# CRISPR Perturbation Cell Atlas

Datasheet for Dataset

    creators: &id001
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      principal_investigator:
        id: https://orcid.org/0000-0002-1708-8454
        name: Ideker T
    - affiliation:
        id: University of California San Francisco
        name: University of California San Francisco
      principal_investigator:
        id: https://orcid.org/0000-0003-4902-337X
        name: Krogan N
    - affiliation:
        id: Stanford University
        name: Stanford University
      principal_investigator:
        id: https://orcid.org/0000-0001-7034-0850
        name: Lundberg E
    - affiliation:
        id: University of Virginia
        name: University of Virginia
      author:
        id: https://orcid.org/0000-0003-4060-7360
        name: Clark T
    - affiliation:
        id: University of California, San Diego
        name: University of California, San Diego
      author:
        id: https://orcid.org/0000-0003-4535-3486
        name: Parker J
    - affiliation:
        id: University of Virginia
        name: University of Virginia
      author:
        id: https://orcid.org/0000-0003-4647-3877
        name: Al Manir S
    - affiliation:
        id: KTH Royal Institute of Technology
        name: KTH Royal Institute of Technology
      author:
        id: ''
        name: Axelsson U
    - affiliation:
        id: Stanford University
        name: Stanford University
      author:
        id: https://orcid.org/0000-0002-4180-422X
        name: Ballllosero Navarro F
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: ''
        name: Chinn B
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0001-9998-705X
        name: Churas CP
    - affiliation:
        id: University of California, San Diego
        name: University of California, San Diego
      author:
        id: https://orcid.org/0000-0002-6711-8260
        name: Dailamy A
    - affiliation:
        id: University of California, San Diego
        name: University of California, San Diego
      author:
        id: https://orcid.org/0009-0009-0483-7506
        name: Doctor Y
    - affiliation:
        id: KTH - Royal Institute of Technology
        name: KTH - Royal Institute of Technology
      author:
        id: ''
        name: Fall J
    - affiliation:
        id: University of California San Francisco
        name: University of California San Francisco
      author:
        id: https://orcid.org/0000-0003-0223-0312
        name: Forget A
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0002-6311-3526
        name: Gao J
    - affiliation:
        id: Stanford University
        name: Stanford University
      author:
        id: https://orcid.org/0000-0002-4650-9094
        name: Hansen JN
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0002-1571-8029
        name: Hu M
    - affiliation:
        id: KTH - Royal Institute of Technology
        name: KTH - Royal Institute of Technology
      author:
        id: ''
        name: Johannesson A
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: ''
        name: Khaliq H
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0003-0917-355X
        name: Lee YH
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0001-7252-8638
        name: Lenkiewicz J
    - affiliation:
        id: University of Virginia
        name: University of Virginia
      author:
        id: https://orcid.org/0000-0003-0384-8499
        name: Levinson MA
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: 0000-0003-3960-420X
        name: Marquez C
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0003-2404-3040
        name: Metallo C
    - affiliation:
        id: University of California San Francisco
        name: University of California San Francisco
      author:
        id: ''
        name: Muralidharan M
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0003-3881-7588
        name: Nourreddine S
    - affiliation:
        id: University of Virginia
        name: University of Virginia
      author:
        id: https://orcid.org/0000-0002-1103-3882
        name: Niestroy J
    - affiliation:
        id: University of California San Francisco
        name: University of California San Francisco
      author:
        id: https://orcid.org/0000-0002-4025-1299
        name: Obernier K
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: ''
        name: Pan E
    - affiliation:
        id: University of California San Francisco
        name: University of California San Francisco
      author:
        id: ''
        name: Polacco B
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0002-1471-9513
        name: Pratt D
