=== 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"
version: "1.4"
conforms_to: "https://w3id.org/ro/crate"
license: "CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)"
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:
  - "Clark T (University of Virginia) - ORCID: https://orcid.org/0000-0003-4060-7360"
  - "Parker J (University of California, San Diego) - ORCID: https://orcid.org/0000-0003-4535-3486"
  - "Al Manir S (University of Virginia) - ORCID: https://orcid.org/0000-0003-4647-3877"
  - "Axelsson U (KTH Royal Institute of Technology)"
  - "Ballllosero Navarro F (Stanford University) - ORCID: https://orcid.org/0000-0002-4180-422X"
  - "Chinn B (University of California San Diego)"
  - "Churas CP (University of California San Diego) - ORCID: https://orcid.org/0000-0001-9998-705X"
  - "Dailamy A (University of California, San Diego) - ORCID: https://orcid.org/0000-0002-6711-8260"
  - "Doctor Y (University of California, San Diego) - ORCID: https://orcid.org/0009-0009-0483-7506"
  - "Fall J (KTH - Royal Institute of Technology)"
  - "Forget A (University of California San Francisco) - ORCID: https://orcid.org/0000-0003-0223-0312"
  - "Gao J (University of California San Diego) - ORCID: https://orcid.org/0000-0002-6311-3526"
  - "Hansen JN (Stanford University) - ORCID: https://orcid.org/0000-0002-4650-9094"
  - "Hu M (University of California San Diego) - ORCID: https://orcid.org/0000-0002-1571-8029"
  - "Johannesson A (KTH - Royal Institute of Technology)"
  - "Khaliq H (University of California San Diego)"
  - "Lee YH (University of California San Diego) - ORCID: https://orcid.org/0000-0003-0917-355X"
  - "Lenkiewicz J (University of California San Diego) - ORCID: https://orcid.org/0000-0001-7252-8638"
  - "Levinson MA (University of Virginia) - ORCID: https://orcid.org/0000-0003-0384-8499"
  - "Marquez C (University of California San Diego) - ORCID: 0000-0003-3960-420X"
  - "Metallo C (University of California San Diego) - ORCID: https://orcid.org/0000-0003-2404-3040"
  - "Muralidharan M (University of California San Francisco)"
  - "Nourreddine S (University of California San Diego) - ORCID: https://orcid.org/0000-0003-3881-7588"
  - "Niestroy J (University of Virginia) - ORCID: https://orcid.org/0000-0002-1103-3882"
  - "Obernier K (University of California San Francisco) - ORCID: https://orcid.org/0000-0002-4025-1299"
  - "Pan E (University of California San Diego)"
  - "Polacco B (University of California San Francisco)"
  - "Pratt D (University of California San Diego) - ORCID: https://orcid.org/0000-0002-1471-9513"
  - "Qian G (University of California San Diego) - ORCID: https://orcid.org/0009-0005-4217-2745"
  - "Schaffer L (University of California San Diego) - ORCID: https://orcid.org/0000-0001-6339-9141"
  - "Sigaeva A (KTH Royal Institute of Technology) - ORCID: https://orcid.org/0000-0003-3361-3797"
  - "Thaker S (University of Alabama at Birmingham) - ORCID: https://orcid.org/0000-0001-6730-2773"
  - "Zhang Y (University of California San Diego)"
  - "Bélisle-Pipon JC (Simon Fraser University) - ORCID: https://orcid.org/0000-0002-8965-8153"
  - "Brandt C (Yale University) - ORCID: https://orcid.org/0000-0001-8179-1796"
  - "Chen JY (The University of Alabama at Birmingham) - ORCID: https://orcid.org/0000-0002-6112-415X"
  - "Ding Y (University of Texas at Austin) - ORCID: https://orcid.org/0000-0003-2567-2009"
  - "Fodeh S (Yale University) - ORCID: https://orcid.org/0000-0003-4664-3143"
  - "Krogan N (University of California San Francisco) - ORCID: https://orcid.org/0000-0003-4902-337X"
  - "Lundberg E (Stanford University) - ORCID: https://orcid.org/0000-0001-7034-0850"
  - "Mali P (University of California San Diego) - ORCID: https://orcid.org/0000-0002-3383-1287"
  - "Payne-Foster P (University of Alabama) - ORCID: https://orcid.org/0000-0002-3508-3577"
  - "Ratcliffe S (University of Virginia) - ORCID: https://orcid.org/0000-0002-6644-8284"
  - "Ravitsky V (University of Montreal) - ORCID: https://orcid.org/0000-0002-7080-8801"
  - "Sali A (University of California San Diego) - ORCID: https://orcid.org/0000-0003-0435-6197"
  - "Schulz W (Yale University) - ORCID: https://orcid.org/0000-0002-2048-4028"
  - "Ideker T (University of California San Diego) - ORCID: https://orcid.org/0000-0002-1708-8454
    (Point of Contact: Ideker Trey, UC San Diego)"
purposes:
  - name: Primary purpose
    response: Provide AI-ready multimodal functional genomics datasets to map human cell architecture and enable machine learning research under Bridge2AI (CM4AI).
