dataverse 10.18130 V3 F3TD5R tab files d4d

Datasheet for Dataset - Human Readable Format

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Motivation

Why was the dataset created?

Response
AI-ready datasets to support research in functional genomics
Enable AI model training using multimodal cellular data (perturb-seq, SEC-MS, IF imaging)
Support analysis of cellular processes and architecture under disease, treatment, and genetic pertur...
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Composition

What do the instances represent?

Data TypeInstance TypeRepresentation
Sequencing-based single-cell expression measurements associated with CRISPRi perturbationsSingle-cell transcriptomic profiles under genetic perturbationsCRISPRi perturb-seq profiles in undifferentiated KOLF2.1J iPSCs
Mass spectrometry spectral data and quantitative interaction featuresProtein complexes and interaction profiles from size-exclusion chromatography mass spectrometryProtein-protein interaction measurements via SEC-MS across multiple cell types
Fluorescence microscopy images and derived featuresCellular protein localization and morphology imagesImmunofluorescence microscopy images in MDA-MB-468 cells with and without chemotherapy (vorinostat, ...
  • Identification
    • Undifferentiated KOLF2.1J iPSCs
    • iPSC-derived NPCs
    • iPSC-derived neurons
    • iPSC-derived cardiomyocytes
    • MDA-MB-468 breast cancer cells (treated and untreated)
  • Description
    • Distributed via University of Virginia Dataverse; external primary data hosted on NCBI SRA (BioProject) and MassIVE repositories
  • Description
    • 2025-10-22 (June 2025 Beta release)
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Collection Process

How was the data acquired?

doi:10.18130/V3/F3TD5R
Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
This dataset is the June 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, iPSC-derived NPCs, neurons, cardiomyocytes, and treated and untreated MDA-MB-468 breast cancer cells - Immunofluorescence (IF) images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel) External data links (see also ExternalResource and RawData sections): - Sequence Read Archive (SRA) Data: NCBI BioProject - Mass Spectrometry Data (Human iPSCs): MassIVE Repository - Mass Spectrometry Data (Human Cancer Cells): MassIVE Repository Data Governance & Ethics: - Human Subjects: No - De-identified Samples: Yes - FDA Regulated: No - Data Governance Committee: Jillian Parker (jillianparker@health.ucsd.edu) - Ethical Review: Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca) Completeness: - Some datasets are under temporary pre-publication embargo - Protein-protein interaction (SEC-MS), protein localization (IF imaging), and CRISPRi perturb-seq datasets interrogate sets of proteins which incompletely overlap - Computed cell maps are not included in this release Maintenance Plan: - Dataset will be regularly updated and augmented through the end of the project in November 2026 - Updates on a quarterly basis - Long-term preservation in the University of Virginia Dataverse, supported by committed institutional funds Intended Use: - AI-ready datasets to support research in functional genomics - AI model training - Cellular process analysis - Analysis of cell architectural changes and interactions under specific disease processes, treatment conditions, or genetic perturbations Limitations: - Interim release; does not contain predicted cell maps (to be added in future releases) - Current release is most suitable for bioinformatics analysis of the individual datasets - Requires domain expertise for meaningful analysis Prohibited Uses: - Not to be used in clinical decision-making or in any context involving patient care without appropriate regulatory oversight and approval Potential Sources of Bias: - Data derived from commercially available de-identified human cell lines - Does not represent all biological variants in the broader population
2025-10-22
  • CM4AI
  • functional genomics
  • AI-ready dataset
  • perturb-seq
  • CRISPRi
  • SEC-MS
  • immunofluorescence imaging
  • iPSC
  • KOLF2.1J
  • MDA-MB-468
  • NPC
  • neurons
  • cardiomyocytes
  • chemotherapy
  • vorinostat
  • paclitaxel
  • Clark T
  • Parker J
  • Al Manir S
  • Axelsson U
  • Ballllosero Navarro F
  • Chinn B
  • Churas CP
  • Dailamy A
  • Doctor Y
  • Fall J
  • Forget A
  • Gao J
  • Hansen JN
  • Hu M
  • Johannesson A
  • Khaliq H
  • Lee YH
  • Lenkiewicz J
  • Levinson MA
  • Marquez C
  • Metallo C
  • Muralidharan M
  • Nourreddine S
  • Niestroy J
  • Obernier K
  • Pan E
  • Polacco B
  • Pratt D
  • Qian G
  • Schaffer L
  • Sigaeva A
  • Thaker S
  • Zhang Y
  • Bélisle-Pipon JC
  • Brandt C
  • Chen JY
  • Ding Y
  • Fodeh S
  • Krogan N
  • Lundberg E
  • Mali P
  • Description
    • Human Subjects
      False
    • De Identified Samples
      True
    • Fda Regulated
      False
    • Ethical Review Contacts
      Vardit Ravitsky (ravitskyv@thehastingscenter.org); Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca)
Description
  • Data derived from commercially available de-identified human cell lines
  • No human subjects; de-identified samples
  • Description
    • Data acquired via high-throughput laboratory instrumentation and imaging; not reported by human subjects
  • Description
    • CRISPRi perturb-seq (single-cell sequencing)
    • Size-exclusion chromatography followed by mass spectrometry (SEC-MS)
    • Immunofluorescence microscopy (IF imaging)
  • External Resources
    • NCBI BioProject (SRA) for sequencing data
    • MassIVE Repository for human iPSC mass spectrometry data
    • MassIVE Repository for human cancer cell mass spectrometry data
    Restrictions
    • Refer to respective repository terms of use for access and reuse conditions
  • Description
    • Raw and/or primary data are accessible via external repositories (SRA/BioProject and MassIVE) linked from the dataset landing resources
  • Description
    • Interim Beta release; some datasets under temporary pre-publication embargo
    • Modalities interrogate overlapping but non-identical protein sets (SEC-MS, IF, perturb-seq)
    • Computed cell maps are not included in this release
  • Description
    • University of Virginia Dataverse (hosting and long-term preservation)
    • Data Governance Committee Contact
      Jillian Parker (jillianparker@health.ucsd.edu)
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Uses

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

Response
AI model training on multimodal biological data
Bioinformatics analyses of perturb-seq, SEC-MS, and IF imaging datasets
Cellular process and protein interaction analysis
  • Description
    • Interim nature and missing computed cell maps may limit end-to-end modeling use cases
    • Multimodal protein target sets only partially overlap across modalities
    • Requires domain expertise for meaningful analysis
    • Potential population bias due to use of specific de-identified cell lines; may not represent all biological variants
  • Description
    • Do not use for clinical decision-making or patient care without appropriate regulatory oversight and approval
Description
  • Prohibited for use in clinical decision-making or patient care without appropriate regulatory oversight and approval
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Distribution

How will the dataset be distributed?

doi:10.18130/V3/F3TD5R
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Maintenance

How will the dataset be maintained?

June 2025 Data Release (Beta)
Description
  • Dataset will be regularly updated and augmented through November 2026
  • Quarterly updates planned
  • Long-term preservation supported by institutional funds at University of Virginia Dataverse
Generated on 2025-11-09 10:17:35 using Bridge2AI Data Sheets Schema