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0009-0005-4217-2745
        name: Qian G
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0001-6339-9141
        name: Schaffer L
    - affiliation:
        id: KTH Royal Institute of Technology
        name: KTH Royal Institute of Technology
      author:
        id: https://orcid.org/0000-0003-3361-3797
        name: Sigaeva A
    - affiliation:
        id: University of Alabama at Birmingham
        name: University of Alabama at Birmingham
      author:
        id: https://orcid.org/0000-0001-6730-2773
        name: Thaker S
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: ''
        name: Zhang Y
    - affiliation:
        id: Simon Fraser University
        name: Simon Fraser University
      author:
        id: https://orcid.org/0000-0002-8965-8153
        name: "B\xE9lisle-Pipon JC"
    - affiliation:
        id: Yale University
        name: Yale University
      author:
        id: https://orcid.org/0000-0001-8179-1796
        name: Brandt C
    - affiliation:
        id: The University of Alabama at Birmingham
        name: The University of Alabama at Birmingham
      author:
        id: https://orcid.org/0000-0002-6112-415X
        name: Chen JY
    - affiliation:
        id: University of Texas at Austin
        name: University of Texas at Austin
      author:
        id: https://orcid.org/0000-0003-2567-2009
        name: Ding Y
    - affiliation:
        id: Yale University
        name: Yale University
      author:
        id: https://orcid.org/0000-0003-4664-3143
        name: Fodeh S
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0002-3383-1287
        name: Mali P
    - affiliation:
        id: University of Alabama
        name: University of Alabama
      author:
        id: https://orcid.org/0000-0002-3508-3577
        name: Payne-Foster P
    - affiliation:
        id: University of Virginia
        name: University of Virginia
      author:
        id: https://orcid.org/0000-0002-6644-8284
        name: Ratcliffe S
    - affiliation:
        id: University of Montreal
        name: University of Montreal
      author:
        id: https://orcid.org/0000-0002-7080-8801
        name: Ravitsky V
    - affiliation:
        id: University of California San Diego
        name: University of California San Diego
      author:
        id: https://orcid.org/0000-0003-0435-6197
        name: Sali A
    - affiliation:
        id: Yale University
        name: Yale University
      author:
        id: https://orcid.org/0000-0002-2048-4028
        name: Schulz W
    description: "This dataset represents an expressed genome-scale CRISPRi Perturbation\
      \ Cell Atlas in undifferentiated KOLF2.1J human induced pluripotent stem cells (hiPSCs)\
      \ mapping transcriptional and fitness phenotypes associated with 11,739 targeted\
      \ genes, as part of the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org)\
      \ Functional Genomics Grand Challenge, a component of the U.S. National Institute\
      \ of Health\u2019s (NIH) Bridge2AI program. We validated these findings via phenotypic,\
      \ protein-interaction, and metabolic tracing assays."
    funders: &id002
    - grant:
        grant_number: 1OT2OD032742-01
        id: 1OT2OD032742-01
        name: ''
      grantor:
        id: NIH
        name: National Institutes of Health
    id: https://doi.org/10.18130/V3/B35XWX#crispr-atlas
    issued: '2025-03-03'
    keywords: &id003
    - CRISPR/Cas9
    - perturb-seq
    - iPSC
    - KOLF2.1J
    - scRNAseq
    resources:
    - acquisition_methods: []
      addressing_gaps: []
      anomalies: []
      bytes: 31100
      cleaning_strategies: []
      collection_mechanisms: []
      collection_timeframes: []
      compression: ''
      confidential_elements: []
      conforms_to:
      - RO-Crate
      - FAIRSCAPE
      conforms_to_class: ''
      conforms_to_schema: ''
      content_warnings: []
      created_by:
      - Niestroy, Justin
      created_on: '2025-02-27'
      creators: *id001
      data_collectors: []
      data_protection_impacts: []
      description: "This dataset represents an expressed genome-scale CRISPRi Perturbation\
        \ Cell Atlas in undifferentiated KOLF2.1J human induced pluripotent stem cells\
        \ (hiPSCs) mapping transcriptional and fitness phenotypes associated with 11,739\
        \ targeted genes, as part of the Cell Maps for Artificial Intelligence (CM4AI;\
        \ CM4AI.org) Functional Genomics Grand Challenge, a component of the U.S. National\
        \ Institute of Health\u2019s (NIH) Bridge2AI program. We validated these findings\
        \ via phenotypic, protein-interaction, and metabolic tracing assays."
