=== YAML Fixing Applied ===
id: "doi:10.18130/V3/F3TD5R"
name: Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
title: Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
description: This dataset is the 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).
language: en
page: "https://doi.org/10.18130/V3/F3TD5R"
doi: "doi:10.18130/V3/F3TD5R"
issued: "2025-07-01"
created_on: "2025-02-27"
publisher: "https://dataverse.lib.virginia.edu"
version: "2.0"
license: CC BY-NC-SA 4.0
keywords:
  - AI
  - artificial intelligence
  - machine learning
  - Bridge2AI
  - CM4AI
  - functional genomics
  - induced pluripotent stem cell
  - iPSC
  - KOLF2.1J
  - neural progenitor cell
  - NPC
  - neuron
  - cardiomyocyte
  - breast cancer
  - MDA-MB-468
  - perturb-seq
  - perturbation sequencing
  - CRISPR/Cas9
  - single-cell RNA sequencing
  - scRNAseq
  - protein-protein interaction
  - size exclusion chromatography
  - SEC-MS
  - mass spectroscopy
  - affinity purification
  - AP-MS
  - protein localization
  - subcellular imaging
  - immunofluorescence
  - confocal microscopy
  - paclitaxel
  - 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
purposes:
  - id: purpose-1
    name: Purpose
    description: AI-ready datasets to support research in functional genomics under the NIH Bridge2AI program.
    response: Create AI-ready multimodal cell maps resources for algorithm development and biomedical discovery (CM4AI).
tasks:
  - id: task-1
    name: Primary intended tasks
    response: AI model training; cellular process analysis; analysis of cell architectural changes and interactions under disease, treatment, or genetic perturbations.
addressing_gaps:
  - id: gap-1
    name: AddressingGap
    response: Provides interim, harmonized AI-ready datasets spanning imaging, proteomics, and perturb-seq for building future computed cell maps.
creators:
  - id: creator-ideker
    name: CM4AI PI - Ideker
    principal_investigator:
      id: person-ideker
      name: Trey Ideker
      description: Point of contact listed for the dataset.
      affiliation:
        - id: org-ucsd
          name: University of California San Diego
    affiliation:
      id: org-ucsd
      name: University of California San Diego
  - id: creator-clark
    name: CM4AI PI - Clark
    principal_investigator:
      id: person-clark
      name: Tim Clark
      affiliation:
        - id: org-uva
          name: University of Virginia
    affiliation:
      id: org-uva
      name: University of Virginia
funders:
  - id: fund-nih-ot2
    name: NIH OT2 Funding
    grantor:
      id: org-nih
      name: National Institutes of Health
    grant:
      id: grant-1OT2OD032742-01
      name: NIH OT2 award
      grant_number: 1OT2OD032742-01
instances:
  - id: inst-perturbseq
    name: Perturb-seq in undifferentiated KOLF2.1J iPSCs
    representation: Single-cell transcriptomic profiles with CRISPRi perturbations (perturb-seq) in KOLF2.1J iPSCs.
    instance_type: Cells and per-cell RNA profiles with perturbation labels.
    data_type: Raw and processed single-cell RNA-seq derived measurements and associated perturbation metadata.
  - id: inst-secms
    name: SEC-MS protein-protein interaction profiles
    representation: Proteomic fractionation and mass spectrometry profiles (size exclusion chromatography mass spectrometry).
    instance_type: Proteins and inferred protein-protein interactions across fractions.
    data_type: Mass spectrometry signal intensities, fractionation profiles, and derived interaction metrics.
  - id: inst-if
    name: Immunofluorescence (IF) imaging in MDA-MB-468 cells
    representation: Microscopy images showing protein localization under treatment and control conditions.
    instance_type: Images per protein target and condition.
    data_type: Confocal microscopy images with multichannel immunofluorescence staining.
sampling_strategies:
  - id: samp-1
    name: SamplingStrategy
    is_sample:
      - yes
    source_data:
      - Commercially available de-identified human cell lines; specific cell types and treatments profiled.
    is_representative:
      - no
    why_not_representative:
      - Derived from selected cell lines and perturbations, not representative of all human biological variation.
collection_mechanisms:
  - id: mech-if
    name: IF imaging collection
    description:
      - Immunofluorescence-based staining (ICC-IF) and confocal microscopy in the Lundberg Lab (Stanford University). Nuclei stained with DAPI (blue), ER with calreticulin antibody (yellow), microtubules with tubulin antibody (red), and protein-of-interest antibody (green).
