# dataverse 10.18130 V3 B35XWX tab metadata d4d

Datasheet for Dataset - Human Readable Format

🎯

## Motivation

Why was the dataset created?

Purposes

- ID
    purpose-1
  Name
    Purpose
  Response
    Provide AI-ready, richly annotated multimodal functional genomics datasets (transcriptomics, proteomics, and microscopy) to enable construction of cell maps and development of AI/ML methods under the NIH Bridge2AI CM4AI program.

Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | NIH Bridge2AI CM4AI | 1OT2OD032742-01

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## Composition

What do the instances represent?

Instances

Counts | Data Type | ID | Instance Type | Name | Representation
--- | --- | --- | --- | --- | ---
11739 | Raw sequencing reads (fastq-equivalent as packaged), RO-Crate JSON metadata and provenance. | inst-perturbseq | Cells with gene perturbations; per-cell scRNAseq reads and derived counts/phenotypes. | Instance | Single-cell transcriptomic profiles and fitness phenotypes from CRISPRi perturb-seq in undifferentia...
| RO-Crate JSON metadata; raw data to be deposited to PRIDE. | inst-secms | Fractionated protein complexes profiled by mass spectrometry in hiPSCs and iPSC-derived NPCs, neuron... | Instance | Protein-protein interaction profiles measured by size exclusion chromatography–mass spectrometry (SE...
563 | ZIP archives of image files plus RO-Crate metadata and provenance. | inst-if | Images across treatment conditions (untreated, paclitaxel, vorinostat) with multi-channel staining. | Instance | Immunofluorescence (IF) confocal microscopy images showing spatial protein localization in MDA-MB-46...

Instance Acquisition Methods

1. ID
     acq-1
   Name
     InstanceAcquisition
   Description
     - Directly observed measurements from sequencing, mass spectrometry, and microscopy; experimental perturbations via CRISPRi.
   Was Directly Observed
     True
   Was Reported By Subjects
     False
   Was Inferred Derived
     True
   Was Validated Verified
     True

Subpopulations

1. ID
     subpop-1
   Name
     Subpopulation
   Identification
     - Mda Mb 468 Breast Cancer Cell Line With Treatment Conditions
         untreated, paclitaxel, vorinostat.
   Distribution
     - Imaging subsets exist for each treatment condition; detailed counts per condition are provided within respective archives.

Distribution Formats

- ID
    distfmt-1
  Name
    DistributionFormat
  Description
    - Dataverse repository (web UI and Data Access API).
    - RO-Crate metadata (JSON-LD).
    - ZIP archives for large image collections.
    - JSON files for metadata packages.

Distribution Dates

- ID
    distdate-1
  Name
    DistributionDate
  Description
    - 2025-03-03 (Version 1.4)

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## Collection Process

How was the data acquired?

ID *
doi:10.18130/V3/B35XWX
Name
Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
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).
Page
https://doi.org/10.18130/V3/B35XWX
Publisher
https://dataverse.lib.virginia.edu
Issued
2025-03-03
Created On
2025-02-27
Language
en
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

Conforms To
https://w3id.org/ro/crate
Created By

- Niestroy, Justin

Addressing Gaps

- ID
    gap-1
  Name
    AddressingGap
  Response
    Addresses the lack of standardized, provenance-rich, multimodal functional genomics datasets spanning perturb-seq, SEC-MS, and subcellular imaging across disease-relevant human cell lines.

Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Ideker T | person-ideker | University of California San Diego
Principal Investigator | Krogan N | person-krogan | University of California San Francisco
Principal Investigator | Lundberg E | person-lundberg | Stanford University
Principal Investigator | Mali P | person-mali | University of California San Diego
Principal Investigator | Clark T | person-clark | University of Virginia

Relationships

- ID
    rel-1
  Name
    Relationships
  Description
    - Multimodal linkage across perturb-seq gene targets, SEC-MS protein interactions, and IF-derived protein localization for integrated cell mapping.

Collection Mechanisms

- ID
    mech-1
  Name
    CollectionMechanism
  Description
    - CRISPRi perturb-seq (single-cell RNA-seq after targeted gene knockdown).
    - Size exclusion chromatography followed by mass spectrometry (SEC-MS).
    - Immunofluorescence-based staining (ICC-IF) and confocal microscopy.

Collection Timeframes

- ID
    timeframe-1
  Name
    CollectionTimeframe
  Description
    - Data Creation Date
        2025-02-27; Public release: 2025-03-03 (March 2025 Beta release).

Ethical Reviews

- ID
    er-1
  Name
    EthicalReview
  Description
    - Data derive from human cell lines and do not include human subject PII; specific IRB details not provided in this record.

Deidentified

ID
  deid-1
Name
  Deidentification
Description
  - Dataset contains measurements from cell lines; no directly identifiable personal data are included.

