# dataverse 10.18130 V3 F3TD5R tab terms d4d

Datasheet for Dataset - Human Readable Format

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## Motivation

Why was the dataset created?

Purposes

- Name
    Primary purpose
  Response
    Provide AI-ready multimodal functional genomics datasets (images, perturb-seq, SEC-MS) to enable research on human cell architecture, processes, and responses to disease, treatments, and genetic perturbations.

Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | Bridge2AI Functional Genomics | 1OT2OD032742-01

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## Composition

What do the instances represent?

Instances

1. Name
     Data modalities and instance structure
   Representation
     Cell-based measurements and derived observations across multiple experimental modalities.
   Instance Type
     Immunofluorescence images, size exclusion chromatography mass spectrometry (SEC-MS) profiles, and CRISPRi perturb-seq single-cell transcriptomes.
   Data Type
     Raw and processed data files per modality (confocal ICC-IF images with multi-channel staining; SEC-MS protein abundance/interaction fractions; scRNA-seq counts/metadata from perturb-seq).
   Label
     Yes; instances include protein of interest and treatment condition (e.g., paclitaxel, vorinostat, untreated) for imaging; perturbation identity for perturb-seq; sample and condition metadata for SEC-MS.

Distribution Formats

- Name
    File formats
  Description
    - ZIP archives for image datasets
    - JSON (RO-Crate metadata)
    - HTML (provenance graphs, datasheet)

Distribution Dates

- Name
    Release dates
  Description
    - 2025-07-01 (Version 2.0 public release)
    - 2025-10-22 (additional IF image ZIP packages)

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## Collection Process

How was the data acquired?

ID *
doi:10.18130/V3/F3TD5R
Name
CM4AI 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).
Language
English
Publisher
https://dataverse.lib.virginia.edu
Issued
2025-07-01
Page
https://doi.org/10.18130/V3/F3TD5R
Created On
2025-02-27
Keywords

- AI
- artificial intelligence
- machine learning
- Bridge2AI
- CM4AI
- induced pluripotent stem cell
- iPSC
- KOLF2.1J
- neural progenitor cell
- NPC
- neuron
- cardiomyocyte
- breast cancer
- MDA-MB-468
- paclitaxel
- vorinostat
- perturb-seq
- perturbation sequencing
- single-cell RNA sequencing
- scRNAseq
- protein-protein interaction
- protein localization
- size exclusion chromatography
- SEC-MS
- mass spectroscopy
- affinity purification

Addressing Gaps

- Name
    Gap addressed
  Response
    Deliver standardized, AI-ready, de-identified cell-based datasets spanning complementary modalities; predicted cell maps are planned for future releases.

Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Trey Ideker | - | University of California San Diego
Principal Investigator | Nevan Krogan | - | University of California San Francisco
Principal Investigator | Emma Lundberg | - | Stanford University
Principal Investigator | Prashant Mali | - | University of California San Diego
Principal Investigator | Tim Clark | - | University of Virginia

Sampling Strategies

1. Name
     Sampling notes
   Is Sample
     - Yes; data derived from commercially available de-identified human cell lines and selected protein sets.
   Is Representative
     - No; does not represent all biological variants in the broader population.
   Why Not Representative
     - Modalities interrogate overlapping but incomplete protein sets; dataset focuses on specific disease-relevant cell lines and conditions.

Relationships

- Name
    Cross-modality relationships
  Description
    - Overlapping protein targets across SEC-MS, IF imaging, and perturb-seq enable integrative analyses of cellular architecture and interactions.

Splits

- Name
    Experimental conditions as natural splits
  Description
    - IF imaging split by treatment condition (untreated, paclitaxel, vorinostat) and protein of interest.

Data Collectors

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Contributor | Data collection contributors | - | -

Collection Mechanisms

- Name
    Experimental methods
  Description
    - ICC-IF confocal microscopy with multi-channel staining (DAPI, calreticulin for ER, tubulin, and target protein antibody).
    - Size exclusion chromatography mass spectrometry (SEC-MS) for protein-protein interactions and complex profiling.
    - CRISPRi perturb-seq single-cell RNA sequencing in KOLF2.1J iPSCs.

Collection Timeframes

- Name
    Dataset timeline
  Description
    - Data Creation Date
        2025-02-27; initial public release: 2025-07-01 (Version 2.0). Additional IF image packages published 2025-10-22.

Ethical Reviews

- Name
    Data governance and ethics
  Description
    - 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 Bélisle-Pipon (jean-christophe_belisle-pipon@sfu.ca).

Is Deidentified

Name
  De-identification status
Description
  - Data derived from commercially available de-identified human cell lines; no human subjects.

External Resources

- Name
    External repositories
  External Resources
    - Sequence Read Archive (sra) Data
        NCBI BioProject
    - Mass Spectrometry Data (human Ipscs)
        MassIVE Repository
    - Mass Spectrometry Data (human Cancer Cells)
        MassIVE Repository

Preprocessing Strategies

- Name
    Imaging channels and staining
  Description
    - Multi-channel ICC-IF imaging with DAPI (nuclei, blue), calreticulin (ER, yellow), tubulin (microtubules, red), and antibody to protein of interest (green).

