISPR/Cas9
  - perturb-seq
  - perturbation sequencing
  - single-cell RNA sequencing
  - scRNAseq
  - protein-protein interaction
  - SEC-MS
  - size exclusion chromatography
  - affinity purification
  - AP-MS
  - mass spectroscopy
  - protein localization
  - subcellular imaging
  - MDA-MB-468
  - breast cancer
  - neural progenitor cell
  - NPC
  - neuron
  - cardiomyocyte
  - paclitaxel
  - vorinostat
purposes:
  - name: Dataset Purpose
    response: Create AI-ready, FAIR, multi-modal functional genomics datasets to map human cell architecture and function across disease-relevant cell lines.
tasks:
  - name: Target Tasks
    response: Modeling and analysis of single-cell perturbation responses, protein-protein interactions, and protein subcellular localization for AI/ML applications.
addressing_gaps:
  - name: Addressed Gap
    response: Provides standardized, provenance-rich, multi-omic and imaging datasets packaged as RO-Crates to accelerate AI methods development in functional genomics.
creators:
  - name: CM4AI Consortium (UC San Diego lead)
    principal_investigator:
      id: trey-ideker
      name: Trey Ideker
      affiliation:
        id: ucsd
        name: University of California San Diego
    affiliation:
      id: ucsd
      name: University of California San Diego
  - name: CM4AI Consortium (UCSF node)
    principal_investigator:
      id: nevan-krogan
      name: Nevan Krogan
      affiliation:
        id: ucsf
        name: University of California San Francisco
    affiliation:
      id: ucsf
      name: University of California San Francisco
  - name: CM4AI Consortium (Stanford node)
    principal_investigator:
      id: emma-lundberg
      name: Emma Lundberg
      affiliation:
        id: stanford
        name: Stanford University
    affiliation:
      id: stanford
      name: Stanford University
funders:
  - name: NIH Bridge2AI
    grantor:
      id: nih
      name: National Institutes of Health
    grant:
      id: bridge2ai-funcgen
      name: Bridge2AI Functional Genomics Grand Challenge
      grant_number: 1OT2OD032742-01
instances:
  - name: Single-cell CRISPRi perturb-seq (KOLF2.1J hiPSCs)
    representation: Single-cell transcriptomes and fitness phenotypes under CRISPRi perturbations targeting 11,739 genes.
    instance_type: Cells and gene-level perturbations
    data_type: Raw sequencing reads and RO-Crate metadata; processed phenotypic summaries when available.
    sampling_strategies:
      - name: Targeted perturbation set
        is_sample:
          - yes
        is_random:
          - no
        source_data:
          - KOLF2.1J human induced pluripotent stem cells
        strategies:
          - Deterministic, targeted genome-scale CRISPRi library
  - name: Protein-protein interactions by SEC-MS
    representation: Protein complex co-fractionation mass spectrometry profiles.
    instance_type: Proteins and protein complexes
    data_type: SEC-MS co-elution profiles and RO-Crate metadata; repository deposition to PRIDE when available.
  - name: Immunofluorescence subcellular imaging (MDA-MB-468)
    representation: Multi-channel confocal images showing subcellular localization of proteins under treatments.
    instance_type: Images of cells and annotated channels
    data_type: ZIP archives of image sets with immunofluorescence channels (DAPI, calreticulin/ER, tubulin/microtubules, protein-of-interest).
collection_mechanisms:
  - name: Data Collection Modalities
    description:
      - CRISPRi perturb-seq in KOLF2.1J hiPSCs
      - Size exclusion chromatography mass spectrometry (SEC-MS)
      - Immunofluorescence staining and confocal microscopy
data_collectors:
  - name: Data Collection Teams
    description:
      - Nevan Krogan Laboratory, UCSF (SEC-MS)
      - Lundberg Lab, Stanford University (IF imaging)
      - UC San Diego (perturb-seq, coordination)
      - University of Virginia (data stewardship)
      - CM4AI consortium member institutions (Yale, UAB, Simon Fraser University, The Hastings Center)
collection_timeframes:
  - name: Initial Release Timeframe
    description:
      - Data creation: 2025-02-27
      - First public release (publication date): 2025-03-03
external_resources:
  - name: External Repository Plans
    external_resources:
      - PRIDE repository (for SEC-MS data; to be uploaded when available)
    future_guarantees:
      - Dataverse persistent DOI and versioning for this collection
    archival:
      - Packaged as RO-Crate with FAIRSCAPE provenance graphs
distribution_formats:
  - name: Distribution Formats
    description:
      - RO-Crate metadata (JSON)
      - ZIP archives (image data)
      - JSON metadata for SEC-MS and sequencing packages
distribution_dates:
  - name: Initial Distribution
    description:
      - 2025-03-03
license_and_use_terms:
  name: CC BY-NC-SA 4.0
  description:
    - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (https://creativecommons.org/licenses/by-nc-sa/4.0/)
    - Non-commercial use; attribution required; share alike.
ip_restrictions:
  name: IP and Copyright
  description:
    - Copyright (c) 2025 The Regents of the University of California except where noted.
