=== YAML Fixing Applied ===
id: "doi:10.18130/V3/F3TD5R"
name: CM4AI June 2025 Data Release (Beta)
title: Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
description: >
  June 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, iPSC-derived NPCs, neurons, cardiomyocytes,
  and treated and untreated MDA-MB-468 breast cancer cells; and IF images in MDA-MB-468
  breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel).
doi: "doi:10.18130/V3/F3TD5R"
version: "2.0"
issued: "2025-07-01"
created_on: "2025-02-27"
last_updated_on: "2025-10-22"
page: "https://doi.org/10.18130/V3/F3TD5R"
publisher: "https://dataverse.lib.virginia.edu/"
license: "https://creativecommons.org/licenses/by-nc-sa/4.0/"
language: en
keywords:
  - AI
  - artificial intelligence
  - machine learning
  - Bridge2AI
  - CM4AI
  - induced pluripotent stem cell
  - iPSC
  - KOLF2.1J
  - neural progenitor cell
  - NPC
  - neuron
  - cardiomyocyte
  - breast cancer
  - MDA-MB-468
  - paclitaxel
  - vorinostat
  - perturb-seq
  - perturbation sequencing
  - single-cell RNA sequencing
  - scRNAseq
  - size exclusion chromatography
  - SEC-MS
  - mass spectrometry
  - protein-protein interaction
  - protein localization
  - subcellular imaging
created_by:
  - Niestroy, Justin (Depositor)
  - CM4AI Project Team
status: "bibo:draft"
purposes:
  - name: Dataset Purpose
    response: >
      Provide AI-ready multimodal functional genomics datasets to support research on
      human cell architecture and cellular processes, enabling AI model training and
      analysis across imaging, proteomics, and perturb-seq modalities.
tasks:
  - name: Intended Tasks
    response: >
      AI model training for functional genomics; cellular process analysis; analysis of
      cell architectural changes and interactions under disease, treatment, or genetic
      perturbations.
addressing_gaps:
  - name: Gap Addressed
    response: >
      Consolidates multimodal cell architecture data to support AI methods; computed
      cell maps are out of scope for this interim release and will be added in future releases.
funders:
  - name: NIH Bridge2AI Program
    grantor:
      id: NIH
      name: National Institutes of Health
    grant:
      id: 1OT2OD032742-01
      name: 1OT2OD032742-01
      grant_number: 1OT2OD032742-01
creators:
  - name: Cell Maps for Artificial Intelligence (CM4AI) Consortium
    principal_investigator:
      id: "https://orcid.org/0000-0002-1708-8454"
      name: Ideker, Trey
      description: Point of Contact listed on Dataverse
      affiliation:
        id: "https://www.ucsd.edu/"
        name: University of California San Diego
    affiliation:
      id: "https://www.ucsd.edu/"
      name: University of California San Diego
instances:
  - name: Data Modalities
    representation: >
      Multimodal instances: (1) immunofluorescence microscopy images; (2) size exclusion
      chromatography-mass spectrometry (SEC-MS) proteomics runs; (3) perturb-seq single-cell
      transcriptomes in human iPSCs.
    instance_type: Images; Proteomics runs; Single-cell profiles
    data_type: Raw and processed experimental data across imaging, proteomics (SEC-MS), and scRNA-seq (perturb-seq).
sampling_strategies:
  - name: Representativeness
    is_sample:
      - Yes
    is_representative:
      - No
    why_not_representative:
      - >
        Data derived from commercially available de-identified human cell lines and does
        not represent all biological variants present in the population.
relationships:
  - name: Cross-modality alignment
    description:
      - >
        Modalities interrogate overlapping but not identical protein sets across SEC-MS,
        IF imaging, and CRISPRi perturb-seq.
subpopulations:
  - name: Cell types and conditions
    identification:
      - KOLF2.1J iPSCs (undifferentiated)
      - iPSC-derived neural progenitor cells (NPCs)
      - iPSC-derived neurons
      - iPSC-derived cardiomyocytes
      - MDA-MB-468 breast cancer cells (untreated)
      - MDA-MB-468 breast cancer cells (vorinostat-treated)
      - MDA-MB-468 breast cancer cells (paclitaxel-treated)
collection_mechanisms:
  - name: Experimental collection mechanisms
    description:
      - Confocal microscopy with ICC-IF staining (DAPI, calreticulin/ER, tubulin/microtubules, protein-of-interest antibody).
      - Size exclusion chromatography followed by mass spectrometry (SEC-MS).
      - CRISPRi perturb-seq (single-cell RNA-seq).
data_collectors:
  - name: Contributing laboratories and institutions
    description:
      - Lundberg Lab (Stanford University) for IF imaging (MDA-MB-468).
      - University of California San Diego.
      - University of California San Francisco.
      - University of Virginia.
collection_timeframes:
  - name: Timeline
    description:
      - Data creation date: 2025-02-27; Release (publication) date: 2025-07-01; Additional image archives published 2025-10-22.
ethical_reviews:
  - name: Data Governance & Ethics
    description:
      - Human Subjects: No; De-identified Samples: Yes; FDA Regulated: No.
      - Data Governance Committee: Jillian Parker (jillianparker@health.ucsd.edu).
