dataverse 10.18130 V3 B35XWX tab metadata d4d

Datasheet for Dataset - Human Readable Format

🎯

Motivation

Why was the dataset created?

  • 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.
GrantorGrant NameGrant Number
National Institutes of HealthNIH Bridge2AI CM4AI1OT2OD032742-01
📊

Composition

What do the instances represent?

CountsData TypeIDInstance TypeNameRepresentation
11739Raw sequencing reads (fastq-equivalent as packaged), RO-Crate JSON metadata and provenance.inst-perturbseqCells with gene perturbations; per-cell scRNAseq reads and derived counts/phenotypes.InstanceSingle-cell transcriptomic profiles and fitness phenotypes from CRISPRi perturb-seq in undifferentia...
RO-Crate JSON metadata; raw data to be deposited to PRIDE.inst-secmsFractionated protein complexes profiled by mass spectrometry in hiPSCs and iPSC-derived NPCs, neuron...InstanceProtein-protein interaction profiles measured by size exclusion chromatography–mass spectrometry (SE...
563ZIP archives of image files plus RO-Crate metadata and provenance.inst-ifImages across treatment conditions (untreated, paclitaxel, vorinostat) with multi-channel staining.InstanceImmunofluorescence (IF) confocal microscopy images showing spatial protein localization in MDA-MB-46...
  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
  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.
  • 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.
  • ID
    distdate-1
    Name
    DistributionDate
    Description
    • 2025-03-03 (Version 1.4)
🔍

Collection Process

How was the data acquired?

doi:10.18130/V3/B35XWX
Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
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).
https://doi.org/10.18130/V3/B35XWX
https://dataverse.lib.virginia.edu
2025-03-03
2025-02-27
en
  • 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
https://w3id.org/ro/crate
  • Niestroy, Justin
  • 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.
RoleNameORCIDAffiliation
Principal InvestigatorIdeker Tperson-idekerUniversity of California San Diego
Principal InvestigatorKrogan Nperson-kroganUniversity of California San Francisco
Principal InvestigatorLundberg Eperson-lundbergStanford University
Principal InvestigatorMali Pperson-maliUniversity of California San Diego
Principal InvestigatorClark Tperson-clarkUniversity of Virginia
  • 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.
  • 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.
  • ID
    timeframe-1
    Name
    CollectionTimeframe
    Description
    • Data Creation Date
      2025-02-27; Public release: 2025-03-03 (March 2025 Beta release).
  • 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.
ID
deid-1
Name
Deidentification
Description
  • Dataset contains measurements from cell lines; no directly identifiable personal data are included.
  • ID
    sens-1
    Name
    SensitiveElement
    Description
    • No sensitive personal data; scientific data from established human cell lines.
  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.
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.
DescriptionIDName
University of Virginia Dataverse (repository hosting and support).maint-1Maintainer
{'Point of contact': 'Ideker T (University of California San Diego) via Dataverse contact mechanism.'}maint-2Maintainer
no
CompressionDescriptionEncodingFormatIDIssuedMd5Media TypeNamePathTitle
Expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J hiPSCs mapping t...UTF-8JSONfile-crispr-atlas-rocrate2025-03-03cbdb263b1c099396d75e16f00a79a818application/jsonro-crate-metadata.jsonCRISPR Perturbation Cell Atlas/ro-crate-metadata.jsonCRISPR Perturbation Cell Atlas/JSON
Raw sequence data from genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs; packaged as ...UTF-8JSONfile-crispr-rawseq-rocrate2025-03-031cafefa32a897998e3e2ba0a29a3ef5capplication/jsonro-crate-metadata.jsonCRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.jsonCRISPR 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-8JSONfile-sec-ms-rocrate2025-03-03cb67e7749b15ce87b9042a9feba9d032application/jsonro-crate-metadata.jsonProtein-protein Interaction SEC-MS/ro-crate-metadata.jsonProtein-protein Interaction SEC-MS/JSON
ZIPSpatial localization of 563 proteins in untreated MDA-MB-468 cells by ICC-IF and confocal microscopy...file-if-untreated-zip2025-03-030b4d129f5fbc3bb7f7ea564cd032cef7application/zipcm4ai-v0.6-beta-if-images-untreated.zipProtein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zipProtein Localization Subcellular Images/ZIP Archive - Untreated
ZIPSpatial localization of 563 proteins in MDA-MB-468 cells treated with paclitaxel by ICC-IF and confo...file-if-paclitaxel-zip2025-03-039422486c80bc9e1d35b2fbbc72a5f043application/zipcm4ai-v0.6-beta-if-images-paclitaxel.zipProtein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zipProtein Localization Subcellular Images/ZIP Archive - Paclitaxel
ZIPSpatial localization of 563 proteins in MDA-MB-468 cells treated with vorinostat by ICC-IF and confo...file-if-vorinostat-zip2025-03-03ac577109a41a9806978461157b777d52application/zipcm4ai-v0.6-beta-if-images-vorinostat.zipProtein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zipProtein Localization Subcellular Images/ZIP Archive - Vorinostat
🚀

Uses

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

  • 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.
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:10.18130/V3/B35XWX
CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)
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?

2025-03-07
1.4
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