      dialect: ''
      discouraged_uses: []
      distribution_dates: []
      distribution_formats: []
      doi: https://doi.org/10.18130/V3/B35XWX
      download_url: ''
      encoding: ''
      errata: []
      ethical_reviews: []
      existing_uses: []
      extension_mechanism: ''
      external_resources: []
      format: JSON
      funders: *id002
      future_use_impacts: []
      hash: ''
      id: https://doi.org/10.18130/V3/B35XWX#crispr-atlas
      instances: []
      ip_restrictions: ''
      is_deidentified:
        description: []
        identifiable_elements_present: ''
      is_tabular: ''
      issued: '2025-03-03'
      keywords: *id003
      labeling_strategies: []
      language: ''
      last_updated_on: '2025-02-27'
      license: https://creativecommons.org/licenses/by-nc-sa/4.0/
      license_and_use_terms:
      - description: Dataset licensed for reuse under Creative Commons Attribution-NonCommercial-ShareAlike
          4.0 International license. Attribution is required to the copyright holders
          and the authors.
      maintainers: []
      md5: cbd...818
      media_type: ''
      modified_by: []
      other_tasks: []
      page: ''
      path: CRISPR Perturbation Cell Atlas/ro-crate-metadata.json
      preprocessing_strategies: []
      publisher: University of Virginia Dataverse
      purposes:
      - response: To provide AI-ready datasets for the Cell Maps for Artificial Intelligence
          (CM4AI) Functional Genomics Grand Challenge, a part of the NIH Bridge2AI program.
      raw_sources: []
      regulatory_restrictions: ''
      retention_limit: ''
      sampling_strategies: []
      sensitive_elements: []
      sha256: ''
      status: ''
      subpopulations: []
      subsets: []
      tasks: []
      title: CRISPR Perturbation Cell Atlas
      updates: []
      use_repository: []
      version: '1.4'
      version_access: []
      was_derived_from: []
    - acquisition_methods: []
      addressing_gaps: []
      anomalies: []
      bytes: 1000100
      cleaning_strategies: []
      collection_mechanisms: []
      collection_timeframes: []
      compression: ''
      confidential_elements: []
      conforms_to:
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      - FAIRSCAPE
      conforms_to_class: ''
      conforms_to_schema: ''
      content_warnings: []
      created_by:
      - Niestroy, Justin
      created_on: '2025-02-27'
      creators:
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        principal_investigator:
          id: https://orcid.org/0000-0002-1708-8454
          name: Ideker T
      - affiliation:
          id: University of California San Francisco
          name: University of California San Francisco
        principal_investigator:
          id: https://orcid.org/0000-0003-4902-337X
          name: Krogan N
      - affiliation:
          id: Stanford University
          name: Stanford University
        principal_investigator:
          id: https://orcid.org/0000-0001-7034-0850
          name: Lundberg E
      - affiliation:
          id: University of Virginia
          name: University of Virginia
        author:
          id: https://orcid.org/0000-0003-4060-7360
          name: Clark T
      - affiliation:
          id: University of California, San Diego
          name: University of California, San Diego
        author:
          id: https://orcid.org/0000-0003-4535-3486
          name: Parker J
      - affiliation:
          id: University of Virginia
          name: University of Virginia
        author:
          id: https://orcid.org/0000-0003-4647-3877
          name: Al Manir S
      - affiliation:
          id: KTH Royal Institute of Technology
          name: KTH Royal Institute of Technology
        author:
          id: ''
          name: Axelsson U
      - affiliation:
          id: Stanford University
          name: Stanford University
        author:
          id: https://orcid.org/0000-0002-4180-422X
          name: Ballllosero Navarro F
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: ''
          name: Chinn B
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0001-9998-705X
          name: Churas CP
      - affiliation:
          id: University of California, San Diego
          name: University of California, San Diego
        author:
          id: https://orcid.org/0000-0002-6711-8260
          name: Dailamy A
      - affiliation:
          id: University of California, San Diego
          name: University of California, San Diego
        author:
          id: https://orcid.org/0009-0009-0483-7506
          name: Doctor Y
      - affiliation:
          id: KTH - Royal Institute of Technology
          name: KTH - Royal Institute of Technology
        author:
          id: ''
          name: Fall J
      - affiliation:
          id: University of California San Francisco
          name: University of California San Francisco
        author:
          id: https://orcid.org/0000-0003-0223-0312
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      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0002-6311-3526
          name: Gao J
      - affiliation:
          id: Stanford University
          name: Stanford University
        author:
          id: https://orcid.org/0000-0002-4650-9094
