# dataverse 10.18130 V3 F3TD5R tab files d4d

Datasheet for Dataset - Human Readable Format

🎯

## Motivation

Why was the dataset created?

Purposes

ID | Name | Response
--- | --- | ---
purpose-1 | Purpose | Provide AI-ready datasets to support research in functional genomics within the CM4AI (Cell Maps for...
purpose-2 | Purpose | Train and evaluate AI/ML models on multimodal cellular data.

Funders

Grantor | Grant Name | Grant Number
--- | --- | ---
National Institutes of Health | NIH OT2OD032742-01 | 1OT2OD032742-01

📊

## Composition

What do the instances represent?

Instances

Data Type | ID | Instance Type | Name | Representation
--- | --- | --- | --- | ---
Raw/processed image data packaged in ZIP archives | instance-if | Image files with multi-channel staining (DAPI, ER, microtubules, protein-of-interest) | Instance | Immunofluorescence (ICC-IF) confocal microscopy images of MDA-MB-468 cells
Processed mass spectrometry outputs and associated metadata | instance-sec-ms | Proteomics datasets across multiple cell types and treatments | Instance | Size exclusion chromatography–mass spectrometry (SEC-MS) protein-protein interaction data
Sequencing reads and/or processed matrices referenced via SRA BioProject | instance-perturb-seq | scRNA-seq profiles under targeted perturbations | Instance | CRISPRi perturb-seq single-cell transcriptomics in KOLF2.1J iPSCs

Subpopulations

- ID
    subpop-1
  Name
    Subpopulation
  Identification
    - Cell lines and derived cell types: KOLF2.1J iPSCs, iPSC-derived NPCs, neurons, cardiomyocytes, MDA-MB-468 breast cancer cells; treatments include vorinostat and paclitaxel.

Distribution Formats

- ID
    distfmt-1
  Name
    DistributionFormat
  Description
    - ZIP archives (images)
    - HTML (datasheet and provenance graphs)
    - JSON (RO-Crate metadata)

Distribution Dates

- ID
    distdate-1
  Name
    DistributionDate
  Description
    - Initial Publication
        2025-07-01
    - Additional Image Archives Published
        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
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).
Issued
2025-07-01
Created On
2025-02-27
Page
https://doi.org/10.18130/V3/F3TD5R
Keywords

- AI
- affinity purification
- AP-MS
- artificial intelligence
- breast cancer
- Bridge2AI
- cardiomyocyte
- CM4AI
- CRISPR/Cas9
- induced pluripotent stem cell
- iPSC
- KOLF2.1J
- machine learning
- mass spectroscopy
- MDA-MB-468
- neural progenitor cell
- NPC
- neuron
- paclitaxel
- perturb-seq
- perturbation sequencing
- protein-protein interaction
- protein localization
- single-cell RNA sequencing
- scRNAseq
- SEC-MS
- size exclusion chromatography
- subcellular imaging
- vorinostat

