# dataverse 10.18130 V3 B35XWX d4d

Datasheet for Dataset - Human Readable Format

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## Motivation

Why was the dataset created?

Purposes

- Name
    Purpose
  Response
    Provide AI-ready, FAIR, provenance-rich multimodal functional genomics datasets to map human cell architecture and enable machine learning and AI applications.

Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | NIH OT2 award | 1OT2OD032742-01

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## Composition

What do the instances represent?

Distribution Formats

- Name
    DistributionFormat
  Description
    - RO-Crate JSON-LD
    - ZIP Archive

Distribution Dates

- Name
    DistributionDate
  Description
    - 2025-03-03

🔍

## Collection Process

How was the data acquired?

ID *
doi:10.18130/V3/B35XWX
Name
Cell Maps for Artificial Intelligence
Title
Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
Description
This dataset is the March 2025 Data Release of Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org), the Functional Genomics Grand Challenge in the NIH Bridge2AI program. This Beta release includes perturb-seq data in undifferentiated KOLF2.1J iPSCs; SEC-MS data in undifferentiated KOLF2.1J iPSCs and iPSC-derived NPCs, neurons, and cardiomyocytes; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel). CM4AI output data are packaged with provenance graphs and rich metadata as AI-ready datasets in RO-Crate format using the FAIRSCAPE framework. Data presented here will be augmented regularly through the end of the project. CM4AI is a collaboration of UCSD, UCSF, Stanford, UVA, Yale, UA Birmingham, Simon Fraser University, and the Hastings Center. This data is Copyright (c) 2025 The Regents of the University of California except where otherwise noted. Spatial proteomics raw image data is copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University. Dataset licensed for reuse under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license (https://creativecommons.org/licenses/by-nc-sa/4.0/). Attribution is required to the copyright holders and the authors. Any publications referencing this data or derived products should cite the Related Publication below, as well as directly citing this data collection (2025-03-04). (2025-03-07)
Conforms To

- https://w3id.org/ro/crate
- https://fairscape.net

Created By

- CM4AI Consortium
- Justin Niestroy (Depositor)

Created On
2025-02-27
Issued
2025-03-03
Keywords

- AI
- affinity purification
- AP-MS
- artificial intelligence
- breast cancer
- Bridge2AI
- cardiomyocyte
- CM4AI
- CRISPR/Cas9
- induced pluripotent stem cell
- iPSC
- KOLF2.1J
- machine learning
- mass spectroscopy
- MDA-MB-468
- neural progenitor cell
- NPC
- neuron
- paclitaxel
- perturb-seq
- perturbation sequencing
- protein-protein interaction
- protein localization
- single-cell RNA sequencing
- scRNAseq
- SEC-MS
- size exclusion chromatography
- subcellular imaging
- vorinostat

Language
en
Page
https://doi.org/10.18130/V3/B35XWX
Publisher
https://dataverse.lib.virginia.edu
Status
bibo:draft
Was Derived From
Cell Maps for Artificial Intelligence (CM4AI) program, NIH Bridge2AI
Addressing Gaps

- Name
    AddressingGap
  Response
    Bridge the gap between large-scale experimental cell maps and AI by releasing standardized RO-Crate datasets with complete provenance to support reproducibility and downstream AI use.

Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Contributor | Clark T | - | University of Virginia
Contributor | Parker J | - | University of California, San Diego
Contributor | Al Manir S | - | University of Virginia
Contributor | Axelsson U | - | KTH Royal Institute of Technology
Contributor | Ballllosero Navarro F | - | Stanford University
Contributor | Chinn B | - | University of California San Diego
Contributor | Churas CP | - | University of California San Diego
Contributor | Dailamy A | - | University of California, San Diego
Contributor | Doctor Y | - | University of California, San Diego
Contributor | Fall J | - | KTH - Royal Institute of Technology
Contributor | Forget A | - | University of California San Francisco
Contributor | Gao J | - | University of California San Diego
Contributor | Hansen JN | - | Stanford University
Contributor | Hu M | - | University of California San Diego
Contributor | Johannesson A | - | KTH - Royal Institute of Technology
Contributor | Khaliq H | - | University of California San Diego
Contributor | Lee YH | - | University of California San Diego
Contributor | Lenkiewicz J | - | University of California San Diego
Contributor | Levinson MA | - | University of Virginia
Contributor | Marquez C | - | University of California San Diego
Contributor | Metallo C | - | University of California San Diego
Contributor | Muralidharan M | - | University of California San Francisco
Contributor | Nourreddine S | - | University of California San Diego
Contributor | Niestroy J | - | University of Virginia
Contributor | Obernier K | - | University of California San Francisco
Contributor | Pan E | - | University of California San Diego
Contributor | Polacco B | - | University of California San Francisco
Contributor | Pratt D | - | University of California San Diego
Contributor | Qian G | - | University of California San Diego
Contributor | Schaffer L | - | University of California San Diego
Contributor | Sigaeva A | - | KTH Royal Institute of Technology
Contributor | Thaker S | - | University of Alabama at Birmingham
Contributor | Zhang Y | - | University of California San Diego
Contributor | Bélisle-Pipon JC | - | Simon Fraser University
Contributor | Brandt C | - | Yale University
Contributor | Chen JY | - | The University of Alabama at Birmingham
Contributor | Ding Y | - | University of Texas at Austin
Contributor | Fodeh S | - | Yale University
Contributor | Krogan N | - | University of California San Francisco
Contributor | Lundberg E | - | Stanford University
Contributor | Mali P | - | University of California San Diego
Contributor | Payne-Foster P | - | University of Alabama
Contributor | Ratcliffe S | - | University of Virginia
Contributor | Ravitsky V | - | University of Montreal
Contributor | Sali A | - | University of California San Diego
Contributor | Schulz W | - | Yale University
Contributor | Ideker T | - | University of California San Diego

Collection Timeframes

- Name
    CollectionTimeframe
  Description
    - Data created on 2025-02-27 and first published on 2025-03-03.

Collection Mechanisms

- Name
    CollectionMechanism
  Description
    - CRISPRi perturb-seq in undifferentiated KOLF2.1J hiPSCs.
    - Size exclusion chromatography-mass spectrometry (SEC-MS) in hiPSCs, and iPSC-derived NPCs, neurons, and cardiomyocytes.
    - Immunofluorescence (ICC-IF) confocal microscopy imaging in MDA-MB-468 breast cancer cells, with and without chemotherapy (vorinostat, paclitaxel).

Acquisition Methods

- Name
    InstanceAcquisition
  Description
    - Directly observed imaging (IF confocal microscopy), mass spectrometry (SEC-MS), and single-cell RNA sequencing (perturb-seq).
    - CRISPRi perturbations to assay transcriptional and fitness phenotypes across 11,739 targeted genes.

Data Collectors

- Name
    DataCollector
  Description
    - Lundberg Lab, Stanford University (IF imaging).
    - Nevan Krogan Laboratory, University of California San Francisco (SEC-MS).
    - University of California San Diego CM4AI team (CRISPRi perturb-seq).

Ethical Reviews
Data Protection Impacts
Preprocessing Strategies

- Name
    PreprocessingStrategy
  Description
    - RO-Crate packaging with provenance graphs via FAIRSCAPE framework; modality-specific preprocessing is described in individual RO-Crate metadata files.

Cleaning Strategies
Labeling Strategies
Raw Sources
Ip Restrictions

Name
  IPRestrictions
Description
  - Copyright (c) 2025 The Regents of the University of California except where noted. Spatial proteomics raw image data copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University.

Regulatory Restrictions

Name
  ExportControlRegulatoryRestrictions
Description
  - Collection is under review for potential modification in compliance with Administration directives (per repository notice).

