=== 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 (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: "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (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
created_by:
  - CM4AI Consortium
  - University of California San Diego
  - University of California San Francisco
  - Stanford University
  - University of Virginia
  - Yale University
  - University of Alabama at Birmingham
  - Simon Fraser University
  - The Hastings Center
purposes:
  - name: CM4AI purpose
    response: Enable AI/ML research on human cell architecture by releasing AI-ready multimodal functional genomics data (perturb-seq, SEC-MS, and protein localization imaging) with provenance and rich metadata.
tasks:
  - name: Intended AI/ML tasks
    response: Model cellular architecture and function, including prediction and analysis of protein localization, protein-protein interactions, and cellular transcriptional/fitness responses to genome-scale CRISPRi perturbations.
addressing_gaps:
  - name: Gap addressed
    response: Provide standardized, AI-ready, richly annotated functional genomics datasets from disease-relevant human cell lines to accelerate development and benchmarking of AI systems in cell biology.
creators:
  - name: CM4AI Leadership
    principal_investigator:
      id: "https://orcid.org/0000-0002-1708-8454"
      name: Trey Ideker
      affiliation:
        - id: https://www.ucsd.edu/
          name: University of California San Diego
    affiliation:
      id: "https://www.ucsd.edu/"
      name: University of California San Diego
funders:
  - name: NIH Bridge2AI program
    grantor:
      id: "https://www.nih.gov/"
      name: National Institutes of Health
    grant:
      name: Bridge2AI - Functional Genomics Grand Challenge (CM4AI)
      grant_number: 1OT2OD032742-01
instances:
  - name: CRISPRi Perturb-seq in KOLF2.1J hiPSCs
    representation: Single-cell perturbation profiles (CRISPRi Perturb-seq) in undifferentiated KOLF2.1J human induced pluripotent stem cells (hiPSCs)
    instance_type: scRNA-seq profiles linked to targeted gene perturbations
    data_type: Raw sequencing data and RO-Crate metadata describing transcriptional and fitness phenotypes
    counts: 11739
    label: Transcriptional and fitness phenotypes associated with targeted gene perturbations
  - name: Protein localization imaging (ICC-IF) in MDA-MB-468 cells
    representation: Multichannel immunofluorescence confocal microscopy images of subcellular protein localization under treatment conditions
    instance_type: Images across treatment conditions (untreated, paclitaxel, vorinostat) with multiple cellular markers
    data_type: Confocal microscopy image data with channels for nuclei (DAPI), ER (calreticulin), microtubules (tubulin), and protein-of-interest
    counts: 563
    label: Protein-of-interest fluorescence channel per target protein
  - name: SEC-MS protein-protein interaction data
    representation: Size exclusion chromatography-mass spectrometry (SEC-MS) profiles from KOLF2.1J hiPSCs and iPSC-derived NPCs, neurons, and cardiomyocytes
    instance_type: Proteomic fractionation and mass spectrometry profiles for complex inference
    data_type: Mass spectrometry outputs and RO-Crate metadata
external_resources:
  - name: External data deposition
    external_resources:
      - PRIDE repository (planned) for SEC-MS data
    future_guarantees:
      - SEC-MS data will be uploaded to PRIDE when available (as stated by dataset authors)
    archival:
      - RO-Crate metadata included with dataset for provenance and reproducibility
    restrictions:
      - Dataset license CC BY-NC-SA 4.0 applies; PRIDE repository terms may additionally apply upon deposition
subpopulations:
  - name: Cell line subpopulations
    identification:
      - KOLF2.1J human induced pluripotent stem cells (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:
      - Imaging covers 563 proteins of interest across untreated and chemotherapy-treated MDA-MB-468 cells
acquisition_methods:
  - name: Acquisition - Perturb-seq
    description:
      - Genome-scale CRISPRi perturbations followed by single-cell RNA sequencing in KOLF2.1J hiPSCs
    was_directly_observed: yes
    was_reported_by_subjects: no
    was_inferred_derived: no
    was_validated_verified: yes
  - name: Acquisition - SEC-MS
    description:
      - Size exclusion chromatography followed by mass spectrometry profiling to infer protein-protein interactions
    was_directly_observed: yes
    was_reported_by_subjects: no
    was_inferred_derived: no
    was_validated_verified: yes
  - name: Acquisition - Protein localization imaging
    description:
      - Immunofluorescence-based staining (ICC-IF) and confocal microscopy in MDA-MB-468 cells under multiple treatment conditions