Status
bibo:draft
Resources

Description | Format | ID | Md5 | Media Type | Name | Path | Title
--- | --- | --- | --- | --- | --- | --- | ---
HTML datasheet summarizing key release information. |  | release-ro-crate-datasheet.html | 599c9ece9b88b3ce797b82463b4a1eb4 | text/html | release-ro-crate-datasheet.html | release-ro-crate-datasheet.html | Release RO-Crate datasheet (HTML)
Release RO-Crate with pointers to sub ro-crates. | JSON | release-ro-crate-metadata.json | 99f9e00053bff3020fd9832a3a518bbb | application/json | release-ro-crate-metadata.json | release-ro-crate-metadata.json | Release RO-Crate metadata (JSON)
Spatial localization of 464 proteins in MDA-MB-468 breast cancer cells treated with paclitaxel, imag... |  | Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip | 0d972b80744344ddeede516a0cf6e3d7 | application/zip | cm4ai-ifimages-mda-mb-468-paclitaxel.zip | Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip | CM4AI IF images – MDA-MB-468 treated with paclitaxel (ZIP)
Spatial localization of 464 proteins in untreated MDA-MB-468 breast cancer cells, imaged by ICC-IF c... |  | Images/cm4ai-ifimages-mda-mb-468-untreated.zip | a98affcc05429650c6bb3906cd836d55 | application/zip | cm4ai-ifimages-mda-mb-468-untreated.zip | Images/cm4ai-ifimages-mda-mb-468-untreated.zip | CM4AI IF images – MDA-MB-468 untreated (ZIP)
Spatial localization of 464 proteins in MDA-MB-468 breast cancer cells treated with vorinostat, imag... |  | Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip | ad4e68ccc14b0f3349dad3321e7b81b2 | application/zip | cm4ai-ifimages-mda-mb-468-vorinostat.zip | Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip | CM4AI IF images – MDA-MB-468 treated with vorinostat (ZIP)
HTML provenance graph; requires download to view properly. |  | Images/paclitaxel/Images-paclitaxel-provenance-graph.html | e38e63e4c8dfc5808a5ffa2d7829fc38 | text/html | Images-paclitaxel-provenance-graph.html | Images/paclitaxel/Images-paclitaxel-provenance-graph.html | IF images (paclitaxel) provenance graph (HTML)
HTML provenance graph; requires download to view properly. |  | Images/untreated/Images-untreated-provenance-graph.html | 1a3b510f74d3f8647e07c6559ce64ee8 | text/html | Images-untreated-provenance-graph.html | Images/untreated/Images-untreated-provenance-graph.html | IF images (untreated) provenance graph (HTML)
HTML provenance graph; requires download to view properly. |  | Images/vorinostat/Images-vorinostat-provenance-graph.html | 58935fe4e254b31d33fed019f24c7668 | text/html | Images-vorinostat-provenance-graph.html | Images/vorinostat/Images-vorinostat-provenance-graph.html | IF images (vorinostat) provenance graph (HTML)
HTML provenance graph; requires download to view properly. |  | mass-spec/cancer-cells/mass-spec-cancer-cells-provenance-graph.html | 931ad9b552562024cb84ebe62d1f1838 | text/html | mass-spec-cancer-cells-provenance-graph.html | mass-spec/cancer-cells/mass-spec-cancer-cells-provenance-graph.html | SEC-MS cancer cells provenance graph (HTML)
RO-Crate metadata for SEC-MS cancer cell data. | JSON | mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json | 3a7063bb391ea5e05a32ba5da5f4b2f8 | application/json | mass-spec-cancer-cells-ro-crate-metadata.json | mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json | SEC-MS cancer cells RO-Crate metadata (JSON)

Addressing Gaps

- ID
    gap-1
  Name
    AddressingGap
  Response
    Create harmonized, AI-ready multimodal datasets (imaging, perturb-seq, SEC-MS) from disease-relevant human cell lines to enable data-driven cell architecture maps.

Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Trey Ideker | person-trey-ideker | Cell Maps for Artificial Intelligence (CM4AI)
Principal Investigator | Tim Clark | person-tim-clark | University of Virginia
Principal Investigator | Nevan Krogan | person-nevan-krogan | University of California San Francisco
Principal Investigator | Emma Lundberg | person-emma-lundberg | Stanford University
Principal Investigator | Prashant Mali | person-prashant-mali | University of California San Diego

Sampling Strategies

1. ID
     sampling-1
   Name
     SamplingStrategy
   Strategies
     - Targeted selection of proteins-of-interest and perturbations; datasets in this release interrogate overlapping but not identical protein sets across modalities.
   Is Representative
     - Not representative of all biological variants; derived from specific human cell lines.
   Why Not Representative
     - Commercially available de-identified human cell lines do not represent full population diversity.

Relationships

- ID
    rel-1
  Name
    Relationships
  Description
    - Cross-modality relationships between proteins and cellular structures are implicit across IF imaging, SEC-MS interactions, and perturb-seq responses.

Splits

- ID
    splits-1
  Name
    Splits
  Description
    - No recommended data splits are provided in this interim release.

Anomalies

- ID
    anomaly-1
  Name
    DataAnomaly
  Description
    - Interim (Beta) release; computed cell maps are not included.
    - Protein sets interrogated across modalities incompletely overlap.

External Resources

1. ID
     ext-1
   Name
     ExternalResource
   External Resources
     - Sequence Read Archive (sra) Data
         NCBI BioProject
     - Mass Spectrometry Data (human Ipscs)
         MassIVE Repository
     - Mass Spectrometry Data (human Cancer Cells)
         MassIVE Repository
   Archival
     - Long-term preservation in the University of Virginia Dataverse.

Confidential Elements

- ID
    conf-1
  Name
    Confidentiality
  Description
    - No human subjects; commercially available de-identified human cell lines.

Content Warnings

- ID
    cw-1
  Name
    ContentWarning
  Warnings
    - None noted.