      - Ethical Review contacts: Vardit Ravitsky (ravitskyv@thehastingscenter.org); Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca).
is_deidentified:
  - name: De-identification
    description:
      - De-identified samples from commercially available human cell lines; no human subjects involved.
preprocessing_strategies:
  - name: Imaging channels
    description:
      - Multichannel IF imaging with DAPI (nuclei), calreticulin (ER), tubulin (microtubules), and protein-of-interest antibodies.
raw_sources:
  - name: External raw data repositories
    description:
      - Sequence Read Archive (SRA) Data: NCBI BioProject (perturb-seq).
      - MassIVE Repository: Human iPSC SEC-MS data.
      - MassIVE Repository: Human cancer cell SEC-MS data.
external_resources:
  - name: External Data Links
    external_resources:
      - Sequence Read Archive (SRA) Data: NCBI BioProject
      - Mass Spectrometry Data (Human iPSCs): MassIVE Repository
      - Mass Spectrometry Data (Human Cancer Cells): MassIVE Repository
    archival:
      - >
        Primary raw data for some modalities are hosted externally (SRA/MassIVE); release RO-Crate includes pointers to sub ro-crates.
content_warnings:
  - name: Prohibited Uses
    warnings:
      - Not for clinical decision-making or patient care without appropriate regulatory oversight and approval.
existing_uses:
  - name: Related publications
    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:10.1101/2024.05.21.589311
      - >
        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:10.1101/2024.11.03.621734
future_use_impacts:
  - name: Limitations and risks
    description:
      - Interim release; computed cell maps not included.
      - Some datasets under temporary pre-publication embargo.
      - Modalities interrogate partially overlapping protein sets.
      - Requires domain expertise for meaningful analysis.
discouraged_uses:
  - name: Prohibited Uses
    description:
      - Clinical decision-making or patient care without appropriate regulatory oversight and approval.
distribution_formats:
  - name: Distribution mechanisms and formats
    description:
      - Distributed via University of Virginia Dataverse (DOI landing page).
      - RO-Crate metadata (JSON) and HTML datasheet.
      - Large ZIP archive files for imaging data.
distribution_dates:
  - name: Release dates
    description:
      - Dataset publication date: 2025-07-01 (Version 2.0).
      - Additional image archives published: 2025-10-22.
maintainers:
  - name: Dataset maintenance
    description:
      - Long-term preservation in the University of Virginia Dataverse, supported by committed institutional funds.
      - Point of Contact: Trey Ideker (UC San Diego). Contact owner via Dataverse.
errata: []
updates:
  name: Update plan
  description:
    - Dataset will be regularly updated and augmented through November 2026, with quarterly updates.
version_access:
  name: Versioning
  description:
    - Managed via Dataverse versioning (this is Version 2.0).
subsets:
  - id: cm4ai-ifimages-mda-mb-468-untreated
    name: IF images - MDA-MB-468 untreated
    title: Immunofluorescence images of MDA-MB-468 (untreated)
    description: >
      Spatial localization of 464 proteins in MDA-MB-468 cells imaged by ICC-IF confocal
      microscopy (Lundberg Lab, Stanford). Channels: DAPI (nuclei), calreticulin (ER),
      tubulin (microtubules), protein-of-interest (green).
    path: Images/cm4ai-ifimages-mda-mb-468-untreated.zip
    media_type: application/zip
    compression: ZIP
    md5: a98affcc05429650c6bb3906cd836d55
    issued: "2025-10-22"
    is_data_split: No
    is_subpopulation: Yes
  - id: cm4ai-ifimages-mda-mb-468-paclitaxel
    name: IF images - MDA-MB-468 paclitaxel
    title: Immunofluorescence images of MDA-MB-468 (paclitaxel-treated)
    description: >
      Spatial localization of 464 proteins in MDA-MB-468 cells treated with paclitaxel,
      imaged by ICC-IF confocal microscopy (Lundberg Lab, Stanford). Channels as above.
    path: Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    media_type: application/zip
    compression: ZIP
    md5: 0d972b80744344ddeede516a0cf6e3d7
    issued: "2025-10-22"
    is_data_split: No
    is_subpopulation: Yes
  - id: cm4ai-ifimages-mda-mb-468-vorinostat
    name: IF images - MDA-MB-468 vorinostat
    title: Immunofluorescence images of MDA-MB-468 (vorinostat-treated)
    description: >
      Spatial localization of 464 proteins in MDA-MB-468 cells treated with vorinostat,
      imaged by ICC-IF confocal microscopy (Lundberg Lab, Stanford). Channels as above.
    path: Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip
    media_type: application/zip
    compression: ZIP
    md5: ad4e68ccc14b0f3349dad3321e7b81b2
    issued: "2025-10-22"
    is_data_split: No
    is_subpopulation: Yes
  - id: release-ro-crate-datasheet
    name: Release datasheet (HTML)
    title: Release RO-Crate datasheet
    description: HTML datasheet summarizing key release information.
    path: release-ro-crate-datasheet.html
    media_type: text/html
    md5: 599c9ece9b88b3ce797b82463b4a1eb4
    issued: "2025-07-01"
    is_data_split: No
    is_subpopulation: No
  - id: release-ro-crate-metadata
    name: Release RO-Crate metadata (JSON)
    title: Release RO-Crate metadata
    description: RO-Crate with pointers to sub RO-Crates.
    path: release-ro-crate-metadata.json
    media_type: application/json
    md5: 99f9e00053bff3020fd9832a3a518bbb
    issued: "2025-07-01"
    is_data_split: No
    is_subpopulation: No
license_and_use_terms:
  name: License and Terms
  description:
    - CC BY-NC-SA 4.0. Our Community Norms and good scientific practices expect proper citation using the dataset citation shown on the dataset page.