# CRISPR Perturbation Cell Atlas

Datasheet for Dataset - Human Readable Format

🎯

## Motivation

Why was the dataset created?

Dataset Resource
Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | - | 1OT2OD032742-01

Dataset Resource
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.

Dataset Resource
Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | - | 1OT2OD032742-01

Dataset Resource
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.

Dataset Resource
Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | - | 1OT2OD032742-01

Dataset Resource
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.

Dataset Resource
Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | - | 1OT2OD032742-01

Dataset Resource
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.

Dataset Resource
Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | - | 1OT2OD032742-01

Dataset Resource
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.

Dataset Resource
Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | - | 1OT2OD032742-01

Dataset Resource
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.

📊

## Composition

What do the instances represent?

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🔍

## Collection Process

How was the data acquired?

Dataset Resource
ID *
https://doi.org/10.18130/V3/B35XWX#crispr-atlas
Dataset Resource
Title
CRISPR Perturbation Cell Atlas
Dataset Resource
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.
Dataset Resource
Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Ideker T | 0000-0002-1708-8454 | University of California San Diego
Principal Investigator | Krogan N | 0000-0003-4902-337X | University of California San Francisco
Principal Investigator | Lundberg E | 0000-0001-7034-0850 | Stanford University
Author | Clark T | 0000-0003-4060-7360 | University of Virginia
Author | Parker J | 0000-0003-4535-3486 | University of California, San Diego
Author | Al Manir S | 0000-0003-4647-3877 | University of Virginia
Author | Axelsson U | - | KTH Royal Institute of Technology
Author | Ballllosero Navarro F | 0000-0002-4180-422X | Stanford University
Author | Chinn B | - | University of California San Diego
Author | Churas CP | 0000-0001-9998-705X | University of California San Diego
Author | Dailamy A | 0000-0002-6711-8260 | University of California, San Diego
Author | Doctor Y | 0009-0009-0483-7506 | University of California, San Diego
Author | Fall J | - | KTH - Royal Institute of Technology
Author | Forget A | 0000-0003-0223-0312 | University of California San Francisco
Author | Gao J | 0000-0002-6311-3526 | University of California San Diego
Author | Hansen JN | 0000-0002-4650-9094 | Stanford University
Author | Hu M | 0000-0002-1571-8029 | University of California San Diego
Author | Johannesson A | - | KTH - Royal Institute of Technology
Author | Khaliq H | - | University of California San Diego
Author | Lee YH | 0000-0003-0917-355X | University of California San Diego
Author | Lenkiewicz J | 0000-0001-7252-8638 | University of California San Diego
Author | Levinson MA | 0000-0003-0384-8499 | University of Virginia
Author | Marquez C | 0000-0003-3960-420X | University of California San Diego
Author | Metallo C | 0000-0003-2404-3040 | University of California San Diego
Author | Muralidharan M | - | University of California San Francisco
Author | Nourreddine S | 0000-0003-3881-7588 | University of California San Diego
Author | Niestroy J | 0000-0002-1103-3882 | University of Virginia
Author | Obernier K | 0000-0002-4025-1299 | University of California San Francisco
Author | Pan E | - | University of California San Diego
Author | Polacco B | - | University of California San Francisco
Author | Pratt D | 0000-0002-1471-9513 | University of California San Diego
Author | Qian G | 0009-0005-4217-2745 | University of California San Diego
Author | Schaffer L | 0000-0001-6339-9141 | University of California San Diego
Author | Sigaeva A | 0000-0003-3361-3797 | KTH Royal Institute of Technology
Author | Thaker S | 0000-0001-6730-2773 | University of Alabama at Birmingham
Author | Zhang Y | - | University of California San Diego
Author | Bélisle-Pipon JC | 0000-0002-8965-8153 | Simon Fraser University
Author | Brandt C | 0000-0001-8179-1796 | Yale University
Author | Chen JY | 0000-0002-6112-415X | The University of Alabama at Birmingham
Author | Ding Y | 0000-0003-2567-2009 | University of Texas at Austin
Author | Fodeh S | 0000-0003-4664-3143 | Yale University
Author | Mali P | 0000-0002-3383-1287 | University of California San Diego
Author | Payne-Foster P | 0000-0002-3508-3577 | University of Alabama
Author | Ratcliffe S | 0000-0002-6644-8284 | University of Virginia
Author | Ravitsky V | 0000-0002-7080-8801 | University of Montreal
Author | Sali A | 0000-0003-0435-6197 | University of California San Diego
Author | Schulz W | 0000-0002-2048-4028 | Yale University

