# dataverse 10.18130 V3 F3TD5R tab terms d4d

Datasheet for Dataset - Human Readable Format

🎯

## Motivation

Why was the dataset created?

Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health (NIH) Bridge2AI Program | - | -

Purposes

- Response
    AI-ready datasets to support research in functional genomics

📊

## Composition

What do the instances represent?

Instances

Data Type | Instance Type | Missing Information | Representation
--- | --- | --- | ---
Sequencing-based single-cell perturbation readouts; primary data and/or intermediate processed data | Perturb-seq (CRISPRi) in undifferentiated KOLF2.1J iPSCs | {'missing': 'Computed cell maps', 'why_missing': 'Not included in this release; to be added in future releases'} | Cell line assay data
Mass spectrometry raw and/or processed spectral/protein interaction data | Size exclusion chromatography mass spectrometry (SEC-MS) in iPSCs, iPSC-derived NPCs, neurons, cardi... |  | Proteomics data
Microscopy image data | Immunofluorescence (IF) images in MDA-MB-468 cells with and without chemotherapy (vorinostat and pac... |  | Imaging data

Subpopulations

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

Distribution Formats

- Description
    - University of Virginia Dataverse repository distribution
    - Links to external repositories (NCBI SRA/BioProject, MassIVE)

Distribution Dates

- Description
    - 2025-10-22

🔍

## 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
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-MB468 breast cancer cells; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel). External Data Links Access external data resources related to this dataset: 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 These data are not yet in completed final form: Some datasets are under temporary pre-publication embargo Protein-protein interaction (SEC-MS), protein localization (IF imaging), and CRISPRi perturbSeq data interrogate sets of proteins which incompletely overlap Computed cell maps 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 This dataset is intended for: AI-ready datasets to support research in functional genomics AI model training Cellular process analysis Cell architectural changes and interactions in presence of specific disease processes, treatment conditions, or genetic perturbations Limitations Researchers should be aware of inherent limitations: This is an interim release Does not contain predicted cell maps, which will be added in future releases The current release is most suitable for bioinformatics analysis of the individual datasets Requires domain expertise for meaningful analysis Prohibited Uses These laboratory data are 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 Users should be aware of potential biases: Data in this release was derived from commercially available de-identified human cell lines Does not represent all biological variants which may be seen in the population at large
Issued
2025-10-22
Creators

Name
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

Anomalies

- Description
    - Interim release; some datasets under temporary pre-publication embargo
    - Protein sets across modalities incompletely overlap
    - Computed cell maps not included

External Resources

- External Resources
    - Sequence Read Archive (SRA) via NCBI BioProject
    - MassIVE Repository (Human iPSCs)
    - MassIVE Repository (Human Cancer Cells)
  Restrictions
    - External repositories may have their own licensing/terms of use

Collection Mechanisms

- Description
    - Perturb-seq (CRISPRi-based single-cell transcriptomics)
    - Size exclusion chromatography coupled mass spectrometry (SEC-MS)
    - Immunofluorescence microscopy imaging

Acquisition Methods

1. Description
     - Data directly observed via sequencing, proteomics, and imaging assays
   Was Directly Observed
     True
   Was Reported By Subjects
     False
   Was Inferred Derived
     Some downstream computed cell maps are not included in this release

Ethical Reviews

- Description
    - Ethical review oversight by Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca)

Deidentification

Description
  - Human Subjects
      False
  - De Identified Samples
      True

Sensitive Elements

- Description
    - No patient-identifying information; data derived from de-identified human cell lines

Regulatory Restrictions

- Description
    - Fda Regulated
        False

Maintainers

- Description
    - Long-term preservation and hosting in the University of Virginia Dataverse (supported by institutional funds)
    - Data Governance Committee Contact
        Jillian Parker (jillianparker@health.ucsd.edu)

🚀

## Uses

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

Tasks

Response
AI model training
Cellular process analysis
Analysis of cell architectural changes and interactions under disease, treatment, or genetic perturb...

Future Use Impacts

- Description
    - Data derived from commercially available de-identified human cell lines; may not represent all biological variants
    - Interim release and modality coverage differences may impact integrative analyses

Discouraged Uses

- Description
    - Not for clinical decision-making or patient care without appropriate regulatory oversight and approval

License And Use Terms

- Description
    - Prohibited clinical use without appropriate regulatory oversight and approval
    - Some datasets subject to temporary pre-publication embargo

📤

## Distribution

How will the dataset be distributed?

DOI
doi:10.18130/V3/F3TD5R
🔄

## Maintenance

How will the dataset be maintained?

Version
June 2025 Beta
Updates

Description
  - Dataset will be regularly updated and augmented through November 2026
  - Quarterly updates planned

Generated on 2025-11-09 10:17:35 using Bridge2AI Data Sheets Schema