          name: Hansen JN
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0002-1571-8029
          name: Hu M
      - affiliation:
          id: KTH - Royal Institute of Technology
          name: KTH - Royal Institute of Technology
        author:
          id: ''
          name: Johannesson A
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: ''
          name: Khaliq H
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0003-0917-355X
          name: Lee YH
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0001-7252-8638
          name: Lenkiewicz J
      - affiliation:
          id: University of Virginia
          name: University of Virginia
        author:
          id: https://orcid.org/0000-0003-0384-8499
          name: Levinson MA
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: 0000-0003-3960-420X
          name: Marquez C
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0003-2404-3040
          name: Metallo C
      - affiliation:
          id: University of California San Francisco
          name: University of California San Francisco
        author:
          id: ''
          name: Muralidharan M
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0003-3881-7588
          name: Nourreddine S
      - affiliation:
          id: University of Virginia
          name: University of Virginia
        author:
          id: https://orcid.org/0000-0002-1103-3882
          name: Niestroy J
      - affiliation:
          id: University of California San Francisco
          name: University of California San Francisco
        author:
          id: https://orcid.org/0000-0002-4025-1299
          name: Obernier K
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: ''
          name: Pan E
      - affiliation:
          id: University of California San Francisco
          name: University of California San Francisco
        author:
          id: ''
          name: Polacco B
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0002-1471-9513
          name: Pratt D
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0009-0005-4217-2745
          name: Qian G
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0001-6339-9141
          name: Schaffer L
      - affiliation:
          id: KTH Royal Institute of Technology
          name: KTH Royal Institute of Technology
        author:
          id: https://orcid.org/0000-0003-3361-3797
          name: Sigaeva A
      - affiliation:
          id: University of Alabama at Birmingham
          name: University of Alabama at Birmingham
        author:
          id: https://orcid.org/0000-0001-6730-2773
          name: Thaker S
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: ''
          name: Zhang Y
      - affiliation:
          id: Simon Fraser University
          name: Simon Fraser University
        author:
          id: https://orcid.org/0000-0002-8965-8153
          name: "B\xE9lisle-Pipon JC"
      - affiliation:
          id: Yale University
          name: Yale University
        author:
          id: https://orcid.org/0000-0001-8179-1796
          name: Brandt C
      - affiliation:
          id: The University of Alabama at Birmingham
          name: The University of Alabama at Birmingham
        author:
          id: https://orcid.org/0000-0002-6112-415X
          name: Chen JY
      - affiliation:
          id: University of Texas at Austin
          name: University of Texas at Austin
        author:
          id: https://orcid.org/0000-0003-2567-2009
          name: Ding Y
      - affiliation:
          id: Yale University
          name: Yale University
        author:
          id: https://orcid.org/0000-0003-4664-3143
          name: Fodeh S
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0002-3383-1287
          name: Mali P
      - affiliation:
          id: University of Alabama
          name: University of Alabama
        author:
          id: https://orcid.org/0000-0002-3508-3577
          name: Payne-Foster P
      - affiliation:
          id: University of Virginia
          name: University of Virginia
        author:
          id: https://orcid.org/0000-0002-6644-8284
          name: Ratcliffe S
      - affiliation:
          id: University of Montreal
          name: University of Montreal
        author:
          id: https://orcid.org/0000-0002-7080-8801
          name: Ravitsky V
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        author:
          id: https://orcid.org/0000-0003-0435-6197
          name: Sali A
      - affiliation:
          id: Yale University
          name: Yale University
        author:
          id: https://orcid.org/0000-0002-2048-4028
          name: Schulz W
      data_collectors: []
      data_protection_impacts: []
      description: "This dataset represents raw sequence data from an expressed genome-scale\
        \ CRISPRi Perturbation Cell Atlas in KOLF2.1J human induced pluripotent stem cells\
        \ (hiPSCs) mapping transcriptional and fitness phenotypes associated with 11,739\
        \ targeted genes, as part of the Cell Maps for Artificial Intelligence (CM4AI;\
        \ CM4AI.org) Functional Genomics Grand Challenge, a component of the U.S. National\
        \ Institute of Health\u2019s (NIH) Bridge2AI program."
