# dataverse 10.18130 V3 F3TD5R d4d

Datasheet for Dataset - Human Readable Format

🎯

## Motivation

Why was the dataset created?

Purposes

Name | Response
--- | ---
Functional genomics AI readiness | AI-ready datasets to support research in functional genomics
AI model training | Enable AI model training on multi-modal cellular/omics data
Cellular process analysis | Support analysis of cellular processes and architectures
Perturbation and treatment analysis | Study cell architectural changes and interactions under disease, treatment, or genetic perturbations

📊

## Composition

What do the instances represent?

Instances

Data Type | Name | Representation
--- | --- | ---
Sequencing-based single-cell expression data with perturbation guides | CRISPRi perturb-seq in undifferentiated KOLF2.1J iPSCs | Single-cell transcriptomic profiles under CRISPRi perturbations (perturb-seq)
Proteomics mass spectrometry data across iPSCs, NPCs, neurons, cardiomyocytes, and MDA-MB-468 cells ... | SEC-MS proteomics | Protein-protein interaction measurements via Size Exclusion Chromatography–Mass Spectrometry (SEC-MS...
Microscopy image data (immunofluorescence) under vorinostat and paclitaxel treatment conditions | Immunofluorescence microscopy images | IF images of MDA-MB-468 breast cancer cells with/without chemotherapy

Distribution Formats

- Name
    Distribution channels
  Description
    - University of Virginia Dataverse landing page and downloads
    - External Repositories
        NCBI SRA (BioProject), MassIVE

Distribution Dates

- Name
    Release timeline
  Description
    - June 2025 (Beta data release)
    - 2025-10-22 (Dataverse record date)

🔍

## 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; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel). External Data Links - 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 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 - 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 - 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 - 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
Page
https://doi.org/10.18130/V3/F3TD5R
Keywords

- CM4AI
- Cell Maps for Artificial Intelligence
- functional genomics
- perturb-seq
- CRISPRi
- SEC-MS
- mass spectrometry
- immunofluorescence
- imaging
- iPSC
- KOLF2.1J
- NPCs
- neurons
- cardiomyocytes
- MDA-MB-468
- 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

Sampling Strategies

1. Name
     Cell line-based sampling
   Is Sample
     - True
   Source Data
     - Commercially available de-identified human cell lines
   Is Representative
     - False
   Why Not Representative
     - Derived from specific cell lines and conditions; does not represent all biological variants in the wider population

Collection Mechanisms

Description | Name
--- | ---
Single-cell RNA-seq with CRISPR interference perturbations in KOLF2.1J iPSCs | CRISPRi perturb-seq
Size Exclusion Chromatography coupled to Mass Spectrometry for protein-protein interactions | SEC-MS (proteomics)
IF microscopy of MDA-MB-468 cells under treatment and control conditions | Immunofluorescence imaging

Ethical Reviews

- Name
    Governance and ethics
  Description
    - Human Subjects
        False
    - De Identified Samples
        True
    - Fda Regulated
        False
    - Data Governance Committee
        Jillian Parker (jillianparker@health.ucsd.edu)
    - Ethical Review
        Vardit Ravitsky (ravitskyv@thehastingscenter.org); Jean-Christophe Belisle-Pipon (jean-christophe_belisle-pipon@sfu.ca)

Is Deidentified

Name
  De-identification status
Description
  - De-identified samples; no human subjects

External Resources

- Name
    Related external repositories
  External Resources
    - NCBI SRA (BioProject) for sequencing data
    - MassIVE repository (human iPSCs proteomics)
    - MassIVE repository (human cancer cell proteomics)

Regulatory Restrictions

Name
  Regulatory status
Description
  - Fda Regulated
      False

Maintainers

- Name
    Dataset hosting and governance
  Description
    - University of Virginia Dataverse (hosting and long-term preservation)
    - Cm4ai Data Governance Committee Contact
        Jillian Parker (jillianparker@health.ucsd.edu)

🚀

## Uses

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

Tasks

Name | Response
--- | ---
AI model training | Train machine learning and AI models on perturb-seq, proteomics, and imaging data
Cellular process analysis | Analyze cellular processes and structures from multi-modal assays
Perturbation effect analysis | Assess effects of disease models, chemical treatments, or CRISPRi perturbations

License And Use Terms

Name
  Terms and prohibited uses
Description
  - 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

Future Use Impacts

- Name
    Limitations and considerations
  Description
    - Interim release; computed cell maps not yet included
    - Most suitable for bioinformatics analyses of individual datasets at this stage
    - Requires domain expertise for meaningful analysis

📤

## Distribution

How will the dataset be distributed?

DOI
doi:10.18130/V3/F3TD5R
🔄

## Maintenance

How will the dataset be maintained?

Updates

Name
  Update plan
Description
  - Dataset will be regularly updated and augmented through November 2026
  - Quarterly updates planned
  - Long-term preservation in the University of Virginia Dataverse

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