    was_directly_observed: yes
    was_reported_by_subjects: no
    was_inferred_derived: no
    was_validated_verified: yes
collection_mechanisms:
  - name: Collection methods
    description:
      - CRISPRi perturbation screening followed by scRNA-seq (Perturb-seq)
      - Size exclusion chromatography-mass spectrometry (SEC-MS)
      - Immunofluorescence staining (DAPI, calreticulin, tubulin, protein-of-interest) and confocal microscopy
data_collectors:
  - name: Data collection teams
    description:
      - Nevan Krogan Laboratory (University of California San Francisco) for SEC-MS
      - Lundberg Lab (Stanford University) for protein localization imaging
      - UC San Diego team for Perturb-seq and coordination
collection_timeframes:
  - name: Data timeframe
    description:
      - Data creation date: 2025-02-27; publication date: 2025-03-03
preprocessing_strategies:
  - name: Packaging and provenance
    description:
      - Data packaged as AI-ready RO-Crate with provenance graphs using the FAIRSCAPE framework
raw_sources:
  - name: Raw data availability
    description:
      - Raw RNA sequence data (Perturb-seq) is included in the release
distribution_formats:
  - name: Distribution
    description:
      - Distributed via University of Virginia Dataverse; includes RO-Crate JSON files and large ZIP archives
      - For large files, use the Dataverse Data Access API; whole-dataset ZIP download may be disabled due to size
distribution_dates:
  - name: Release date
    description:
      - 2025-03-03 (publication date)
license_and_use_terms:
  name: License and attribution
  description:
    - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
    - Attribution required to the copyright holders (The Regents of the University of California; The Board of Trustees of the Leland Stanford Junior University for spatial proteomics raw images) and the authors
    - Cite related publications and the dataset (doi:10.18130/V3/B35XWX)
maintainers:
  - name: Dataset contact
    description:
      - Point of Contact: Trey Ideker (University of California San Diego) via UVA Dataverse contact form
updates:
  name: Update plan
  description:
    - Data will be augmented regularly through the end of the project
is_deidentified:
  name: Deidentification status
  description:
    - Dataset contains in vitro cell line data (no direct personal identifiers); no human subject PII present per dataset description
subsets:
  - id: subset:crisperta-rocrate
    name: CRISPR Perturbation Cell Atlas - RO-Crate metadata
    title: ro-crate-metadata.json
    description: This dataset represents an expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes associated with 11,739 targeted genes.
    format: JSON
    media_type: application/json
    path: CRISPR Perturbation Cell Atlas/ro-crate-metadata.json
    md5: cbdb263b1c099396d75e16f00a79a818
    issued: "2025-03-03"
  - id: subset:crispr-rawseq-rocrate
    name: CRISPR Perturbation RNA Sequences - Raw Sequences - RO-Crate metadata
    title: ro-crate-metadata.json
    description: Raw sequence data from an expressed genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs.
    format: JSON
    media_type: application/json
    path: CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json
    md5: 1cafefa32a897998e3e2ba0a29a3ef5c
    issued: "2025-03-03"
  - id: subset:if-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 and confocal microscopy (Lundberg Lab, Stanford).
    compression: ZIP
    media_type: application/zip
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip
    md5: 9422486c80bc9e1d35b2fbbc72a5f043
    issued: "2025-03-03"
  - id: subset:if-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 and confocal microscopy (Lundberg Lab, Stanford).
    compression: ZIP
    media_type: application/zip
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip
    md5: 0b4d129f5fbc3bb7f7ea564cd032cef7
    issued: "2025-03-03"
  - id: subset:if-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 and confocal microscopy (Lundberg Lab, Stanford).
    compression: ZIP
    media_type: application/zip
    path: Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip
    md5: ac577109a41a9806978461157b777d52
    issued: "2025-03-03"
  - id: subset:secms-rocrate
    name: Protein-protein Interaction SEC-MS - RO-Crate metadata
    title: ro-crate-metadata.json
    description: SEC-MS on undifferentiated KOLF2.1J hiPSCs (Nevan Krogan laboratory, UCSF). Data to be uploaded to PRIDE when available.
    format: JSON
    media_type: application/json
    path: Protein-protein Interaction SEC-MS/ro-crate-metadata.json
    md5: cb67e7749b15ce87b9042a9feba9d032
    issued: "2025-03-03"