dataverse 10.18130 V3 B35XWX tab files d4d

Datasheet for Dataset - Human Readable Format

🎯

Motivation

Why was the dataset created?

GrantorGrant NameGrant Number
National Institutes of HealthBridge2AI - CM4AI1OT2OD032742-01
📊

Composition

What do the instances represent?

  • Description
    • Public Release Date
      2025-03-03
  • Description
    • RO-Crate JSON metadata
    • ZIP archives of image data
    • Proteomics RO-Crate JSON metadata
🔍

Collection Process

How was the data acquired?

doi:10.18130/V3/B35XWX
CM4AI 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)
https://doi.org/10.18130/V3/B35XWX
2025-03-03
2025-02-27
bibo:draft
  • 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
  • CM4AI Consortium
  • Clark T
  • Ideker T
  • Krogan N
  • Lundberg E
  • Mali P
Description
  • Copyrights as noted; reuse under CC BY-NC-SA 4.0.
Description
Description
  • University of Virginia Dataverse (hosting)
  • Point Of Contact
    Trey Ideker (University of California San Diego)
Description
  • Dataset contains measurements from cell lines and iPSC-derived cells; no directly identifiable human subject data.
Acquisition MethodsCollection MechanismsCompressionDescriptionExternal ResourcesFormatFundersIDInstancesIs TabularIssuedLicenseMd5Media TypeNamePathPurposesSubpopulationsTasksTitle
{'description': ['CRISPRi perturb-seq in undifferentiated KOLF2.1J hiPSCs; phenotypic, protein-interaction, and metabolic tracing assays used for validation']}{'description': ['Packaged as RO-Crate using the FAIRSCAPE framework']}This dataset represents an expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiate...JSON{'grantor': {'name': 'National Institutes of Health'}, 'grant': {'name': 'Bridge2AI - CM4AI', 'grant_number': '1OT2OD032742-01'}}doi:10.18130/V3/B35XWX#crisper-perturbation-cell-atlas-ro-crate{'representation': 'RO-Crate metadata and provenance for the CRISPRi Perturbation Cell Atlas', 'data_type': 'JSON metadata describing files, provenance graphs, and AI-ready packaging'}no2025-03-03CC BY-NC-SA 4.0 https://creativecommons.org/licenses/by-nc-sa/4.0/cbdb263b1c099396d75e16f00a79a818application/jsonro-crate-metadata.json (CRISPR Perturbation Cell Atlas)CRISPR Perturbation Cell Atlas/ro-crate-metadata.json{'response': 'Support AI/ML on cell architecture and functional genomics perturbation effects'}{'identification': ['KOLF2.1J human induced pluripotent stem cells (hiPSCs)']}{'response': 'AI-ready data packaging and provenance for downstream ML and analysis'}CRISPR Perturbation Cell Atlas RO-Crate metadata
{'description': ['CRISPRi perturb-seq in KOLF2.1J hiPSCs', {'was_directly_observed': True}]}{'description': ['Packaged as RO-Crate using the FAIRSCAPE framework']}Raw sequence data from a genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs mapping tra...JSON{'grantor': {'name': 'National Institutes of Health'}, 'grant': {'name': 'Bridge2AI - CM4AI', 'grant_number': '1OT2OD032742-01'}}doi:10.18130/V3/B35XWX#crisper-perturbation-rna-raw-ro-crate{'representation': 'RO-Crate metadata for raw RNA sequence files from CRISPRi perturb-seq', 'data_type': 'JSON metadata describing raw sequence data and provenance'}no2025-03-03CC BY-NC-SA 4.0 https://creativecommons.org/licenses/by-nc-sa/4.0/1cafefa32a897998e3e2ba0a29a3ef5capplication/jsonro-crate-metadata.json (CRISPR Perturbation RNA Sequences - Raw Sequences)CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json{'response': 'Provide AI-ready raw sequence data for modeling gene perturbations'}{'identification': ['KOLF2.1J human induced pluripotent stem cells (hiPSCs)']}{'response': 'Single-cell transcriptomics analysis; ML on perturbation effects'}CRISPR Perturbation RNA Sequences - Raw Sequences RO-Crate metadata
{'description': ['Immunofluorescence-based staining (ICC-IF) and confocal microscopy (Lundberg Lab, Stanford University)']}ZIPSpatial localization of 563 proteins of interest in untreated MDA-MB-468 breast cancer cells imaged ...{'grantor': {'name': 'National Institutes of Health'}, 'grant': {'name': 'Bridge2AI - CM4AI', 'grant_number': '1OT2OD032742-01'}}doi:10.18130/V3/B35XWX#if-images-untreated{'representation': 'Immunofluorescence-based subcellular protein localization images', 'instance_type': 'Confocal microscopy image files', 'data_type': 'Multichannel confocal images (DAPI, ER, microtubules, protein of interest)'}no2025-03-03CC BY-NC-SA 4.0 https://creativecommons.org/licenses/by-nc-sa/4.0/0b4d129f5fbc3bb7f7ea564cd032cef7application/zipcm4ai-v0.6-beta-if-images-untreated.zipProtein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip{'response': 'Enable AI/ML models to learn subcellular protein localization patterns under baseline conditions'}{'identification': ['MDA-MB-468 breast cancer cell line (untreated)']}{'response': 'Protein localization image analysis; subcellular structure mapping; ML for cell architecture'}Protein Localization Subcellular Images (untreated)
