dataverse 10.18130 V3 B35XWX tab versions d4d

Datasheet for Dataset - Human Readable Format

🎯

Motivation

Why was the dataset created?

  • Name
    CM4AI goal
    Response
    Provide AI-ready datasets and provenance for mapping human cell architecture from disease-relevant cell lines, enabling machine learning and AI research on genomics, proteomics, and imaging modalities.
GrantorGrant NameGrant Number
National Institutes of HealthBridge2AI program1OT2OD032742-01
📊

Composition

What do the instances represent?

CountsData TypeInstance TypeLabelNameRepresentation
11739Raw sequencing reads and processed gene-expression/fitness features (per RO-Crate packages).Single cells; gene perturbationsTranscriptional and fitness phenotypes per targeted gene perturbation.CRISPRi perturb-seq in KOLF2.1J hiPSCsSingle-cell transcriptomes and fitness phenotypes from CRISPRi perturbations in undifferentiated KOL...
563Multi-channel immunofluorescence images under untreated and drug-treated conditions (vorinostat, pac...Cell images; protein localizationProtein-of-interest localization patterns across conditions.Protein localization IF imaging in MDA-MB-468Immunofluorescence confocal microscopy images with four channels (DAPI, ER/calreticulin, tubulin, pr...
Mass spectrometry intensity profiles indicative of protein complex size distributions.Proteins; chromatographic fractionsProtein-protein interaction SEC-MSSize exclusion chromatography–mass spectrometry profiles from undifferentiated KOLF2.1J iPSCs and iP...
  • Identification
    • Undifferentiated KOLF2.1J human iPSCs and iPSC-derived NPCs, neurons, and cardiomyocytes.
    • MDA-MB-468 breast cancer cells (untreated and treated with vorinostat or paclitaxel).
    Distribution
    • Multiple experimental conditions including presence/absence of chemotherapy.
  • Description
    • RO-Crate JSON metadata packages.
    • ZIP archives for imaging data distributions.
    Used Software
    NameURL
    RO-Cratehttps://www.researchobject.org/ro-crate/
    FAIRSCAPEhttps://fairscape.net
  • Description
    • 2025-03-03 (publication date on Dataverse).
🔍

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). (2025-03-07)
en
https://dataverse.lib.virginia.edu
2025-03-03
https://doi.org/10.18130/V3/B35XWX
  • 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
2025-02-27
https://w3id.org/ro/crate
no
  • Name
    AI-ready cell maps
    Response
    Create standardized, provenance-rich, FAIR AI-ready datasets to accelerate AI methods for functional genomics and cell architecture mapping.
RoleNameORCIDAffiliation
Principal InvestigatorTrey Ideker-Cell Maps for Artificial Intelligence (CM4AI)
Principal InvestigatorEmma Lundberg-Stanford University
Principal InvestigatorNevan Krogan-University of California San Francisco
  1. Description
    • Data acquired via high-throughput scRNAseq (perturb-seq), confocal fluorescence microscopy (IF), and SEC-MS proteomics.
    Was Directly Observed
    True
    Was Reported By Subjects
    False
    Was Inferred Derived
    partial
    Was Validated Verified
    not specified
  • Description
    • Hardware and instruments include sequencing platforms for scRNAseq, confocal microscopes for IF imaging, and mass spectrometers for SEC-MS; datasets packaged as RO-Crates using the FAIRSCAPE framework.
  • Description
    • Lundberg Lab at Stanford University (IF imaging).
    • Nevan Krogan Laboratory at UCSF (SEC-MS).
    • CM4AI collaboration across UCSD, UCSF, Stanford, UVA, Yale, UAB, Simon Fraser University, and the Hastings Center.
  • Description
    • Data creation date 2025-02-27; published 2025-03-03.
  1. External Resources
    • SEC-MS data will be uploaded to PRIDE when available.
    Future Guarantees
    • Not specified.
    Archival
    • Planned archival in PRIDE for proteomics data.
    Restrictions
    • Subject to repository terms and the dataset’s CC BY-NC-SA 4.0 license.
Description
  • No individually identifiable human data; experiments are on established human cell lines.
  • Description
    • Point Of Contact
      Trey Ideker (University of California San Diego). Contact via Dataverse dataset page.
CompressionDescriptionFormatIs TabularIssuedMd5Media TypeNameTitle
RO-Crate metadata for the expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated...JSONno2025-03-03cbdb263b1c099396d75e16f00a79a818application/jsonCRISPR Perturbation Cell Atlas ro-crate-metadata.jsonro-crate-metadata.json
RO-Crate metadata for raw sequence data from the CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs.JSONno2025-03-031cafefa32a897998e3e2ba0a29a3ef5capplication/jsonCRISPR Perturbation RNA Sequences - Raw Sequences ro-crate-metadata.jsonro-crate-metadata.json
ZIPSpatial localization of 563 proteins in MDA-MB-468 cells treated with paclitaxel imaged by ICC-IF an...no2025-03-039422486c80bc9e1d35b2fbbc72a5f043application/zipcm4ai-v0.6-beta-if-images-paclitaxel.zipProtein Localization Subcellular Images (paclitaxel)
ZIPSpatial localization of 563 proteins in untreated MDA-MB-468 cells imaged by ICC-IF and confocal mic...no2025-03-030b4d129f5fbc3bb7f7ea564cd032cef7application/zipcm4ai-v0.6-beta-if-images-untreated.zipProtein Localization Subcellular Images (untreated)
ZIPSpatial localization of 563 proteins in MDA-MB-468 cells treated with vorinostat imaged by ICC-IF an...no2025-03-03ac577109a41a9806978461157b777d52application/zipcm4ai-v0.6-beta-if-images-vorinostat.zipProtein Localization Subcellular Images (vorinostat)
RO-Crate metadata for SEC-MS dataset from undifferentiated KOLF2.1J hiPSCs (with additional iPSC-der...JSONno2025-03-03cb67e7749b15ce87b9042a9feba9d032application/jsonProtein-protein Interaction SEC-MS ro-crate-metadata.jsonro-crate-metadata.json
🚀

Uses

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

  • Name
    AI/ML analysis across modalities
    Response
    Analysis and model development using CRISPRi perturb-seq scRNAseq, SEC-MS protein interaction profiling, and immunofluorescence protein localization images.
Description
  • Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). Attribution required to the copyright holders and the authors.
  • Description
    • Related publications include bioRxiv preprints on CM4AI cell maps and the perturbation cell atlas (e.g., doi:10.1101/2024.05.21.589311; doi:10.1101/2024.11.03.621734).
📤

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/)
🔄

Maintenance

How will the dataset be maintained?

1.4
2025-03-07
Description
  • Data will be augmented regularly through the end of the project; subsequent releases expected.
Generated on 2025-11-09 10:17:35 using Bridge2AI Data Sheets Schema