Maintainers

Description | Name
--- | ---
Ideker T (Point of Contact; University of California San Diego) via Dataverse contact. | Maintainer
University of Virginia Dataverse Support | Maintainer

Errata
Retention Limit
Extension Mechanism
Resources

Acquisition Methods | Collection Mechanisms | Compression | Data Collectors | Description | Distribution Dates | External Resources | Format | ID | Instances | Issued | Md5 | Media Type | Name | Path | Title
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
{'name': 'InstanceAcquisition', 'description': ['CRISPRi perturbations with single-cell RNA sequencing readouts in undifferentiated KOLF2.1J hiPSCs.']} | {'name': 'CollectionMechanism', 'description': ['Perturb-seq experimental pipeline and RO-Crate packaging.']} |  | {'name': 'DataCollector', 'description': ['University of California San Diego CM4AI team']} | This dataset represents an expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiate... | {'name': 'DistributionDate', 'description': ['2025-03-03']} |  | JSON | CRISPR Perturbation Cell Atlas/ro-crate-metadata.json | {'name': 'Instance', 'representation': 'CRISPRi perturb-seq profiles and fitness phenotypes in KOLF2.1J hiPSCs', 'data_type': 'Single-cell RNA sequencing-derived gene expression and phenotype summaries', 'counts': 11739} | 2025-03-03 | cbdb263b1c099396d75e16f00a79a818 | application/json | CRISPR Perturbation Cell Atlas RO-Crate metadata | CRISPR Perturbation Cell Atlas/ro-crate-metadata.json | ro-crate-metadata.json (CRISPR Perturbation Cell Atlas)
{'name': 'InstanceAcquisition', 'description': ['Single-cell RNA sequencing following CRISPRi perturbations.']} |  |  | {'name': 'DataCollector', 'description': ['University of California San Diego CM4AI team']} | Raw sequence data from an expressed genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs ... | {'name': 'DistributionDate', 'description': ['2025-03-03']} |  | JSON | CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json | {'name': 'Instance', 'representation': 'Raw RNA sequencing data associated with CRISPRi perturbations in KOLF2.1J hiPSCs', 'data_type': 'Raw sequencing reads metadata (see RO-Crate)', 'counts': 11739} | 2025-03-03 | 1cafefa32a897998e3e2ba0a29a3ef5c | application/json | CRISPR Perturbation RNA Sequences (Raw) RO-Crate metadata | CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json | ro-crate-metadata.json (CRISPR Perturbation RNA Sequences - Raw Sequences)
| {'name': 'CollectionMechanism', 'description': ['ICC-IF staining and confocal microscopy imaging under paclitaxel treatment.']} | ZIP | {'name': 'DataCollector', 'description': ['Lundberg Lab, Stanford University']} | Spatial localization of 563 proteins of interest in MDA-MB-468 cells treated with paclitaxel, imaged... | {'name': 'DistributionDate', 'description': ['2025-03-03']} |  |  | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip | {'name': 'Instance', 'representation': 'Immunofluorescence confocal microscopy images of protein localization in MDA-MB-468 cells (paclitaxel treated)', 'data_type': 'Multichannel TIFF/JPEG images packaged in ZIP (see RO-Crate for specifics)', 'counts': 563} | 2025-03-03 | 9422486c80bc9e1d35b2fbbc72a5f043 | application/zip | Protein Localization Subcellular Images (paclitaxel) | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip | cm4ai-v0.6-beta-if-images-paclitaxel.zip
| {'name': 'CollectionMechanism', 'description': ['ICC-IF staining and confocal microscopy imaging in untreated condition.']} | ZIP | {'name': 'DataCollector', 'description': ['Lundberg Lab, Stanford University']} | Spatial localization of 563 proteins of interest in untreated MDA-MB-468 cells, imaged by ICC-IF con... | {'name': 'DistributionDate', 'description': ['2025-03-03']} |  |  | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip | {'name': 'Instance', 'representation': 'Immunofluorescence confocal microscopy images of protein localization in MDA-MB-468 cells (untreated controls)', 'data_type': 'Multichannel TIFF/JPEG images packaged in ZIP (see RO-Crate for specifics)', 'counts': 563} | 2025-03-03 | 0b4d129f5fbc3bb7f7ea564cd032cef7 | application/zip | Protein Localization Subcellular Images (untreated) | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip | cm4ai-v0.6-beta-if-images-untreated.zip
| {'name': 'CollectionMechanism', 'description': ['ICC-IF staining and confocal microscopy imaging under vorinostat treatment.']} | ZIP | {'name': 'DataCollector', 'description': ['Lundberg Lab, Stanford University']} | Spatial localization of 563 proteins of interest in MDA-MB-468 cells treated with vorinostat, imaged... | {'name': 'DistributionDate', 'description': ['2025-03-03']} |  |  | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip | {'name': 'Instance', 'representation': 'Immunofluorescence confocal microscopy images of protein localization in MDA-MB-468 cells (vorinostat treated)', 'data_type': 'Multichannel TIFF/JPEG images packaged in ZIP (see RO-Crate for specifics)', 'counts': 563} | 2025-03-03 | ac577109a41a9806978461157b777d52 | application/zip | Protein Localization Subcellular Images (vorinostat) | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip | cm4ai-v0.6-beta-if-images-vorinostat.zip
| {'name': 'CollectionMechanism', 'description': ['Size exclusion chromatography followed by mass spectrometry (SEC-MS).']} |  | {'name': 'DataCollector', 'description': ['Nevan Krogan Laboratory, University of California San Francisco']} | Size exclusion chromatography–mass spectrometry (SEC-MS) dataset in undifferentiated KOLF2.1J hiPSCs... | {'name': 'DistributionDate', 'description': ['2025-03-03']} | {'name': 'ExternalResource', 'external_resources': ['PRIDE repository (planned archival)'], 'future_guarantees': ['Repository submission planned when available.'], 'archival': ['Hosted on UVA Dataverse; PRIDE archival forthcoming.'], 'restrictions': ['CC BY-NC-SA 4.0 license applies.']} | JSON | Protein-protein Interaction SEC-MS/ro-crate-metadata.json | {'name': 'Instance', 'representation': 'SEC-MS protein complex profiles in KOLF2.1J hiPSCs and iPSC-derived lineages', 'data_type': 'Mass spectrometry fractionation profiles (see RO-Crate)'} | 2025-03-03 | cb67e7749b15ce87b9042a9feba9d032 | application/json | Protein–protein Interaction SEC-MS RO-Crate metadata | Protein-protein Interaction SEC-MS/ro-crate-metadata.json | ro-crate-metadata.json (Protein–protein Interaction SEC-MS)