{'description': ['Immunofluorescence-based staining (ICC-IF) and confocal microscopy (Lundberg Lab, Stanford University)']}ZIPSpatial localization of 563 proteins of interest in MDA-MB-468 cells treated with paclitaxel, imaged...{'grantor': {'name': 'National Institutes of Health'}, 'grant': {'name': 'Bridge2AI - CM4AI', 'grant_number': '1OT2OD032742-01'}}doi:10.18130/V3/B35XWX#if-images-paclitaxel{'representation': 'Immunofluorescence-based subcellular protein localization images under paclitaxel treatment', 'instance_type': 'Confocal microscopy image files', 'data_type': 'Multichannel confocal images (DAPI, ER, microtubules, protein of interest)'}no2025-03-03CC BY-NC-SA 4.0 https://creativecommons.org/licenses/by-nc-sa/4.0/9422486c80bc9e1d35b2fbbc72a5f043application/zipcm4ai-v0.6-beta-if-images-paclitaxel.zipProtein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip{'response': 'Compare protein localization patterns under chemotherapy treatment vs. baseline'}{'identification': ['MDA-MB-468 breast cancer cell line (paclitaxel-treated)']}{'response': 'Treatment-response image analysis; ML for drug-induced subcellular changes'}Protein Localization Subcellular Images (paclitaxel-treated)
{'description': ['Immunofluorescence-based staining (ICC-IF) and confocal microscopy (Lundberg Lab, Stanford University)']}ZIPSpatial localization of 563 proteins of interest in MDA-MB-468 cells treated with vorinostat, imaged...{'grantor': {'name': 'National Institutes of Health'}, 'grant': {'name': 'Bridge2AI - CM4AI', 'grant_number': '1OT2OD032742-01'}}doi:10.18130/V3/B35XWX#if-images-vorinostat{'representation': 'Immunofluorescence-based subcellular protein localization images under vorinostat treatment', 'instance_type': 'Confocal microscopy image files', 'data_type': 'Multichannel confocal images (DAPI, ER, microtubules, protein of interest)'}no2025-03-03CC BY-NC-SA 4.0 https://creativecommons.org/licenses/by-nc-sa/4.0/ac577109a41a9806978461157b777d52application/zipcm4ai-v0.6-beta-if-images-vorinostat.zipProtein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip{'response': 'Compare protein localization patterns under chemotherapy treatment vs. baseline'}{'identification': ['MDA-MB-468 breast cancer cell line (vorinostat-treated)']}{'response': 'Treatment-response image analysis; ML for drug-induced subcellular changes'}Protein Localization Subcellular Images (vorinostat-treated)
{'description': ['Size exclusion chromatography-mass spectrometry (SEC-MS) on undifferentiated KOLF2.1J hiPSCs']}{'description': ['Packaged as RO-Crate using the FAIRSCAPE framework']}Size exclusion chromatography-mass spectroscopy (SEC-MS) dataset on undifferentiated KOLF2.1J hiPSCs...{'external_resources': ['Planned archival deposition to PRIDE (when available)'], 'archival': ['PRIDE repository planned'], 'restrictions': ['None beyond CC BY-NC-SA 4.0 for this collection metadata']}JSON{'grantor': {'name': 'National Institutes of Health'}, 'grant': {'name': 'Bridge2AI - CM4AI', 'grant_number': '1OT2OD032742-01'}}doi:10.18130/V3/B35XWX#sec-ms-ro-crate{'representation': 'RO-Crate metadata and provenance for SEC-MS proteomics', 'data_type': 'JSON metadata describing SEC-MS experimental outputs and provenance'}no2025-03-03CC BY-NC-SA 4.0 https://creativecommons.org/licenses/by-nc-sa/4.0/cb67e7749b15ce87b9042a9feba9d032application/jsonro-crate-metadata.json (Protein-protein Interaction SEC-MS)Protein-protein Interaction SEC-MS/ro-crate-metadata.json{'response': 'Provide AI-ready proteomics metadata to support interaction network inference'}{'identification': ['KOLF2.1J human induced pluripotent stem cells (hiPSCs)']}{'response': 'Protein complex and protein-protein interaction analysis; ML on proteomics-derived interaction signals'}Protein-protein Interaction SEC-MS RO-Crate metadata
RoleNameORCIDAffiliation
Principal InvestigatorTrey Ideker0000-0002-1708-8454CM4AI (Cell Maps for Artificial Intelligence) Consortium
  • Description
    • Data Creation Date
      2025-02-27
no
🚀

Uses

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

Description
  • Dataset licensed for reuse under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). Attribution is required to the copyright holders and the authors.
  • 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.
📤

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?

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