      dialect: ''
      discouraged_uses: []
      distribution_dates: []
      distribution_formats: []
      doi: https://doi.org/10.18130/V3/B35XWX
      download_url: ''
      encoding: ''
      errata: []
      ethical_reviews: []
      existing_uses: []
      extension_mechanism: ''
      external_resources: []
      format: JSON
      funders:
      - grant:
          grant_number: 1OT2OD032742-01
          id: 1OT2OD032742-01
          name: ''
        grantor:
          id: NIH
          name: National Institutes of Health
      future_use_impacts: []
      hash: ''
      id: https://doi.org/10.18130/V3/B35XWX#crispr-raw
      instances: []
      ip_restrictions: ''
      is_deidentified:
        description: []
        identifiable_elements_present: ''
      is_tabular: ''
      issued: '2025-03-03'
      keywords:
      - CRISPR/Cas9
      - perturb-seq
      - iPSC
      - KOLF2.1J
      - scRNAseq
      labeling_strategies: []
      language: ''
      last_updated_on: '2025-02-27'
      license: https://creativecommons.org/licenses/by-nc-sa/4.0/
      license_and_use_terms:
      - description: Dataset licensed for reuse under Creative Commons Attribution-NonCommercial-ShareAlike
          4.0 International license. Attribution is required to the copyright holders
          and the authors.
      maintainers: []
      md5: 1ca...f5c
      media_type: ''
      modified_by: []
      other_tasks: []
      page: ''
      path: CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json
      preprocessing_strategies: []
      publisher: University of Virginia Dataverse
      purposes:
      - response: To provide AI-ready datasets for the Cell Maps for Artificial Intelligence
          (CM4AI) Functional Genomics Grand Challenge, a part of the NIH Bridge2AI program.
      raw_sources: []
      regulatory_restrictions: ''
      retention_limit: ''
      sampling_strategies: []
      sensitive_elements: []
      sha256: ''
      status: ''
      subpopulations: []
      subsets: []
      tasks: []
      title: CRISPR Perturbation RNA Sequences - Raw Sequences
      updates: []
      use_repository: []
      version: '1.4'
      version_access: []
      was_derived_from: []
    - acquisition_methods: []
      addressing_gaps: []
      anomalies: []
      bytes: 2791728742
      cleaning_strategies: []
      collection_mechanisms: []
      collection_timeframes: []
      compression: ZIP
      confidential_elements: []
      conforms_to:
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      - FAIRSCAPE
      conforms_to_class: ''
      conforms_to_schema: ''
      content_warnings: []
      created_by:
      - Niestroy, Justin
      created_on: '2025-02-27'
      creators:
      - affiliation:
          id: University of California San Diego
          name: University of California San Diego
        principal_investigator:
          id: https://orcid.org/0000-0002-1708-8454
          name: Ideker T
      - affiliation:
          id: University of California San Francisco
          name: University of California San Francisco
        principal_investigator:
          id: https://orcid.org/0000-0003-4902-337X
          name: Krogan N
      - affiliation:
          id: Stanford University
          name: Stanford University
        principal_investigator:
          id: https://orcid.org/0000-0001-7034-0850
          name: Lundberg E
      - affiliation:
          id: University of Virginia
          name: University of Virginia
        author:
          id: https://orcid.org/0000-0003-4060-7360
          name: Clark T
      - affiliation:
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        author:
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      description: "This dataset was generated by size exclusion chromatography-mass spectroscopy\
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          name: ''
        grantor:
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          name: National Institutes of Health
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      - SEC-MS
      - mass spectroscopy
      - iPSC
      - KOLF2.1J
      labeling_strategies: []
      language: ''
      last_updated_on: '2025-02-27'
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          and the authors.
      maintainers: []
      md5: cb6...032
      media_type: ''
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      regulatory_restrictions: ''
      retention_limit: ''
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      title: Protein-protein Interaction SEC-MS
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      use_repository: []
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      was_derived_from: []
    title: CRISPR Perturbation Cell Atlas
    version: '1.4'

Generated on 2025-08-14 19:52:46