Dataset Resource
Issued
2025-03-03
Dataset Resource
Keywords

- CRISPR/Cas9
- perturb-seq
- iPSC
- KOLF2.1J
- scRNAseq

Dataset Resource
Collection Timeframes
Dataset Resource
Conforms To

- RO-Crate
- FAIRSCAPE

Dataset Resource
Preprocessing Strategies
Dataset Resource
Cleaning Strategies
Dataset Resource
Is Deidentified

Identifiable Elements Present
Description

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Sensitive Elements
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Acquisition Methods
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Compression
Dataset Resource
Conforms To Class
Dataset Resource
Conforms To Schema
Dataset Resource
Created By

- Niestroy, Justin

Dataset Resource
Created On
2025-02-27
Dataset Resource
Language
Dataset Resource
Modified By
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Page
Dataset Resource
Publisher
University of Virginia Dataverse
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Status
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Was Derived From
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Dialect
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Encoding
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Format
JSON
Dataset Resource
Hash
Dataset Resource
Md5
cbd...818
Dataset Resource
Media Type
Dataset Resource
Path
CRISPR Perturbation Cell Atlas/ro-crate-metadata.json
Dataset Resource
Sha256
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Addressing Gaps
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Subsets
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Anomalies
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External Resources
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Confidential Elements
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Content Warnings
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Collection Mechanisms
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Sampling Strategies
Dataset Resource
Data Collectors
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Ethical Reviews
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Data Protection Impacts
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Labeling Strategies
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Raw Sources
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Ip Restrictions
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Regulatory Restrictions
Dataset Resource
Maintainers
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Errata
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Retention Limit
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Extension Mechanism
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Is Tabular
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ID *
https://doi.org/10.18130/V3/B35XWX#crispr-raw
Dataset Resource
Title
CRISPR Perturbation RNA Sequences - Raw Sequences
Dataset Resource
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.
Dataset Resource
Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Ideker T | 0000-0002-1708-8454 | University of California San Diego
Principal Investigator | Krogan N | 0000-0003-4902-337X | University of California San Francisco
Principal Investigator | Lundberg E | 0000-0001-7034-0850 | Stanford University
Author | Clark T | 0000-0003-4060-7360 | University of Virginia
Author | Parker J | 0000-0003-4535-3486 | University of California, San Diego
Author | Al Manir S | 0000-0003-4647-3877 | University of Virginia
Author | Axelsson U | - | KTH Royal Institute of Technology
Author | Ballllosero Navarro F | 0000-0002-4180-422X | Stanford University
Author | Chinn B | - | University of California San Diego
Author | Churas CP | 0000-0001-9998-705X | University of California San Diego
Author | Dailamy A | 0000-0002-6711-8260 | University of California, San Diego
Author | Doctor Y | 0009-0009-0483-7506 | University of California, San Diego
Author | Fall J | - | KTH - Royal Institute of Technology
Author | Forget A | 0000-0003-0223-0312 | University of California San Francisco
Author | Gao J | 0000-0002-6311-3526 | University of California San Diego
Author | Hansen JN | 0000-0002-4650-9094 | Stanford University
Author | Hu M | 0000-0002-1571-8029 | University of California San Diego
Author | Johannesson A | - | KTH - Royal Institute of Technology
Author | Khaliq H | - | University of California San Diego
Author | Lee YH | 0000-0003-0917-355X | University of California San Diego
Author | Lenkiewicz J | 0000-0001-7252-8638 | University of California San Diego
Author | Levinson MA | 0000-0003-0384-8499 | University of Virginia
Author | Marquez C | 0000-0003-3960-420X | University of California San Diego
Author | Metallo C | 0000-0003-2404-3040 | University of California San Diego
Author | Muralidharan M | - | University of California San Francisco
Author | Nourreddine S | 0000-0003-3881-7588 | University of California San Diego
Author | Niestroy J | 0000-0002-1103-3882 | University of Virginia
Author | Obernier K | 0000-0002-4025-1299 | University of California San Francisco
Author | Pan E | - | University of California San Diego
Author | Polacco B | - | University of California San Francisco
Author | Pratt D | 0000-0002-1471-9513 | University of California San Diego
Author | Qian G | 0009-0005-4217-2745 | University of California San Diego
Author | Schaffer L | 0000-0001-6339-9141 | University of California San Diego
Author | Sigaeva A | 0000-0003-3361-3797 | KTH Royal Institute of Technology
Author | Thaker S | 0000-0001-6730-2773 | University of Alabama at Birmingham
Author | Zhang Y | - | University of California San Diego
Author | Bélisle-Pipon JC | 0000-0002-8965-8153 | Simon Fraser University
Author | Brandt C | 0000-0001-8179-1796 | Yale University
Author | Chen JY | 0000-0002-6112-415X | The University of Alabama at Birmingham
Author | Ding Y | 0000-0003-2567-2009 | University of Texas at Austin
Author | Fodeh S | 0000-0003-4664-3143 | Yale University
Author | Mali P | 0000-0002-3383-1287 | University of California San Diego
Author | Payne-Foster P | 0000-0002-3508-3577 | University of Alabama
Author | Ratcliffe S | 0000-0002-6644-8284 | University of Virginia
Author | Ravitsky V | 0000-0002-7080-8801 | University of Montreal
Author | Sali A | 0000-0003-0435-6197 | University of California San Diego
Author | Schulz W | 0000-0002-2048-4028 | Yale University

