# D4D_-_CM4AI_Dataverse_v3 - Data Sheet

Generated using Bridge2AI Data Sheets Schema

This report shows data from a text file following the Bridge2AI Data Sheets Schema.

Schema ID: `https://w3id.org/bridge2ai/data-sheets-schema`

## Collection

### DatasetCollection

resources:

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## Metadata

### DatasetCollection_resources

id: https://doi.org/10.18130/V3/B35XWX#crispr-atlas
title: CRISPR Perturbation Cell Atlas
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’s (NIH) Bridge2AI program. We validated these findings via phenotypic, protein-interaction, and metabolic tracing assays.
creators:

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        "principal_investigator": {
          "id": "https://orcid.org/0000-0002-1708-8454",
          "name": "Ideker T"
        },
        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
      },
      {
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          "id": "https://orcid.org/0000-0003-4902-337X",
          "name": "Krogan N"
        },
        "affiliation": {
          "id": "University of California San Francisco",
          "name": "University of California San Francisco"
        }
      },
      {
        "principal_investigator": {
          "id": "https://orcid.org/0000-0001-7034-0850",
          "name": "Lundberg E"
        },
        "affiliation": {
          "id": "Stanford University",
          "name": "Stanford University"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0003-4060-7360",
          "name": "Clark T"
        },
        "affiliation": {
          "id": "University of Virginia",
          "name": "University of Virginia"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0003-4535-3486",
          "name": "Parker J"
        },
        "affiliation": {
          "id": "University of California, San Diego",
          "name": "University of California, San Diego"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0003-4647-3877",
          "name": "Al Manir S"
        },
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          "id": "University of Virginia",
          "name": "University of Virginia"
        }
      },
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          "id": "",
          "name": "Axelsson U"
        },
        "affiliation": {
          "id": "KTH Royal Institute of Technology",
          "name": "KTH Royal Institute of Technology"
        }
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          "id": "https://orcid.org/0000-0002-4180-422X",
          "name": "Ballllosero Navarro F"
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        "affiliation": {
          "id": "Stanford University",
          "name": "Stanford University"
        }
      },
      {
        "author": {
          "id": "",
          "name": "Chinn B"
        },
        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
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      {
        "author": {
          "id": "https://orcid.org/0000-0001-9998-705X",
          "name": "Churas CP"
        },
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          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
      },
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        "author": {
          "id": "https://orcid.org/0000-0002-6711-8260",
          "name": "Dailamy A"
        },
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          "id": "University of California, San Diego",
          "name": "University of California, San Diego"
        }
      },
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        "author": {
          "id": "https://orcid.org/0009-0009-0483-7506",
          "name": "Doctor Y"
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        "affiliation": {
          "id": "University of California, San Diego",
          "name": "University of California, San Diego"
        }
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          "id": "",
          "name": "Fall J"
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        "affiliation": {
          "id": "KTH - Royal Institute of Technology",
          "name": "KTH - Royal Institute of Technology"
        }
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        "author": {
          "id": "https://orcid.org/0000-0003-0223-0312",
          "name": "Forget A"
        },
        "affiliation": {
          "id": "University of California San Francisco",
          "name": "University of California San Francisco"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0002-6311-3526",
          "name": "Gao J"
        },
        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0002-4650-9094",
          "name": "Hansen JN"
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        "affiliation": {
          "id": "Stanford University",
          "name": "Stanford University"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0002-1571-8029",
          "name": "Hu M"
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          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
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      {
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          "id": "",
          "name": "Johannesson A"
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          "name": "KTH - Royal Institute of Technology"
        }
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      {
        "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 California San Diego",
          "name": "University of California San Diego"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0003-0384-8499",
          "name": "Levinson MA"
        },
        "affiliation": {
          "id": "University of Virginia",
          "name": "University of Virginia"
        }
      },
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        "author": {
          "id": "0000-0003-3960-420X",
          "name": "Marquez C"
        },
        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
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        "author": {
          "id": "https://orcid.org/0000-0003-2404-3040",
          "name": "Metallo C"
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        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
      },
      {
        "author": {
          "id": "",
          "name": "Muralidharan M"
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        "affiliation": {
          "id": "University of California San Francisco",
