=== 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)."
language: English
page: "https://doi.org/10.18130/V3/B35XWX"
doi: "doi:10.18130/V3/B35XWX"
issued: 2025-03-03
created_on: 2025-02-27
conforms_to: "https://w3id.org/ro/crate"
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
purposes:
  - name: Purpose
    response: Create AI-ready maps of human cell architecture from disease-relevant cell lines and modalities (scRNAseq perturb-seq, protein–protein interactions, and subcellular imaging) with rich provenance for machine learning.
tasks:
  - name: Task
    response: Training and evaluating AI/ML models for cellular architecture mapping, protein localization, perturbation effect prediction, and protein–protein interaction inference.
addressing_gaps:
  - name: AddressingGap
    response: Provides standardized, multi-modal, provenance-rich functional genomics datasets across key human cell models to address the lack of integrated, AI-ready resources.
creators:
  - name: CM4AI Consortium
    affiliation:
      id: CM4AI
      name: Cell Maps for Artificial Intelligence (CM4AI)
      description: NIH Bridge2AI Functional Genomics Grand Challenge consortium.
    principal_investigator:
      id: "person:ideker_t"
      name: Trey Ideker
      affiliation:
        - id: org:ucsd
          name: University of California San Diego
  - name: UCSF Team
    affiliation:
      id: "org:ucsf"
      name: University of California San Francisco
    principal_investigator:
      id: "person:krogan_n"
      name: Nevan Krogan
      affiliation:
        - id: org:ucsf
          name: University of California San Francisco
  - name: Stanford Team
    affiliation:
      id: "org:stanford"
      name: Stanford University
    principal_investigator:
      id: "person:lundberg_e"
      name: Emma Lundberg
      affiliation:
        - id: org:stanford
          name: Stanford University
  - name: UCSD Genome Engineering Team
    affiliation:
      id: "org:ucsd"
      name: University of California San Diego
    principal_investigator:
      id: "person:mali_p"
      name: Prashant Mali
      affiliation:
        - id: org:ucsd
          name: University of California San Diego
  - name: UVA Team
    affiliation:
      id: "org:uva"
      name: University of Virginia
    principal_investigator:
      id: "person:clark_t"
      name: Tim Clark
      affiliation:
        - id: org:uva
          name: University of Virginia
funders:
  - name: NIH Bridge2AI Program
    grantor:
      id: "org:nih"
      name: National Institutes of Health
    grant:
      name: Bridge2AI Functional Genomics Grand Challenge (CM4AI)
      grant_number: 1OT2OD032742-01
instances:
  - name: scRNAseq perturb-seq instances
    representation: Single-cell RNA sequencing measurements from KOLF2.1J iPSCs under CRISPRi perturbations.
    instance_type: Cells and associated perturbation targets.
    data_type: Raw RNA sequence reads and processed counts/metadata as described by RO-Crate.
  - name: Protein–protein interaction instances (SEC-MS)
    representation: Protein complex size-exclusion chromatography followed by mass spectrometry profiles in KOLF2.1J iPSCs and derived NPCs, neurons, and cardiomyocytes.
    instance_type: Proteins and co-elution interaction signals across fractions.
    data_type: Mass spectrometry-derived interaction evidence packaged via RO-Crate metadata.
  - name: Subcellular imaging instances (IF)
    representation: Immunofluorescence images of MDA-MB-468 cells with treatment conditions (vorinostat, paclitaxel, untreated).
    instance_type: Cells and protein-of-interest localization channels.
    data_type: Multi-channel confocal microscopy images (DAPI, calreticulin/ER, tubulin/microtubules, protein-of-interest).
subpopulations:
  - name: Subpopulation
    identification:
      - Undifferentiated KOLF2.1J iPSCs
      - iPSC-derived NPCs
      - iPSC-derived neurons
      - iPSC-derived cardiomyocytes
      - MDA-MB-468 breast cancer cells (treated and untreated)
acquisition_methods:
  - name: InstanceAcquisition
    description:
      - Data acquired via direct observation technologies: scRNAseq perturb-seq (sequencing), SEC-MS (mass spectrometry), and confocal IF imaging.