Sensitive Elements

- ID
    sens-1
  Name
    SensitiveElement
  Description
    - No sensitive personal data; scientific data from established human cell lines.

External Resources

1. ID
     ext-1
   Name
     ExternalResource
   External Resources
     - Future deposition of SEC-MS raw data to PRIDE (Proteomics Identifications Database) is planned.
     - Related Publications On Biorxiv (e.g., DOI
         10.1101/2024.05.21.589311; doi:10.1101/2024.11.03.621734).
   Future Guarantees
     - SEC-MS raw data availability will be ensured upon PRIDE deposition (not yet available at time of release).
   Archival
     - Dataset packaged as RO-Crate with provenance to support long-term archival references.

Ip Restrictions

ID
  ipr-1
Name
  IPRestrictions
Description
  - Copyright (c) 2025 The Regents of the University of California except where otherwise noted.
  - Spatial proteomics raw image data copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University.

Maintainers

Description | ID | Name
--- | --- | ---
University of Virginia Dataverse (repository hosting and support). | maint-1 | Maintainer
{'Point of contact': 'Ideker T (University of California San Diego) via Dataverse contact mechanism.'} | maint-2 | Maintainer

Is Tabular
no
Resources

Compression | Description | Encoding | Format | ID | Issued | Md5 | Media Type | Name | Path | Title
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
| Expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J hiPSCs mapping t... | UTF-8 | JSON | file-crispr-atlas-rocrate | 2025-03-03 | cbdb263b1c099396d75e16f00a79a818 | application/json | ro-crate-metadata.json | CRISPR Perturbation Cell Atlas/ro-crate-metadata.json | CRISPR Perturbation Cell Atlas/JSON
| Raw sequence data from genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs; packaged as ... | UTF-8 | JSON | file-crispr-rawseq-rocrate | 2025-03-03 | 1cafefa32a897998e3e2ba0a29a3ef5c | application/json | ro-crate-metadata.json | CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json | CRISPR Perturbation RNA Sequences - Raw Sequences/JSON
| SEC-MS dataset (KOLF2.1J hiPSCs) from the Krogan lab; packaged as RO-Crate. Raw data will be uploade... | UTF-8 | JSON | file-sec-ms-rocrate | 2025-03-03 | cb67e7749b15ce87b9042a9feba9d032 | application/json | ro-crate-metadata.json | Protein-protein Interaction SEC-MS/ro-crate-metadata.json | Protein-protein Interaction SEC-MS/JSON
ZIP | Spatial localization of 563 proteins in untreated MDA-MB-468 cells by ICC-IF and confocal microscopy... |  |  | file-if-untreated-zip | 2025-03-03 | 0b4d129f5fbc3bb7f7ea564cd032cef7 | application/zip | cm4ai-v0.6-beta-if-images-untreated.zip | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip | Protein Localization Subcellular Images/ZIP Archive - Untreated
ZIP | Spatial localization of 563 proteins in MDA-MB-468 cells treated with paclitaxel by ICC-IF and confo... |  |  | file-if-paclitaxel-zip | 2025-03-03 | 9422486c80bc9e1d35b2fbbc72a5f043 | application/zip | cm4ai-v0.6-beta-if-images-paclitaxel.zip | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip | Protein Localization Subcellular Images/ZIP Archive - Paclitaxel
ZIP | Spatial localization of 563 proteins in MDA-MB-468 cells treated with vorinostat by ICC-IF and confo... |  |  | file-if-vorinostat-zip | 2025-03-03 | ac577109a41a9806978461157b777d52 | application/zip | cm4ai-v0.6-beta-if-images-vorinostat.zip | Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip | Protein Localization Subcellular Images/ZIP Archive - Vorinostat

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## Uses

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

Tasks

- ID
    task-1
  Name
    Task
  Response
    AI/ML research on cell architecture and function, including training and benchmarking models for perturbation-response prediction, protein localization, and protein-protein interaction mapping.

License And Use Terms

ID
  lic-1
Name
  LicenseAndUseTerms
Description
  - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
  - Proper citation and attribution to copyright holders and authors required; follow Dataverse community norms.

📤

## Distribution

How will the dataset be distributed?

DOI
doi:10.18130/V3/B35XWX
License
CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)
Version Access

ID
  veracc-1
Name
  VersionAccess
Description
  - Prior versions and release history are available via the Dataverse Versions interface for this DOI landing page.

🔄

## Maintenance

How will the dataset be maintained?

Last Updated On
2025-03-07
Version
1.4
Updates

ID
  update-1
Name
  UpdatePlan
Description
  - Data will be augmented regularly through the end of the project; subsequent releases will add new instances and modalities and correct any issues.

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