Maintainers

- Name
    Preservation and governance
  Description
    - University of Virginia Dataverse (long-term preservation supported by institutional funds)
    - Data Governance Committee Contact
        Jillian Parker (jillianparker@health.ucsd.edu)

Status
https://purl.org/spar/bibo/status/published
Subsets

Description | ID | Is Data Split | Is Subpopulation | Md5 | Media Type | Name | Path
--- | --- | --- | --- | --- | --- | --- | ---
Immunofluorescence images of 464 proteins of interest in untreated MDA-MB-468 breast cancer cells; I... | cm4ai-ifimages-mda-mb-468-untreated | no | no | a98affcc05429650c6bb3906cd836d55 | application/zip | IF images - MDA-MB-468 untreated | Images/cm4ai-ifimages-mda-mb-468-untreated.zip
Immunofluorescence images of 464 proteins of interest in MDA-MB-468 cells treated with paclitaxel; I... | cm4ai-ifimages-mda-mb-468-paclitaxel | no | no | 0d972b80744344ddeede516a0cf6e3d7 | application/zip | IF images - MDA-MB-468 paclitaxel | Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip
Immunofluorescence images of 464 proteins of interest in MDA-MB-468 cells treated with vorinostat; I... | cm4ai-ifimages-mda-mb-468-vorinostat | no | no | ad4e68ccc14b0f3349dad3321e7b81b2 | application/zip | IF images - MDA-MB-468 vorinostat | Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip
HTML datasheet summarizing key release information. | release-ro-crate-datasheet |  |  | 599c9ece9b88b3ce797b82463b4a1eb4 | text/html | Release datasheet (RO-Crate HTML) | release-ro-crate-datasheet.html
RO-Crate metadata with pointers to sub RO-Crates. | release-ro-crate-metadata |  |  | 99f9e00053bff3020fd9832a3a518bbb | application/json | Release RO-Crate metadata (JSON) | release-ro-crate-metadata.json
HTML provenance graph; download to view properly. | images-provenance-paclitaxel |  |  | e38e63e4c8dfc5808a5ffa2d7829fc38 | text/html | IF images paclitaxel provenance graph (HTML) | Images/paclitaxel/Images-paclitaxel-provenance-graph.html
HTML provenance graph; download to view properly. | images-provenance-untreated |  |  | 1a3b510f74d3f8647e07c6559ce64ee8 | text/html | IF images untreated provenance graph (HTML) | Images/untreated/Images-untreated-provenance-graph.html
HTML provenance graph; download to view properly. | images-provenance-vorinostat |  |  | 58935fe4e254b31d33fed019f24c7668 | text/html | IF images vorinostat provenance graph (HTML) | Images/vorinostat/Images-vorinostat-provenance-graph.html
RO-Crate metadata for mass spectrometry cancer cell data. | mass-spec-cancer-cells-ro-crate |  |  | 3a7063bb391ea5e05a32ba5da5f4b2f8 | application/json | Mass spec (cancer cells) RO-Crate metadata (JSON) | mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json

Is Tabular
no
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## Uses

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

Tasks

- Name
    Intended analytical tasks
  Response
    AI model training; cellular process analysis; bioinformatics analysis of modality-specific datasets (IF imaging, SEC-MS, perturb-seq).

Existing Uses

- Name
    Related publications
  Description
    - Clark T Et Al. Cell Maps For Artificial Intelligence
        AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. 2024. doi: http://doi.org/10.1101/2024.05.21.589311
    - Nourreddine S et al. A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS. bioRxiv. 2024 Nov 4;2024.11.03.621734. https://doi.org/10.1101/2024.11.03.621734

Other Tasks

- Name
    Additional potential uses
  Description
    - Cross-modality integration; benchmarking AI methods for multimodal cell data; treatment effect studies; protein localization and interaction mapping.

Future Use Impacts

- Name
    Limitations and biases impacting future use
  Description
    - Interim release; computed cell maps not included yet.
    - Modalities interrogate overlapping but incomplete protein sets.
    - Domain expertise required for meaningful analysis.
    - Data from selected de-identified cell lines may not generalize to all biological variants.

Discouraged Uses

- Name
    Prohibited uses
  Description
    - Not for clinical decision-making or any patient care context without appropriate regulatory oversight and approval.

Use Repository

- Name
    Dataverse exports
  Description
    - OAI_ORE, DataCite, OpenAIRE, Schema.org JSON-LD, DDI Codebook v2, Dublin Core, DDI HTML Codebook, JSON available via Dataverse export tools.

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## Distribution

How will the dataset be distributed?

DOI
doi:10.18130/V3/F3TD5R
License
CC BY-NC-SA 4.0
Version Access

Name
  Versioning and access
Description
  - Older versions are preserved in Dataverse; current described version is 2.0 with subsequent file additions recorded under the dataset.

🔄

## Maintenance

How will the dataset be maintained?

Last Updated On
2025-10-22
Updates

Name
  Maintenance and update plan
Description
  - Dataset will be regularly updated and augmented through November 2026
  - Updates on a quarterly basis
  - Long-term preservation in the University of Virginia Dataverse

Version
2.0
Generated on 2025-11-09 10:17:34 using Bridge2AI Data Sheets Schema