🚀

## Uses

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

Tasks

- Name
    Task
  Response
    Train and benchmark AI/ML models for cellular phenotype prediction, protein localization, and protein interaction inference using perturb-seq, SEC-MS, and IF imaging.

Existing Uses

- Name
    ExistingUse
  Description
    - Related Publications
        2024 preprints cited in the dataset record (bioRxiv doi:10.1101/2024.05.21.589311; doi:10.1101/2024.11.03.621734).

Other Tasks

- Name
    OtherTask
  Description
    - Multimodal integration, network inference, phenotype prediction, and benchmarking AI readiness of cell maps.

Future Use Impacts

- Name
    FutureUseImpact
  Description
    - Dataset will be augmented regularly; users should monitor versions and provenance to ensure comparability across releases.

Discouraged Uses
License And Use Terms

Name
  LicenseAndUseTerms
Description
  - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). Attribution required to the copyright holders and authors. https://creativecommons.org/licenses/by-nc-sa/4.0/

📤

## Distribution

How will the dataset be distributed?

DOI
doi:10.18130/V3/B35XWX
License
https://creativecommons.org/licenses/by-nc-sa/4.0/
Version Access

Name
  VersionAccess
Description
  - Hosted on Dataverse with versioned releases; older versions remain accessible per repository policies.

🔄

## Maintenance

How will the dataset be maintained?

Version
1.4
Updates

Name
  UpdatePlan
Description
  - Data will be augmented regularly through the end of the project; users should check the Dataverse record for updated versions.

Generated on 2025-11-09 10:17:34 using Bridge2AI Data Sheets Schema