  - id: mech-secms
    name: SEC-MS collection
    description:
      - Size exclusion chromatography followed by mass spectrometry to profile protein-protein interactions across fractions.
  - id: mech-perturbseq
    name: Perturb-seq collection
    description:
      - CRISPRi-based perturbation combined with single-cell RNA sequencing in undifferentiated KOLF2.1J iPSCs.
acquisition_methods:
  - id: acq-if
    name: Imaging acquisition
    description:
      - Directly observed microscopy images via ICC-IF and confocal imaging.
    was_directly_observed: yes
    was_reported_by_subjects: no
    was_inferred_derived: no
  - id: acq-secms
    name: Proteomics acquisition
    description:
      - Directly observed mass spectrometry measurements following chromatographic fractionation.
    was_directly_observed: yes
    was_reported_by_subjects: no
    was_inferred_derived: no
  - id: acq-perturbseq
    name: Perturb-seq acquisition
    description:
      - Directly observed single-cell RNA counts post CRISPRi perturbations.
    was_directly_observed: yes
    was_reported_by_subjects: no
    was_inferred_derived: no
data_collectors:
  - id: collectors-1
    name: Data collection teams
    description:
      - Stanford University (Lundberg Lab) for IF imaging.
      - University of California San Diego for perturb-seq.
      - University of California San Francisco for proteomics.
collection_timeframes:
  - id: timeframe-1
    name: Collection and release dates
    description:
      - Data creation date: 2025-02-27; initial public release: 2025-07-01 (Version 2.0). Some image archives carry later publication dates as listed in file metadata.
ethical_reviews:
  - id: ethics-1
    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: Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Bélisle-Pipon (jean-christophe_belisle-pipon@sfu.ca).
external_resources:
  - id: ext-sra
    name: Sequence Read Archive (SRA) Data
    external_resources:
      - NCBI BioProject (perturb-seq raw data)
  - id: ext-massive-ipsc
    name: Mass Spectrometry Data (Human iPSCs)
    external_resources:
      - MassIVE Repository (SEC-MS iPSC data)
  - id: ext-massive-cancer
    name: Mass Spectrometry Data (Human Cancer Cells)
    external_resources:
      - MassIVE Repository (SEC-MS cancer cell data)
subpopulations:
  - id: subpops-1
    name: Cell types and conditions
    identification:
      - Undifferentiated KOLF2.1J iPSCs
      - iPSC-derived neural progenitor cells (NPCs)
      - iPSC-derived neurons
      - iPSC-derived cardiomyocytes
      - MDA-MB-468 breast cancer cells (treated with vorinostat, treated with paclitaxel, untreated)
deidentification:
  id: deid-1
  name: Deidentification
  description:
    - De-identified Samples: Yes. Data derived from commercially available de-identified human cell lines; Human Subjects: No.
confidential_elements:
  - id: conf-1
    name: Confidentiality
    description:
      - No confidential patient data; laboratory datasets from de-identified cell lines.
distribution_formats:
  - id: dist-1
    name: Distribution formats
    description:
      - Dataverse-hosted files (HTML, JSON, ZIP archives) and links to external repositories (NCBI SRA, MassIVE).
distribution_dates:
  - id: distdate-1
    name: Initial release
    description:
      - 2025-07-01 (Version 2.0)
  - id: distdate-2
    name: Additional file publications
    description:
      - Some image archives list publication date 2025-10-22 as per file table.
license_and_use_terms:
  id: ltu-1
  name: License and Terms of Use
  description:
    - License: CC BY-NC-SA 4.0. Community norms expect proper citation as shown on the dataset page.
discouraged_uses:
  - id: disuse-1
    name: Prohibited Uses
    description:
      - Not to be used for clinical decision-making or any patient care context without appropriate regulatory oversight and approval.
future_use_impacts:
  - id: future-1
    name: Limitations and potential impacts
    description:
      - Interim release; computed cell maps are not included.
      - Protein sets interrogated across modalities incompletely overlap.
      - Best suited for bioinformatics analyses of individual datasets; domain expertise required.
      - Data derived from selected, commercially available cell lines and may not represent all biological variants in the wider population.
existing_uses:
  - id: use-1
    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
maintainers:
  - id: maint-1
    name: University of Virginia Dataverse
    description:
      - Long-term preservation in the University of Virginia Dataverse supported by institutional funds.