Dataset Resource
Issued
2025-03-03
Dataset Resource
Keywords

- CRISPR/Cas9
- perturb-seq
- iPSC
- KOLF2.1J
- scRNAseq

Dataset Resource
Collection Timeframes
Dataset Resource
Conforms To

- RO-Crate
- FAIRSCAPE

Dataset Resource
Preprocessing Strategies
Dataset Resource
Cleaning Strategies
Dataset Resource
Is Deidentified

Identifiable Elements Present
Description

Dataset Resource
Sensitive Elements
Dataset Resource
Acquisition Methods
Dataset Resource
Compression
Dataset Resource
Conforms To Class
Dataset Resource
Conforms To Schema
Dataset Resource
Created By

- Niestroy, Justin

Dataset Resource
Created On
2025-02-27
Dataset Resource
Language
Dataset Resource
Modified By
Dataset Resource
Page
Dataset Resource
Publisher
University of Virginia Dataverse
Dataset Resource
Status
Dataset Resource
Was Derived From
Dataset Resource
Dialect
Dataset Resource
Encoding
Dataset Resource
Format
JSON
Dataset Resource
Hash
Dataset Resource
Md5
1ca...f5c
Dataset Resource
Media Type
Dataset Resource
Path
CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json
Dataset Resource
Sha256
Dataset Resource
Addressing Gaps
Dataset Resource
Subsets
Dataset Resource
Anomalies
Dataset Resource
External Resources
Dataset Resource
Confidential Elements
Dataset Resource
Content Warnings
Dataset Resource
Collection Mechanisms
Dataset Resource
Sampling Strategies
Dataset Resource
Data Collectors
Dataset Resource
Ethical Reviews
Dataset Resource
Data Protection Impacts
Dataset Resource
Labeling Strategies
Dataset Resource
Raw Sources
Dataset Resource
Ip Restrictions
Dataset Resource
Regulatory Restrictions
Dataset Resource
Maintainers
Dataset Resource
Errata
Dataset Resource
Retention Limit
Dataset Resource
Extension Mechanism
Dataset Resource
Is Tabular
Dataset Resource
ID *
https://doi.org/10.18130/V3/B35XWX#images-paclitaxel
Dataset Resource
Title
Protein Localization Subcellular Images - Paclitaxel
Dataset Resource
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 paclitaxel 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).
Dataset Resource
Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Ideker T | 0000-0002-1708-8454 | University of California San Diego
Principal Investigator | Krogan N | 0000-0003-4902-337X | University of California San Francisco
Principal Investigator | Lundberg E | 0000-0001-7034-0850 | Stanford University
Author | Clark T | 0000-0003-4060-7360 | University of Virginia
Author | Parker J | 0000-0003-4535-3486 | University of California, San Diego
Author | Al Manir S | 0000-0003-4647-3877 | University of Virginia
Author | Axelsson U | - | KTH Royal Institute of Technology
Author | Ballllosero Navarro F | 0000-0002-4180-422X | Stanford University
Author | Chinn B | - | University of California San Diego
Author | Churas CP | 0000-0001-9998-705X | University of California San Diego
Author | Dailamy A | 0000-0002-6711-8260 | University of California, San Diego
Author | Doctor Y | 0009-0009-0483-7506 | University of California, San Diego
Author | Fall J | - | KTH - Royal Institute of Technology