tasks:
  - name: Modeling tasks
    response: >
      Machine learning on single-cell perturb-seq, protein-protein interaction profiling (SEC-MS),
      and subcellular protein localization imaging to build cell maps and predict gene/protein function.
addressing_gaps:
  - name: Gap addressed
    response: Lack of standardized, AI-ready, multimodal datasets with rich provenance to map human cell architecture across disease-relevant cell lines.
creators:
  - name: CM4AI Consortium
    principal_investigator:
      id: "person:trey_ideker"
      name: Trey Ideker
      affiliation:
        - id: org:ucsd
          name: University of California San Diego
    affiliation:
      id: "org:cm4ai"
      name: Cell Maps for Artificial Intelligence (CM4AI)
funders:
  - name: NIH Bridge2AI Award
    grantor:
      id: "org:nih"
      name: National Institutes of Health
    grant:
      name: Bridge2AI CM4AI
      grant_number: 1OT2OD032742-01
instances:
  - name: CRISPRi perturb-seq in KOLF2.1J iPSCs
    representation: Single-cell RNA sequencing following genome-scale CRISPRi perturbations.
    instance_type: Cells and gene perturbations.
    data_type: Raw sequence reads and processed AI-ready RO-Crate metadata.
    counts: 11739
    label: Transcriptional and fitness phenotypes associated with targeted genes.
  - name: Protein-protein interaction profiling (SEC-MS)
    representation: Size exclusion chromatography-mass spectrometry fractions and profiles.
    instance_type: Protein complexes and fractions across cell types.
    data_type: Mass spectrometry data and RO-Crate metadata.
  - name: Immunofluorescence subcellular imaging (MDA-MB-468)
    representation: Confocal microscopy images with multi-channel immunofluorescence.
    instance_type: Protein localization images under treatment conditions.
    data_type: ZIP archives containing images and RO-Crate metadata.
    counts: 563
sampling_strategies: []
relationships: []
anomalies: []
external_resources:
  - name: External resources
    external_resources:
      - https://cm4ai.org
      - FAIRSCAPE framework (provenance graphs and RO-Crate packaging)
      - PRIDE repository (SEC-MS deposition planned when available)
collection_mechanisms:
  - name: Data collection methods
    description:
      - Genome-scale CRISPRi perturb-seq in undifferentiated KOLF2.1J iPSCs.
      - Size exclusion chromatography-mass spectrometry (SEC-MS) in iPSCs and iPSC-derived NPCs, neurons, cardiomyocytes.
      - Immunofluorescence (ICC-IF) and confocal microscopy in MDA-MB-468 breast cancer cells under vorinostat, paclitaxel, and untreated conditions.
data_collectors:
  - name: Collecting laboratories
    description:
      - Lundberg Lab (Stanford University) for IF imaging.
      - Nevan Krogan Laboratory (UCSF) for SEC-MS.
      - CM4AI consortium sites including UCSD, UCSF, Stanford, UVA, Yale, UAB, SFU, and the Hastings Center.
collection_timeframes:
  - name: Data creation and release timeline
    description:
      - Data creation date: 2025-02-27.
      - Public release: 2025-03-03.
instance_acquisition:
  - name: Acquisition details
    was_directly_observed: Yes (imaging and mass spectrometry measurements).
    was_reported_by_subjects: No.
    was_inferred_derived: >
      Raw measurements are directly observed; RO-Crates may include derived analyses with full provenance.
    was_validated_verified: Yes; validated via phenotypic, protein-interaction, and metabolic tracing assays.
subpopulations:
  - name: Cell types and treatments
    identification:
      - Cell types: undifferentiated KOLF2.1J iPSCs; iPSC-derived NPCs, neurons, cardiomyocytes.