Deidentification

ID
  deid-1
Name
  Deidentification
Description
  - Human Subjects
      False
  - De Identified Samples
      True
  - Fda Regulated
      False

Acquisition Methods

- ID
    acq-1
  Name
    InstanceAcquisition
  Description
    - Data were directly observed/measured via ICC-IF confocal microscopy (imaging), SEC-MS (proteomics), and CRISPRi perturb-seq (scRNA-seq).

Collection Mechanisms

- ID
    mech-1
  Name
    CollectionMechanism
  Description
    - ICC-IF staining and confocal microscopy (multi-channel imaging).
    - Size exclusion chromatography followed by mass spectrometry (SEC-MS).
    - CRISPR interference (CRISPRi) perturb-seq single-cell RNA sequencing.

Data Collectors

- ID
    collectors-1
  Name
    DataCollector
  Description
    - CM4AI consortium labs at UC San Diego, UC San Francisco, Stanford University, and University of Virginia.

Collection Timeframes

- ID
    time-1
  Name
    CollectionTimeframe
  Description
    - Data Creation Date
        2025-02-27; release designated June 2025; published 2025-07-01.
    - Additional image archives published 2025-10-22.

Ethical Reviews

- ID
    er-1
  Name
    EthicalReview
  Description
    - Ethical review oversight noted: Vardit Ravitsky and Jean-Christophe Bélisle-Pipon.
    - Data Governance Committee
        Jillian Parker (contact provided on dataset page).

Data Protection Impacts

- ID
    dpi-1
  Name
    DataProtectionImpact
  Description
    - Minimal data protection risks anticipated as datasets are derived from de-identified human cell lines; no human subjects involved.

Preprocessing Strategies

- ID
    prep-1
  Name
    PreprocessingStrategy
  Description
    - Imaging channels include DAPI (nuclei), calreticulin (ER), tubulin (microtubules), and protein-of-interest antibody; modality-specific preprocessing details may be described in RO-Crates and provenance graphs.

Raw Sources

- ID
    raw-1
  Name
    RawData
  Description
    - External Repositories Host Raw/primary Data
        NCBI SRA BioProject and MassIVE.

Maintainers

Description | ID | Name
--- | --- | ---
Long-term preservation in the University of Virginia Dataverse with committed institutional funds; dataset point of contact listed as Trey Ideker. | maint-1 | Maintainer
{'Data Governance Committee': 'Jillian Parker (contact listed on dataset page).'} | maint-2 | Maintainer

Is Deidentified

ID
  deid-collection
Name
  Deidentification
Description
  - De-identified samples; no human subjects.

Is Tabular
no
🚀

## Uses

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

Tasks

ID | Name | Response
--- | --- | ---
task-1 | Task | AI model training and benchmarking on cellular imaging, scRNAseq, and proteomics.
task-2 | Task | Cellular process analysis and mapping of cell architecture under treatments or perturbations.

Existing Uses

- ID
    uses-1
  Name
    ExistingUse
  Description
    - Related publications include 2024 preprints describing CM4AI and a perturbation cell atlas; see dataset "Related Publication" section for details.

Other Tasks

- ID
    other-1
  Name
    OtherTask
  Description
    - Benchmarking of multimodal integration methods and cross-modality representation learning.

Future Use Impacts

- ID
    fut-1
  Name
    FutureUseImpact
  Description
    - Potential biases due to use of specific human cell lines; not representative of all biological variants. Interim release lacks computed cell maps; modality-specific protein coverage differs, which may affect integrative analyses.

Discouraged Uses

- ID
    no-clinical
  Name
    DiscouragedUse
  Description
    - Not for clinical decision-making or any context involving patient care without appropriate regulatory oversight and approval.

License And Use Terms

ID
  lic-1
Name
  LicenseAndUseTerms
Description
  - CC BY-NC-SA 4.0; proper citation required as per repository community norms.

📤

## Distribution

How will the dataset be distributed?

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

ID
  veracc-1
Name
  VersionAccess
Description
  - Versioned in the University of Virginia Dataverse; this record reflects Version 2.0.

🔄

## Maintenance

How will the dataset be maintained?

Version
2.0
Last Updated On
2025-10-22
Updates

ID
  update-plan-1
Name
  UpdatePlan
Description
  - Dataset will be regularly updated and augmented through the end of the project in November 2026.
  - Updates on a quarterly basis.

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