Author | Forget A | 0000-0003-0223-0312 | University of California San Francisco
Author | Gao J | 0000-0002-6311-3526 | University of California San Diego
Author | Hansen JN | 0000-0002-4650-9094 | Stanford University
Author | Hu M | 0000-0002-1571-8029 | University of California San Diego
Author | Johannesson A | - | KTH - Royal Institute of Technology
Author | Khaliq H | - | University of California San Diego
Author | Lee YH | 0000-0003-0917-355X | University of California San Diego
Author | Lenkiewicz J | 0000-0001-7252-8638 | University of California San Diego
Author | Levinson MA | 0000-0003-0384-8499 | University of Virginia
Author | Marquez C | 0000-0003-3960-420X | University of California San Diego
Author | Metallo C | 0000-0003-2404-3040 | University of California San Diego
Author | Muralidharan M | - | University of California San Francisco
Author | Nourreddine S | 0000-0003-3881-7588 | University of California San Diego
Author | Niestroy J | 0000-0002-1103-3882 | University of Virginia
Author | Obernier K | 0000-0002-4025-1299 | University of California San Francisco
Author | Pan E | - | University of California San Diego
Author | Polacco B | - | University of California San Francisco
Author | Pratt D | 0000-0002-1471-9513 | University of California San Diego
Author | Qian G | 0009-0005-4217-2745 | University of California San Diego
Author | Schaffer L | 0000-0001-6339-9141 | University of California San Diego
Author | Sigaeva A | 0000-0003-3361-3797 | KTH Royal Institute of Technology
Author | Thaker S | 0000-0001-6730-2773 | University of Alabama at Birmingham
Author | Zhang Y | - | University of California San Diego
Author | Bélisle-Pipon JC | 0000-0002-8965-8153 | Simon Fraser University
Author | Brandt C | 0000-0001-8179-1796 | Yale University
Author | Chen JY | 0000-0002-6112-415X | The University of Alabama at Birmingham
Author | Ding Y | 0000-0003-2567-2009 | University of Texas at Austin
Author | Fodeh S | 0000-0003-4664-3143 | Yale University
Author | Mali P | 0000-0002-3383-1287 | University of California San Diego
Author | Payne-Foster P | 0000-0002-3508-3577 | University of Alabama
Author | Ratcliffe S | 0000-0002-6644-8284 | University of Virginia
Author | Ravitsky V | 0000-0002-7080-8801 | University of Montreal
Author | Sali A | 0000-0003-0435-6197 | University of California San Diego
Author | Schulz W | 0000-0002-2048-4028 | Yale University

Dataset Resource
Issued
2025-03-03
Dataset Resource
Keywords

- protein localization
- subcellular imaging
- breast cancer
- MDA-MB-468
- paclitaxel

Dataset Resource
Collection Timeframes
Dataset Resource
Conforms To

- RO-Crate
- FAIRSCAPE

Dataset Resource
Preprocessing Strategies
Dataset Resource
Cleaning Strategies
Dataset Resource
Is Deidentified

Identifiable Elements Present
Description

Dataset Resource
Sensitive Elements
Dataset Resource
Acquisition Methods
Dataset Resource
Compression
ZIP
Dataset Resource
Conforms To Class
Dataset Resource
Conforms To Schema
Dataset Resource
Created By