    - Spatial proteomics raw image data copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University.
maintainers:
  - name: Repository Maintainer
    description:
      - University of Virginia Dataverse (LibraData: UVa's Scholarly Research)
updates:
  name: Update Plan
  description:
    - Data will be augmented regularly throughout the project; subsequent versions will be released via Dataverse with versioning.
version_access:
  name: Version Access and Persistence
  description:
    - Prior versions remain accessible via Dataverse dataset versioning under the persistent DOI.
is_tabular: "no"
subsets:
  - id: ro-crate-crispri-perturbation-cell-atlas
    name: CRISPR Perturbation Cell Atlas RO-Crate
    title: ro-crate-metadata.json (CRISPR Perturbation Cell Atlas)
    description: Expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes for 11,739 targeted genes.
    format: JSON
    media_type: application/json
    md5: cbdb263b1c099396d75e16f00a79a818
    path: CRISPR Perturbation Cell Atlas/ro-crate-metadata.json
  - id: ro-crate-crispri-raw-sequences
    name: CRISPR Perturbation RNA Sequences - Raw Sequences RO-Crate
    title: ro-crate-metadata.json (CRISPR Perturbation RNA Sequences - Raw)
    description: Raw sequence data from genome-scale CRISPRi perturbations in KOLF2.1J hiPSCs.
    format: JSON
    media_type: application/json
    md5: 1cafefa32a897998e3e2ba0a29a3ef5c
    path: CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json
  - id: ro-crate-sec-ms
    name: Protein-protein Interaction SEC-MS RO-Crate
    title: ro-crate-metadata.json (Protein-protein Interaction SEC-MS)
    description: SEC-MS dataset on undifferentiated KOLF2.1J hiPSCs; data to be uploaded to PRIDE when available.
    format: JSON
    media_type: application/json
    md5: cb67e7749b15ce87b9042a9feba9d032
    path: Protein-protein Interaction SEC-MS/ro-crate-metadata.json
  - id: if-images-untreated
    name: Protein Localization Subcellular Images - Untreated
    title: cm4ai-v0.6-beta-if-images-untreated.zip
    description: Spatial localization of 563 proteins in untreated MDA-MB-468 breast cancer cells imaged by ICC-IF and confocal microscopy; channels include DAPI (blue), calreticulin/ER (yellow), tubulin/microtubules (red), and protein-of-interest (green).
    compression: ZIP
    media_type: application/zip
    md5: 0b4d129f5fbc3bb7f7ea564cd032cef7
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip
  - id: if-images-paclitaxel
    name: Protein Localization Subcellular Images - Paclitaxel
    title: cm4ai-v0.6-beta-if-images-paclitaxel.zip
    description: Spatial localization of 563 proteins in MDA-MB-468 cells treated with paclitaxel; ICC-IF confocal imaging with multi-channel stains as described.
    compression: ZIP
    media_type: application/zip
    md5: 9422486c80bc9e1d35b2fbbc72a5f043
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip
  - id: if-images-vorinostat
    name: Protein Localization Subcellular Images - Vorinostat
    title: cm4ai-v0.6-beta-if-images-vorinostat.zip
    description: Spatial localization of 563 proteins in MDA-MB-468 cells treated with vorinostat; ICC-IF confocal imaging with multi-channel stains as described.
    compression: ZIP
    media_type: application/zip
    md5: ac577109a41a9806978461157b777d52
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip
use_repository:
  - name: Related Publications
    description:
      - Clark T, Parker J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle-Pipon JC, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T. 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, Doctor Y, Dailamy A, Forget A, Lee YH, Chinn B, Khaliq H, Polacco B, Muralidharan M, Pan E, Zhang Y, Sigaeva A, Hansen JN, Gao J, Parker JA, Obernier K, Clark T, Chen JY, Metallo C, Lundberg E, Ideker T, Krogan N, Mali P. A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS. bioRxiv. 2024 Nov 4;2024.11.03.621734. doi: https://doi.org/10.1101/2024.11.03.621734
subpopulations:
  - name: Cell Types and Conditions
    identification:
      - KOLF2.1J hiPSCs
      - iPSC-derived neural progenitor cells (NPCs)
      - iPSC-derived neurons
      - iPSC-derived cardiomyocytes
      - MDA-MB-468 breast cancer cells (untreated, paclitaxel-treated, vorinostat-treated)
    distribution:
      - Multiple modalities across listed cell types; counts vary by assay (see modality-specific subsets).