  - id: maint-2
    name: Data Governance Committee
    description:
      - Jillian Parker (jillianparker@health.ucsd.edu)
updates:
  id: updates-1
  name: Maintenance and update plan
  description:
    - Dataset will be regularly updated and augmented through November 2026; updates on a quarterly basis; long-term preservation in UVA Dataverse.
subsets:
  - id: subset-release-datasheet
    name: release-ro-crate-datasheet.html
    title: HTML datasheet summarizing key release information
    description: HTML datasheet summarizing key release information.
    path: release-ro-crate-datasheet.html
    md5: 599c9ece9b88b3ce797b82463b4a1eb4
    media_type: text/html
    issued: "2025-07-01"
  - id: subset-release-rocrate
    name: release-ro-crate-metadata.json
    title: Release RO-Crate with pointers to sub ro-crates
    description: RO-Crate metadata file listing sub-crates for the release.
    path: release-ro-crate-metadata.json
    md5: 99f9e00053bff3020fd9832a3a518bbb
    media_type: application/json
    format: JSON
    issued: "2025-07-01"
  - id: subset-if-paclitaxel-zip
    name: cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    title: IF images - MDA-MB-468 treated with paclitaxel
    description: Spatial localization of 464 proteins in MDA-MB-468 cells treated with paclitaxel (ICC-IF confocal microscopy).
    path: Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
    md5: 0d972b80744344ddeede516a0cf6e3d7
    media_type: application/zip
    issued: "2025-10-22"
  - id: subset-if-untreated-zip
    name: cm4ai-ifimages-mda-mb-468-untreated.zip
    title: IF images - MDA-MB-468 untreated
    description: Spatial localization of 464 proteins in untreated MDA-MB-468 cells (ICC-IF confocal microscopy).
    path: Images/cm4ai-ifimages-mda-mb-468-untreated.zip
    md5: a98affcc05429650c6bb3906cd836d55
    media_type: application/zip
    issued: "2025-10-22"
  - id: subset-if-vorinostat-zip
    name: cm4ai-ifimages-mda-mb-468-vorinostat.zip
    title: IF images - MDA-MB-468 treated with vorinostat
    description: Spatial localization of 464 proteins in MDA-MB-468 cells treated with vorinostat (ICC-IF confocal microscopy).
    path: Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip
    md5: ad4e68ccc14b0f3349dad3321e7b81b2
    media_type: application/zip
    issued: "2025-10-22"
  - id: subset-if-paclitaxel-prov
    name: Images-paclitaxel-provenance-graph.html
    title: Provenance graph (paclitaxel images)
    description: HTML provenance graph for paclitaxel image workflow (download to view properly).
    path: Images/paclitaxel/Images-paclitaxel-provenance-graph.html
    md5: e38e63e4c8dfc5808a5ffa2d7829fc38
    media_type: text/html
    issued: "2025-07-01"
  - id: subset-if-untreated-prov
    name: Images-untreated-provenance-graph.html
    title: Provenance graph (untreated images)
    description: HTML provenance graph for untreated image workflow (download to view properly).
    path: Images/untreated/Images-untreated-provenance-graph.html
    md5: 1a3b510f74d3f8647e07c6559ce64ee8
    media_type: text/html
    issued: "2025-07-01"
  - id: subset-if-vorinostat-prov
    name: Images-vorinostat-provenance-graph.html
    title: Provenance graph (vorinostat images)
    description: HTML provenance graph for vorinostat image workflow (download to view properly).
    path: Images/vorinostat/Images-vorinostat-provenance-graph.html
    md5: 58935fe4e254b31d33fed019f24c7668
    media_type: text/html
    issued: "2025-07-01"
  - id: subset-ms-cancer-prov
    name: mass-spec-cancer-cells-provenance-graph.html
    title: Provenance graph (mass spec - cancer cells)
    description: HTML provenance graph for cancer cell SEC-MS workflow (download to view properly).
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-provenance-graph.html
    md5: 931ad9b552562024cb84ebe62d1f1838
    media_type: text/html
    issued: "2025-07-01"
  - id: subset-ms-cancer-rocrate
    name: mass-spec-cancer-cells-ro-crate-metadata.json
    title: RO-Crate metadata (mass spec - cancer cells)
    description: RO-Crate metadata for SEC-MS cancer cell sub-crate.
    path: mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json
    md5: 3a7063bb391ea5e05a32ba5da5f4b2f8
    media_type: application/json
    format: JSON
    issued: "2025-07-01"
is_deidentified:
  id: isdeid
  name: Is Deidentified
  description:
    - Yes — samples are de-identified cell lines; no human subjects.
is_tabular: "no"