# dataverse 10.18130 V3 F3TD5R tab files d4d

Datasheet for Dataset - Human Readable Format

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## Motivation

Why was the dataset created?

Purposes

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?

Instances

Data Type | Instance Type | Representation
--- | --- | ---
Sequencing-based single-cell expression measurements associated with CRISPRi perturbations | Single-cell transcriptomic profiles under genetic perturbations | CRISPRi perturb-seq profiles in undifferentiated KOLF2.1J iPSCs
Mass spectrometry spectral data and quantitative interaction features | Protein complexes and interaction profiles from size-exclusion chromatography mass spectrometry | Protein-protein interaction measurements via SEC-MS across multiple cell types
Fluorescence microscopy images and derived features | Cellular protein localization and morphology images | Immunofluorescence microscopy images in MDA-MB-468 cells with and without chemotherapy (vorinostat, ...

Subpopulations

- Identification
    - Undifferentiated KOLF2.1J iPSCs
    - iPSC-derived NPCs
    - iPSC-derived neurons
    - iPSC-derived cardiomyocytes
    - MDA-MB-468 breast cancer cells (treated and untreated)

Distribution Formats

- Description
    - Distributed via University of Virginia Dataverse; external primary data hosted on NCBI SRA (BioProject) and MassIVE repositories

Distribution Dates

- Description
    - 2025-10-22 (June 2025 Beta release)

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## Collection Process

How was the data acquired?

ID *
doi:10.18130/V3/F3TD5R
Name
Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
Title
Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
Description
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
Issued
2025-10-22
Keywords

- 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

Created By

- 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

Ethical Reviews

- 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)

Is Deidentified

Description
  - Data derived from commercially available de-identified human cell lines
  - No human subjects; de-identified samples

Acquisition Methods

- Description
    - Data acquired via high-throughput laboratory instrumentation and imaging; not reported by human subjects

Collection Mechanisms

- Description
    - CRISPRi perturb-seq (single-cell sequencing)
    - Size-exclusion chromatography followed by mass spectrometry (SEC-MS)
    - Immunofluorescence microscopy (IF imaging)

External Resources

- 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

Raw Sources

- Description
    - Raw and/or primary data are accessible via external repositories (SRA/BioProject and MassIVE) linked from the dataset landing resources

Anomalies

- 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

Maintainers

- 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?

Tasks

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

Future Use Impacts

- 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

Discouraged Uses

- Description
    - Do not use for clinical decision-making or patient care without appropriate regulatory oversight and approval

License And Use Terms

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
doi:10.18130/V3/F3TD5R
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## Maintenance

How will the dataset be maintained?

Version
June 2025 Data Release (Beta)
Updates

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