- Niestroy, Justin

Dataset Resource
Created On
2025-02-27
Dataset Resource
Language
Dataset Resource
Modified By
Dataset Resource
Page
Dataset Resource
Publisher
University of Virginia Dataverse
Dataset Resource
Status
Dataset Resource
Was Derived From
Dataset Resource
Dialect
Dataset Resource
Encoding
Dataset Resource
Format
ZIP
Dataset Resource
Hash
Dataset Resource
Md5
942...043
Dataset Resource
Media Type
Dataset Resource
Path
Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip
Dataset Resource
Sha256
Dataset Resource
Addressing Gaps
Dataset Resource
Subsets
Dataset Resource
Anomalies
Dataset Resource
External Resources
Dataset Resource
Confidential Elements
Dataset Resource
Content Warnings
Dataset Resource
Collection Mechanisms
Dataset Resource
Sampling Strategies
Dataset Resource
Data Collectors
Dataset Resource
Ethical Reviews
Dataset Resource
Data Protection Impacts
Dataset Resource
Labeling Strategies
Dataset Resource
Raw Sources
Dataset Resource
Ip Restrictions
Dataset Resource
Regulatory Restrictions
Dataset Resource
Maintainers
Dataset Resource
Errata
Dataset Resource
Retention Limit
Dataset Resource
Extension Mechanism
Dataset Resource
Is Tabular
Dataset Resource
ID *
https://doi.org/10.18130/V3/B35XWX#images-untreated
Dataset Resource
Title
Protein Localization Subcellular Images - Untreated
Dataset Resource
Description
This data set displays the spatial localization of 563 proteins of interest in untreated cells of the breast cancer cell line MDA-MB-468 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).
Dataset Resource
Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Ideker T | 0000-0002-1708-8454 | University of California San Diego
Principal Investigator | Krogan N | 0000-0003-4902-337X | University of California San Francisco
Principal Investigator | Lundberg E | 0000-0001-7034-0850 | Stanford University
Author | Clark T | 0000-0003-4060-7360 | University of Virginia
Author | Parker J | 0000-0003-4535-3486 | University of California, San Diego
Author | Al Manir S | 0000-0003-4647-3877 | University of Virginia
Author | Axelsson U | - | KTH Royal Institute of Technology
Author | Ballllosero Navarro F | 0000-0002-4180-422X | Stanford University
Author | Chinn B | - | University of California San Diego
Author | Churas CP | 0000-0001-9998-705X | University of California San Diego
Author | Dailamy A | 0000-0002-6711-8260 | University of California, San Diego
Author | Doctor Y | 0009-0009-0483-7506 | University of California, San Diego
Author | Fall J | - | KTH - Royal Institute of Technology
Author | Forget A | 0000-0003-0223-0312 | University of California San Francisco
Author | Gao J | 0000-0002-6311-3526 | University of California San Diego
Author | Hansen JN | 0000-0002-4650-9094 | Stanford University
Author | Hu M | 0000-0002-1571-8029 | University of California San Diego
Author | Johannesson A | - | KTH - Royal Institute of Technology
Author | Khaliq H | - | University of California San Diego
Author | Lee YH | 0000-0003-0917-355X | University of California San Diego
Author | Lenkiewicz J | 0000-0001-7252-8638 | University of California San Diego
Author | Levinson MA | 0000-0003-0384-8499 | University of Virginia
Author | Marquez C | 0000-0003-3960-420X | University of California San Diego
Author | Metallo C | 0000-0003-2404-3040 | University of California San Diego
Author | Muralidharan M | - | University of California San Francisco
Author | Nourreddine S | 0000-0003-3881-7588 | University of California San Diego
Author | Niestroy J | 0000-0002-1103-3882 | University of Virginia
Author | Obernier K | 0000-0002-4025-1299 | University of California San Francisco
Author | Pan E | - | University of California San Diego
Author | Polacco B | - | University of California San Francisco
Author | Pratt D | 0000-0002-1471-9513 | University of California San Diego
Author | Qian G | 0009-0005-4217-2745 | University of California San Diego
Author | Schaffer L | 0000-0001-6339-9141 | University of California San Diego
Author | Sigaeva A | 0000-0003-3361-3797 | KTH Royal Institute of Technology
Author | Thaker S | 0000-0001-6730-2773 | University of Alabama at Birmingham
Author | Zhang Y | - | University of California San Diego
Author | Bélisle-Pipon JC | 0000-0002-8965-8153 | Simon Fraser University
Author | Brandt C | 0000-0001-8179-1796 | Yale University
Author | Chen JY | 0000-0002-6112-415X | The University of Alabama at Birmingham
Author | Ding Y | 0000-0003-2567-2009 | University of Texas at Austin
Author | Fodeh S | 0000-0003-4664-3143 | Yale University
Author | Mali P | 0000-0002-3383-1287 | University of California San Diego
Author | Payne-Foster P | 0000-0002-3508-3577 | University of Alabama
Author | Ratcliffe S | 0000-0002-6644-8284 | University of Virginia
Author | Ravitsky V | 0000-0002-7080-8801 | University of Montreal
Author | Sali A | 0000-0003-0435-6197 | University of California San Diego
Author | Schulz W | 0000-0002-2048-4028 | Yale University

Dataset Resource
Issued
2025-03-03
Dataset Resource
Keywords

- protein localization
- subcellular imaging
- breast cancer
- MDA-MB-468

Dataset Resource
Collection Timeframes
Dataset Resource
Conforms To

- RO-Crate
- FAIRSCAPE

Dataset Resource
Preprocessing Strategies
Dataset Resource
Cleaning Strategies
Dataset Resource
Is Deidentified