      - Cell line: MDA-MB-468; Treatments: vorinostat, paclitaxel, untreated.
    distribution:
      - Imaging panel includes 563 proteins across treatment conditions.
deidentification:
  - name: Deidentification
    description:
      - Dataset comprises experimental measurements from human cell lines and iPSC-derived cells; no individual-level identifiers are included.
preprocessing_strategies:
  - name: Packaging and provenance
    description:
      - AI-ready packaging in RO-Crate format with provenance graphs using the FAIRSCAPE framework.
raw_sources:
  - name: Raw sequencing availability
    description:
      - Raw RNA sequences are included in the release (see CRISPR Perturbation RNA Sequences - Raw Sequences).
existing_uses:
  - name: Related publications
    description:
      - "Clark T, Parker J, Schaffer L, Obernier K, 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"
      - "Nourreddine S, Doctor Y, Dailamy A, Forget A, 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"
use_repository:
  - name: Dataset landing page
    description:
      - https://doi.org/10.18130/V3/B35XWX
other_tasks:
  - name: Potential additional uses
    description:
      - Benchmarking multimodal integration methods.
      - Protein localization classification and segmentation.
      - Inferring protein complex membership from SEC-MS.
      - Gene function prediction from perturb-seq profiles.
future_use_impacts:
  - name: Considerations for downstream use
    description:
      - Treatment-specific imaging subsets (vorinostat, paclitaxel, untreated) should be considered when training models to avoid confounding by condition.
discouraged_uses: []
distribution_formats:
  - name: Distribution channels and formats
    description:
      - Dataverse web interface (public files) and Data Access API.
      - RO-Crate JSON metadata files for each component dataset.
      - ZIP archives for immunofluorescence image collections.
distribution_dates:
  - name: Public release
    description:
      - "2025-03-03"
license_and_use_terms:
  name: License and 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/
    - Proper citation and attribution to copyright holders and authors are required.
ip_restrictions:
  name: Copyright and IP notes
  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: Dataset maintainers
    description:
      - Point of Contact: Ideker Trey (University of California San Diego).
      - Repository support: University of Virginia Dataverse Support.
updates:
  name: Update plan
  description:
    - Data will be augmented regularly through the end of the project; updates communicated via the Dataverse dataset versioning.
version_access:
  name: Versioning and access to prior versions
  description:
    - Dataset versions are managed by Dataverse; previous versions remain accessible through the repository version history.
subsets:
  - id: subset:crisper_atlas_rocrate
    name: CRISPR Perturbation Cell Atlas RO-Crate metadata
    path: ro-crate-metadata.json
    format: JSON
    media_type: application/json
    md5: cbdb263b1c099396d75e16f00a79a818
    description: >
      Expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J hiPSCs mapping
      transcriptional and fitness phenotypes associated with 11,739 targeted genes.
  - id: subset:crisper_rawseq_rocrate
    name: CRISPR Perturbation RNA Sequences - Raw Sequences RO-Crate metadata
    path: ro-crate-metadata.json
    format: JSON
    media_type: application/json
    md5: 1cafefa32a897998e3e2ba0a29a3ef5c
    description: >
      Raw sequence data from an expressed genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs.
  - id: subset:secms_rocrate
    name: Protein-protein Interaction SEC-MS RO-Crate metadata
    path: ro-crate-metadata.json
    format: JSON
    media_type: application/json
    md5: cb67e7749b15ce87b9042a9feba9d032
    description: >
      SEC-MS dataset generated in undifferentiated KOLF2.1J hiPSCs (Nevan Krogan lab, UCSF). Data will be uploaded to PRIDE when available.
  - id: subset:if_images_paclitaxel_zip
    name: cm4ai-v0.6-beta-if-images-paclitaxel.zip
    path: cm4ai-v0.6-beta-if-images-paclitaxel.zip
    compression: ZIP
    media_type: application/zip
    md5: 9422486c80bc9e1d35b2fbbc72a5f043
    is_subpopulation: "true"
    description: >
      Spatial localization of 563 proteins in MDA-MB-468 cells treated with paclitaxel, imaged by ICC-IF and confocal microscopy (Lundberg Lab, Stanford).
  - id: subset:if_images_untreated_zip
    name: cm4ai-v0.6-beta-if-images-untreated.zip
    path: cm4ai-v0.6-beta-if-images-untreated.zip
    compression: ZIP
    media_type: application/zip
    md5: 0b4d129f5fbc3bb7f7ea564cd032cef7
    is_subpopulation: "true"
    description: >
      Spatial localization of 563 proteins in untreated MDA-MB-468 cells, imaged by ICC-IF and confocal microscopy (Lundberg Lab, Stanford).
  - id: subset:if_images_vorinostat_zip
    name: cm4ai-v0.6-beta-if-images-vorinostat.zip
    path: cm4ai-v0.6-beta-if-images-vorinostat.zip
    compression: ZIP
    media_type: application/zip
    md5: ac577109a41a9806978461157b777d52
    is_subpopulation: "true"
    description: >
      Spatial localization of 563 proteins in MDA-MB-468 cells treated with vorinostat, imaged by ICC-IF and confocal microscopy (Lundberg Lab, Stanford).