          "name": "University of California San Francisco"
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        "author": {
          "id": "https://orcid.org/0000-0003-3881-7588",
          "name": "Nourreddine S"
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          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
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      {
        "author": {
          "id": "https://orcid.org/0000-0002-1103-3882",
          "name": "Niestroy J"
        },
        "affiliation": {
          "id": "University of Virginia",
          "name": "University of Virginia"
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        "author": {
          "id": "https://orcid.org/0000-0002-4025-1299",
          "name": "Obernier K"
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        "affiliation": {
          "id": "University of California San Francisco",
          "name": "University of California San Francisco"
        }
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      {
        "author": {
          "id": "",
          "name": "Pan E"
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        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
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          "id": "",
          "name": "Polacco B"
        },
        "affiliation": {
          "id": "University of California San Francisco",
          "name": "University of California San Francisco"
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      {
        "author": {
          "id": "https://orcid.org/0000-0002-1471-9513",
          "name": "Pratt D"
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        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
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        "author": {
          "id": "https://orcid.org/0009-0005-4217-2745",
          "name": "Qian G"
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          "id": "University of California San Diego",
          "name": "University of California San Diego"
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      {
        "author": {
          "id": "https://orcid.org/0000-0001-6339-9141",
          "name": "Schaffer L"
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        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
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      {
        "author": {
          "id": "https://orcid.org/0000-0003-3361-3797",
          "name": "Sigaeva A"
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        "affiliation": {
          "id": "KTH Royal Institute of Technology",
          "name": "KTH Royal Institute of Technology"
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      {
        "author": {
          "id": "https://orcid.org/0000-0001-6730-2773",
          "name": "Thaker S"
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        "affiliation": {
          "id": "University of Alabama at Birmingham",
          "name": "University of Alabama at Birmingham"
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        "author": {
          "id": "",
          "name": "Zhang Y"
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        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
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        "author": {
          "id": "https://orcid.org/0000-0002-8965-8153",
          "name": "B\u00e9lisle-Pipon JC"
        },
        "affiliation": {
          "id": "Simon Fraser University",
          "name": "Simon Fraser University"
        }
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        "author": {
          "id": "https://orcid.org/0000-0001-8179-1796",
          "name": "Brandt C"
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        "affiliation": {
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          "name": "Yale University"
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        "author": {
          "id": "https://orcid.org/0000-0002-6112-415X",
          "name": "Chen JY"
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        "affiliation": {
          "id": "The University of Alabama at Birmingham",
          "name": "The University of Alabama at Birmingham"
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        "author": {
          "id": "https://orcid.org/0000-0003-2567-2009",
          "name": "Ding Y"
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        "affiliation": {
          "id": "University of Texas at Austin",
          "name": "University of Texas at Austin"
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      {
        "author": {
          "id": "https://orcid.org/0000-0003-4664-3143",
          "name": "Fodeh S"
        },
        "affiliation": {
          "id": "Yale University",
          "name": "Yale University"
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        "author": {
          "id": "https://orcid.org/0000-0002-3383-1287",
          "name": "Mali P"
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          "id": "University of California San Diego",
          "name": "University of California San Diego"
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        "author": {
          "id": "https://orcid.org/0000-0002-3508-3577",
          "name": "Payne-Foster P"
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        "affiliation": {
          "id": "University of Alabama",
          "name": "University of Alabama"
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      {
        "author": {
          "id": "https://orcid.org/0000-0002-6644-8284",
          "name": "Ratcliffe S"
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        "affiliation": {
          "id": "University of Virginia",
          "name": "University of Virginia"
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      },
      {
        "author": {
          "id": "https://orcid.org/0000-0002-7080-8801",
          "name": "Ravitsky V"
        },
        "affiliation": {
          "id": "University of Montreal",
          "name": "University of Montreal"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0003-0435-6197",
          "name": "Sali A"
        },
        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0002-2048-4028",
          "name": "Schulz W"
        },
        "affiliation": {
          "id": "Yale University",
          "name": "Yale University"
        }
      }
    ]

funders:

    [
      {
        "grantor": {
          "id": "NIH",
          "name": "National Institutes of Health"
        },
        "grant": {
          "id": "1OT2OD032742-01",
          "name": "",
          "grant_number": "1OT2OD032742-01"
        }
      }
    ]

issued: 2025-03-03
version: 1.4
keywords:

    [
      "CRISPR/Cas9",
      "perturb-seq",
      "iPSC",
      "KOLF2.1J",
      "scRNAseq"
    ]

license: https://creativecommons.org/licenses/by-nc-sa/4.0/
doi: https://doi.org/10.18130/V3/B35XWX
download_url:
bytes: 31100
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."
      }
    ]

instances:

    []

subpopulations:

    []

collection_timeframes:

    []

conforms_to:

    [
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    ]

preprocessing_strategies:

    []

cleaning_strategies:

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    {
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      "description": []
    }

sensitive_elements:

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existing_uses:

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discouraged_uses:

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updates:

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version_access:

    []

distribution_formats:

    []

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."
      }
    ]

acquisition_methods:

    []

compression:
conforms_to_class:
conforms_to_schema:
created_by:

    [
      "Niestroy, Justin"
    ]

created_on: 2025-02-27
language:
last_updated_on: 2025-02-27
modified_by:

    []

page:
publisher: University of Virginia Dataverse
status:
was_derived_from:

    []

dialect:
encoding:
format: JSON
hash:
md5: cbd...818
media_type:
path: CRISPR Perturbation Cell Atlas/ro-crate-metadata.json
sha256:
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content_warnings:

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sampling_strategies:

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data_collectors:

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labeling_strategies:

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raw_sources:

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use_repository:

    []

other_tasks:

    []

future_use_impacts:

    []

distribution_dates:

    []

ip_restrictions:
regulatory_restrictions:
maintainers:

    []

errata:

    []

retention_limit:
extension_mechanism:
is_tabular:
id: https://doi.org/10.18130/V3/B35XWX#crispr-raw
title: CRISPR Perturbation RNA Sequences - Raw Sequences
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’s (NIH) Bridge2AI program.
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    [
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        "principal_investigator": {
          "id": "https://orcid.org/0000-0002-1708-8454",
          "name": "Ideker T"
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          "name": "University of California San Diego"
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          "name": "Krogan N"
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        "affiliation": {
          "id": "University of California San Francisco",
          "name": "University of California San Francisco"
        }
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      {
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          "name": "Lundberg E"
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          "id": "Stanford University",
          "name": "Stanford University"
        }
      },
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        "author": {
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          "name": "University of California, San Diego"
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          "name": "University of Virginia"
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          "name": "KTH Royal Institute of Technology"
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          "name": "University of California San Diego"
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          "name": "University of California, San Diego"
        }
      },
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          "name": "Fall J"
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          "name": "University of California San Francisco"
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      },
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          "name": "Gao J"
        },
        "affiliation": {
          "id": "University of California San Diego",
          "name": "University of California San Diego"
        }
      },
      {
        "author": {
          "id": "https://orcid.org/0000-0002-4650-9094",
          "name": "Hansen JN"
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          "name": "Stanford University"
        }
      },
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          "name": "Muralidharan M"
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          "name": "University of California San Francisco"
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          "name": "University of California San Diego"
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issued: 2025-03-03
version: 1.4
keywords:

    [
      "protein localization",
      "subcellular imaging",
      "breast cancer",
      "MDA-MB-468"
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license: https://creativecommons.org/licenses/by-nc-sa/4.0/
doi: https://doi.org/10.18130/V3/B35XWX
download_url:
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id: https://doi.org/10.18130/V3/B35XWX#images-vorinostat
title: Protein Localization Subcellular Images - Vorinostat
description: This data set displays the spatial localization of 563 proteins of interest in cells of the breast cancer cell line MDA-MB-468 treated with vorinostat as imaged by immunofluorescence-based staining (ICC-IF) and confocal microscopy in the Lundberg Lab at Stanford University, as part of the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org) project. Nuclei were stained with DAPI (blue channel); endoplasmic reticulum with a calreticulin antibody (yellow channel); microtubules with tubulin antibody (red channel); and antibody against protein of interest (green channel).
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Generated on: 2025-07-09 23:12:31