Identifiable Elements Present
Description

Dataset Resource
Sensitive Elements
Dataset Resource
Acquisition Methods
Dataset Resource
Compression
ZIP
Dataset Resource
Conforms To Class
Dataset Resource
Conforms To Schema
Dataset Resource
Created By

- Niestroy, Justin

Dataset Resource
Created On
2025-02-27
Dataset Resource
Language
Dataset Resource
Modified By
Dataset Resource
Page
Dataset Resource
Publisher
University of Virginia Dataverse
Dataset Resource
Status
Dataset Resource
Was Derived From
Dataset Resource
Dialect
Dataset Resource
Encoding
Dataset Resource
Format
ZIP
Dataset Resource
Hash
Dataset Resource
Md5
0b4...ef7
Dataset Resource
Media Type
Dataset Resource
Path
Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip
Dataset Resource
Sha256
Dataset Resource
Addressing Gaps
Dataset Resource
Subsets
Dataset Resource
Anomalies
Dataset Resource
External Resources
Dataset Resource
Confidential Elements
Dataset Resource
Content Warnings
Dataset Resource
Collection Mechanisms
Dataset Resource
Sampling Strategies
Dataset Resource
Data Collectors
Dataset Resource
Ethical Reviews
Dataset Resource
Data Protection Impacts
Dataset Resource
Labeling Strategies
Dataset Resource
Raw Sources
Dataset Resource
Ip Restrictions
Dataset Resource
Regulatory Restrictions
Dataset Resource
Maintainers
Dataset Resource
Errata
Dataset Resource
Retention Limit
Dataset Resource
Extension Mechanism
Dataset Resource
Is Tabular
Dataset Resource
ID *
https://doi.org/10.18130/V3/B35XWX#images-vorinostat
Dataset Resource
Title
Protein Localization Subcellular Images - Vorinostat
Dataset Resource
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).
Dataset Resource
Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Ideker T | 0000-0002-1708-8454 | University of California San Diego
Principal Investigator | Krogan N | 0000-0003-4902-337X | University of California San Francisco
Principal Investigator | Lundberg E | 0000-0001-7034-0850 | Stanford University
Author | Clark T | 0000-0003-4060-7360 | University of Virginia
Author | Parker J | 0000-0003-4535-3486 | University of California, San Diego
Author | Al Manir S | 0000-0003-4647-3877 | University of Virginia
Author | Axelsson U | - | KTH Royal Institute of Technology
Author | Ballllosero Navarro F | 0000-0002-4180-422X | Stanford University
Author | Chinn B | - | University of California San Diego
Author | Churas CP | 0000-0001-9998-705X | University of California San Diego
Author | Dailamy A | 0000-0002-6711-8260 | University of California, San Diego
Author | Doctor Y | 0009-0009-0483-7506 | University of California, San Diego
Author | Fall J | - | KTH - Royal Institute of Technology
Author | Forget A | 0000-0003-0223-0312 | University of California San Francisco
Author | Gao J | 0000-0002-6311-3526 | University of California San Diego
Author | Hansen JN | 0000-0002-4650-9094 | Stanford University
Author | Hu M | 0000-0002-1571-8029 | University of California San Diego
Author | Johannesson A | - | KTH - Royal Institute of Technology
Author | Khaliq H | - | University of California San Diego
Author | Lee YH | 0000-0003-0917-355X | University of California San Diego
Author | Lenkiewicz J | 0000-0001-7252-8638 | University of California San Diego
Author | Levinson MA | 0000-0003-0384-8499 | University of Virginia
Author | Marquez C | 0000-0003-3960-420X | University of California San Diego
Author | Metallo C | 0000-0003-2404-3040 | University of California San Diego
Author | Muralidharan M | - | University of California San Francisco
Author | Nourreddine S | 0000-0003-3881-7588 | University of California San Diego
Author | Niestroy J | 0000-0002-1103-3882 | University of Virginia
Author | Obernier K | 0000-0002-4025-1299 | University of California San Francisco
Author | Pan E | - | University of California San Diego
Author | Polacco B | - | University of California San Francisco
Author | Pratt D | 0000-0002-1471-9513 | University of California San Diego
Author | Qian G | 0009-0005-4217-2745 | University of California San Diego
Author | Schaffer L | 0000-0001-6339-9141 | University of California San Diego
Author | Sigaeva A | 0000-0003-3361-3797 | KTH Royal Institute of Technology
Author | Thaker S | 0000-0001-6730-2773 | University of Alabama at Birmingham
Author | Zhang Y | - | University of California San Diego
Author | Bélisle-Pipon JC | 0000-0002-8965-8153 | Simon Fraser University
Author | Brandt C | 0000-0001-8179-1796 | Yale University
Author | Chen JY | 0000-0002-6112-415X | The University of Alabama at Birmingham
Author | Ding Y | 0000-0003-2567-2009 | University of Texas at Austin
Author | Fodeh S | 0000-0003-4664-3143 | Yale University
Author | Mali P | 0000-0002-3383-1287 | University of California San Diego
Author | Payne-Foster P | 0000-0002-3508-3577 | University of Alabama
Author | Ratcliffe S | 0000-0002-6644-8284 | University of Virginia
Author | Ravitsky V | 0000-0002-7080-8801 | University of Montreal
Author | Sali A | 0000-0003-0435-6197 | University of California San Diego
Author | Schulz W | 0000-0002-2048-4028 | Yale University