      - Validation reported via phenotypic, protein-interaction, and metabolic tracing assays (per dataset description).
    was_directly_observed: yes
    was_reported_by_subjects: no
    was_inferred_derived: Some downstream features may be derived; primary data are observed measurements.
    was_validated_verified: yes
collection_mechanisms:
  - name: CollectionMechanism
    description:
      - CRISPRi perturbation sequencing workflows (undifferentiated KOLF2.1J iPSCs)
      - Size exclusion chromatography–mass spectrometry (SEC-MS)
      - Immunofluorescence staining and confocal microscopy (DAPI, calreticulin/ER, tubulin, protein-of-interest)
data_collectors:
  - name: DataCollector
    description:
      - Nevan Krogan laboratory (UCSF) – SEC-MS
      - Lundberg Lab (Stanford University) – Subcellular imaging
      - UC San Diego teams – CRISPR perturb-seq and integration
collection_timeframes:
  - name: CollectionTimeframe
    description:
      - Data creation date: 2025-02-27
      - Initial public release: 2025-03-03
preprocessing_strategies:
  - name: PreprocessingStrategy
    description:
      - Packaging in RO-Crate format with provenance graphs and rich metadata using the FAIRSCAPE framework.
labeling_strategies:
  - name: LabelingStrategy
    description:
      - IF imaging channels labeled as: nuclei (DAPI, blue), endoplasmic reticulum (calreticulin antibody, yellow), microtubules (tubulin antibody, red), protein-of-interest (green).
raw_sources:
  - name: RawData
    description:
      - Raw sequences provided in "CRISPR Perturbation RNA Sequences - Raw Sequences" data file.
existing_uses:
  - name: ExistingUse
    description:
      - Clark T, Parker J, Schaffer L, Obernier K, Al Manir S, Churas CP, 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
  - name: ExistingUse
    description:
      - Nourreddine S, Doctor Y, Dailamy A, Forget A, Lee YH, Chinn B, 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
other_tasks:
  - name: OtherTask
    description:
      - Multi-modal representation learning across sequencing, proteomics, and imaging
      - Drug response phenotype modeling in cell lines
      - Protein localization and interaction network inference
future_use_impacts:
  - name: FutureUseImpact
    description:
      - Users should respect modality-specific caveats (e.g., treatment conditions in imaging; cell-type specificity in SEC-MS and perturb-seq) to avoid misgeneralization across biological contexts.
discouraged_uses:
  - name: DiscouragedUse
    description:
      - Commercial use is not permitted under CC BY-NC-SA 4.0.
distribution_formats:
  - name: DistributionFormat
    description:
      - UVA Dataverse distribution; individual files downloadable (JSON, ZIP). Programmatic access via Dataverse Data Access API. Packaged as RO-Crate where applicable.
distribution_dates:
  - name: DistributionDate
    description:
      - 2025-03-03 (initial public release)
license_and_use_terms:
  name: LicenseAndUseTerms
  description:
    - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
    - Attribution required to copyright holders and authors; cite the dataset and related publication as indicated on the landing page.
ip_restrictions:
  name: IPRestrictions
  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:
  - name: Maintainer
    description:
      - University of Virginia Dataverse (host)
      - Point of Contact: Trey Ideker (University of California San Diego)
      - Depositor: Justin Niestroy
updates:
  name: UpdatePlan
  description:
    - Data will be augmented regularly through the end of the project; updates occur via new dataset versions on UVA Dataverse.
version_access:
  name: VersionAccess
  description:
    - Hosted on Dataverse with versioning; older versions remain accessible per Dataverse policies.
external_resources:
  - name: ExternalResource
    external_resources:
      - SEC-MS data will be uploaded to PRIDE when available.
    future_guarantees:
      - Hosted primary distributions are on UVA Dataverse; external repository availability subject to respective repository policies.
    archival:
      - DOIs minted via DataCite; Dataverse preserves released versions.
    restrictions:
      - External repository (PRIDE) terms may apply when deposited.

subsets:
  - id: subset:crispr-cell-atlas-ro-crate
    name: CRISPR Perturbation Cell Atlas - RO-Crate metadata
    title: ro-crate-metadata.json
    description: Expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes associated with 11,739 targeted genes.
    path: CRISPR Perturbation Cell Atlas/ro-crate-metadata.json
    format: JSON
    media_type: application/json
    md5: cbdb263b1c099396d75e16f00a79a818
  - id: subset:crispr-raw-rna-sequences
    name: CRISPR Perturbation RNA Sequences - Raw Sequences (RO-Crate metadata)
    title: ro-crate-metadata.json
    description: Raw sequence data from 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
  - id: subset: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 microscopy).
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip
    compression: ZIP
    media_type: application/zip
    md5: 9422486c80bc9e1d35b2fbbc72a5f043
  - id: subset: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 cells (ICC-IF, confocal microscopy).
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip
    compression: ZIP
    media_type: application/zip
    md5: 0b4d129f5fbc3bb7f7ea564cd032cef7
  - id: subset: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 microscopy).
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip
    compression: ZIP
    media_type: application/zip
    md5: ac577109a41a9806978461157b777d52
  - id: subset:sec-ms-ro-crate
    name: Protein–protein Interaction SEC-MS - RO-Crate metadata
    title: ro-crate-metadata.json
    description: Size exclusion chromatography–mass spectrometry (SEC-MS) on undifferentiated KOLF2.1J hiPSCs (Nevan Krogan lab, UCSF); 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