Dataset Resource
Issued
2025-03-03
Dataset Resource
Keywords

- protein localization
- subcellular imaging
- breast cancer
- MDA-MB-468
- vorinostat

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Collection Timeframes
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Conforms To

- RO-Crate
- FAIRSCAPE

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Is Deidentified

Identifiable Elements Present
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Compression
ZIP
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Conforms To Class
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Conforms To Schema
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Created By

- Niestroy, Justin

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Created On
2025-02-27
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Language
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Page
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Publisher
University of Virginia Dataverse
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Was Derived From
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Encoding
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Format
ZIP
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Hash
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Md5
ac5...d52
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Media Type
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Path
Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip
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ID *
https://doi.org/10.18130/V3/B35XWX#ppi-secms
Dataset Resource
Title
Protein-protein Interaction SEC-MS
Dataset Resource
Description
This dataset was generated by size exclusion chromatography-mass spectroscopy (SEC-MS) on undifferentiated KOLF2.1J human induced pluripotent stem cells (hiPSCs), in the Nevan Krogan laboratory at the University of California San Francisco, 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. The data will be uploaded to Pride when available.
Dataset Resource
Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Ideker T | 0000-0002-1708-8454 | University of California San Diego
Principal Investigator | Krogan N | 0000-0003-4902-337X | University of California San Francisco
Principal Investigator | Lundberg E | 0000-0001-7034-0850 | Stanford University
Author | Clark T | 0000-0003-4060-7360 | University of Virginia
Author | Parker J | 0000-0003-4535-3486 | University of California, San Diego
Author | Al Manir S | 0000-0003-4647-3877 | University of Virginia
Author | Axelsson U | - | KTH Royal Institute of Technology
Author | Ballllosero Navarro F | 0000-0002-4180-422X | Stanford University
Author | Chinn B | - | University of California San Diego
Author | Churas CP | 0000-0001-9998-705X | University of California San Diego
Author | Dailamy A | 0000-0002-6711-8260 | University of California, San Diego
Author | Doctor Y | 0009-0009-0483-7506 | University of California, San Diego
Author | Fall J | - | KTH - Royal Institute of Technology
Author | Forget A | 0000-0003-0223-0312 | University of California San Francisco
Author | Gao J | 0000-0002-6311-3526 | University of California San Diego
Author | Hansen JN | 0000-0002-4650-9094 | Stanford University
Author | Hu M | 0000-0002-1571-8029 | University of California San Diego
Author | Johannesson A | - | KTH - Royal Institute of Technology
Author | Khaliq H | - | University of California San Diego
Author | Lee YH | 0000-0003-0917-355X | University of California San Diego
Author | Lenkiewicz J | 0000-0001-7252-8638 | University of California San Diego
Author | Levinson MA | 0000-0003-0384-8499 | University of Virginia
Author | Marquez C | 0000-0003-3960-420X | University of California San Diego
Author | Metallo C | 0000-0003-2404-3040 | University of California San Diego
Author | Muralidharan M | - | University of California San Francisco
Author | Nourreddine S | 0000-0003-3881-7588 | University of California San Diego
Author | Niestroy J | 0000-0002-1103-3882 | University of Virginia
Author | Obernier K | 0000-0002-4025-1299 | University of California San Francisco
Author | Pan E | - | University of California San Diego
Author | Polacco B | - | University of California San Francisco
Author | Pratt D | 0000-0002-1471-9513 | University of California San Diego
Author | Qian G | 0009-0005-4217-2745 | University of California San Diego
Author | Schaffer L | 0000-0001-6339-9141 | University of California San Diego
Author | Sigaeva A | 0000-0003-3361-3797 | KTH Royal Institute of Technology
Author | Thaker S | 0000-0001-6730-2773 | University of Alabama at Birmingham
Author | Zhang Y | - | University of California San Diego
Author | Bélisle-Pipon JC | 0000-0002-8965-8153 | Simon Fraser University
Author | Brandt C | 0000-0001-8179-1796 | Yale University
Author | Chen JY | 0000-0002-6112-415X | The University of Alabama at Birmingham
Author | Ding Y | 0000-0003-2567-2009 | University of Texas at Austin
Author | Fodeh S | 0000-0003-4664-3143 | Yale University
Author | Mali P | 0000-0002-3383-1287 | University of California San Diego
Author | Payne-Foster P | 0000-0002-3508-3577 | University of Alabama
Author | Ratcliffe S | 0000-0002-6644-8284 | University of Virginia
Author | Ravitsky V | 0000-0002-7080-8801 | University of Montreal
Author | Sali A | 0000-0003-0435-6197 | University of California San Diego
Author | Schulz W | 0000-0002-2048-4028 | Yale University

Dataset Resource
Issued
2025-03-03
Dataset Resource
Keywords

- protein-protein interaction
- SEC-MS
- mass spectroscopy
- iPSC
- KOLF2.1J

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Collection Timeframes
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Conforms To

- RO-Crate
- FAIRSCAPE

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Preprocessing Strategies
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Cleaning Strategies
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Is Deidentified

Identifiable Elements Present
Description

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Sensitive Elements
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Acquisition Methods
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Compression
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Conforms To Class
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Conforms To Schema
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Created By

- Niestroy, Justin

Dataset Resource
Created On
2025-02-27
Dataset Resource
Language
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Modified By
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Page
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Publisher
University of Virginia Dataverse
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Status
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Was Derived From
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Encoding
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Format
JSON
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Hash
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Md5
cb6...032
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Media Type
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Path
Protein-protein Interaction SEC-MS/ro-crate-metadata.json
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Sha256
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Is Tabular
🚀

## Uses

What (other) tasks could the dataset be used for?

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Role | Name | ORCID | Affiliation
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📤

## Distribution

How will the dataset be distributed?

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License
https://creativecommons.org/licenses/by-nc-sa/4.0/
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DOI
https://doi.org/10.18130/V3/B35XWX
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Download URL
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Bytes
31,100
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Version Access
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License
https://creativecommons.org/licenses/by-nc-sa/4.0/
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DOI
https://doi.org/10.18130/V3/B35XWX
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Download URL
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Bytes
1,000,100
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Version Access
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License
https://creativecommons.org/licenses/by-nc-sa/4.0/
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DOI
https://doi.org/10.18130/V3/B35XWX
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Download URL
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Bytes
2,791,728,742
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License
https://creativecommons.org/licenses/by-nc-sa/4.0/
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DOI
https://doi.org/10.18130/V3/B35XWX
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Download URL
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Bytes
3,435,973,836
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License
https://creativecommons.org/licenses/by-nc-sa/4.0/
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DOI
https://doi.org/10.18130/V3/B35XWX
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Download URL
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Bytes
3,006,477,107
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Version Access
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License
https://creativecommons.org/licenses/by-nc-sa/4.0/
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DOI
https://doi.org/10.18130/V3/B35XWX
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Download URL
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Bytes
2,900
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Version Access
🔄

## Maintenance

How will the dataset be maintained?

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Version
1.4
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Updates
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Last Updated On
2025-02-27
Dataset Resource
Version
1.4
Dataset Resource
Updates
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Last Updated On
2025-02-27
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Version
1.4
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Updates
Dataset Resource
Last Updated On
2025-02-27
Dataset Resource
Version
1.4
Dataset Resource
Updates
Dataset Resource
Last Updated On
2025-02-27
Dataset Resource
Version
1.4
Dataset Resource
Updates
Dataset Resource
Last Updated On
2025-02-27
Dataset Resource
Version
1.4
Dataset Resource
Updates
Dataset Resource
Last Updated On
2025-02-27
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