# dataverse 10.18130 V3 F3TD5R tab metadata d4d

Datasheet for Dataset - Human Readable Format

🎯

## Motivation

Why was the dataset created?

Purposes

- Name
    CM4AI project purpose
  Response
    Provide AI-ready multimodal datasets to support research in functional genomics and enable AI model training on cellular architecture and processes.

Funders

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

📊

## Composition

What do the instances represent?

Instances

Data Type | Instance Type | Name | Representation
--- | --- | --- | ---
Single-cell RNA sequencing (perturb-seq) counts/metadata. | scRNA-seq cells and perturbation targets. | Perturb-seq in KOLF2.1J iPSCs | Single-cell transcriptomic profiles under CRISPRi perturbations.
Mass spectrometry-based proteomics (SEC-MS) across iPSCs, NPCs, neurons, cardiomyocytes, and MDA-MB-... | Protein fractions, peptide/spectral features, quantified complexes. | SEC-MS across cell types | Protein-protein interaction and complex abundance via size exclusion chromatography mass spectrometr...
Immunofluorescence microscopy images for 464 proteins under untreated, paclitaxel, and vorinostat tr... | Confocal microscopy images with multiple channels (DAPI, calreticulin/ER, tubulin, protein-of-intere... | IF images in MDA-MB-468 with treatments | Subcellular protein localization images under chemotherapy conditions.

Subpopulations

- Name
    Cell types and conditions
  Identification
    - KOLF2.1J human iPSCs
    - iPSC-derived NPCs
    - iPSC-derived neurons
    - iPSC-derived cardiomyocytes
    - MDA-MB-468 breast cancer cells (untreated, paclitaxel, vorinostat)
  Distribution
    - Modality coverage varies by protein set; SEC-MS, IF, and perturb-seq protein targets incompletely overlap in this release.

Distribution Formats

- Name
    Distribution channels and formats
  Description
    - Public distribution via University of Virginia Dataverse; files include ZIP archives (images), HTML (datasheet, provenance graphs), and JSON (RO-Crate metadata).

Distribution Dates

Description | Name
--- | ---
2025-07-01 (Version 2.0) | Initial publication
2025-10-22 (IF image ZIP archives) | Imaging archives publication

🔍

## 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).
Page
https://doi.org/10.18130/V3/F3TD5R
Issued
2025-07-01
Created On
2025-02-27
Publisher
https://dataverse.lib.virginia.edu
Keywords

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

Created By

- Clark T (university Of Virginia) Orcid
    https://orcid.org/0000-0003-4060-7360
- Parker J (university Of California, San Diego) Orcid
    https://orcid.org/0000-0003-4535-3486
- Al Manir S (university Of Virginia) Orcid
    https://orcid.org/0000-0003-4647-3877
- Axelsson U (KTH Royal Institute of Technology)
- Ballllosero Navarro F (stanford University) Orcid
    https://orcid.org/0000-0002-4180-422X
- Chinn B (University of California San Diego)
- Churas Cp (university Of California San Diego) Orcid
    https://orcid.org/0000-0001-9998-705X
- Dailamy A (university Of California, San Diego) Orcid
    https://orcid.org/0000-0002-6711-8260
- Doctor Y (university Of California, San Diego) Orcid
    https://orcid.org/0009-0009-0483-7506
- Fall J (KTH - Royal Institute of Technology)
- Forget A (university Of California San Francisco) Orcid
    https://orcid.org/0000-0003-0223-0312
- Gao J (university Of California San Diego) Orcid
    https://orcid.org/0000-0002-6311-3526
- Hansen Jn (stanford University) Orcid
    https://orcid.org/0000-0002-4650-9094
- Hu M (university Of California San Diego) Orcid
    https://orcid.org/0000-0002-1571-8029
- Johannesson A (KTH - Royal Institute of Technology)
- Khaliq H (University of California San Diego)
- Lee Yh (university Of California San Diego) Orcid
    https://orcid.org/0000-0003-0917-355X
- Lenkiewicz J (university Of California San Diego) Orcid
    https://orcid.org/0000-0001-7252-8638
- Levinson Ma (university Of Virginia) Orcid
    https://orcid.org/0000-0003-0384-8499
- Marquez C (university Of California San Diego) Orcid
    https://orcid.org/0000-0003-3960-420X
- Metallo C (university Of California San Diego) Orcid
    https://orcid.org/0000-0003-2404-3040
- Muralidharan M (University of California San Francisco)
- Nourreddine S (university Of California San Diego) Orcid
    https://orcid.org/0000-0003-3881-7588
- Niestroy J (university Of Virginia) Orcid
    https://orcid.org/0000-0002-1103-3882
- Obernier K (university Of California San Francisco) Orcid
    https://orcid.org/0000-0002-4025-1299
- Pan E (University of California San Diego)
- Polacco B (University of California San Francisco)
- Pratt D (university Of California San Diego) Orcid
    https://orcid.org/0000-0002-1471-9513
- Qian G (university Of California San Diego) Orcid
    https://orcid.org/0009-0005-4217-2745
- Schaffer L (university Of California San Diego) Orcid
    https://orcid.org/0000-0001-6339-9141
- Sigaeva A (kth Royal Institute Of Technology) Orcid
    https://orcid.org/0000-0003-3361-3797
- Thaker S (university Of Alabama At Birmingham) Orcid
    https://orcid.org/0000-0001-6730-2773
- Zhang Y (University of California San Diego)
- Bélisle Pipon Jc (simon Fraser University) Orcid
    https://orcid.org/0000-0002-8965-8153
- Brandt C (yale University) Orcid
    https://orcid.org/0000-0001-8179-1796
- Chen Jy (the University Of Alabama At Birmingham) Orcid
    https://orcid.org/0000-0002-6112-415X
- Ding Y (university Of Texas At Austin) Orcid
    https://orcid.org/0000-0003-2567-2009
- Fodeh S (yale University) Orcid
    https://orcid.org/0000-0003-4664-3143
- Krogan N (university Of California San Francisco) Orcid
    https://orcid.org/0000-0003-4902-337X
- Lundberg E (stanford University) Orcid
    https://orcid.org/0000-0001-7034-0850
- Mali P (university Of California San Diego) Orcid
    https://orcid.org/0000-0002-3383-1287
- Payne Foster P (university Of Alabama) Orcid
    https://orcid.org/0000-0002-3508-3577
- Ratcliffe S (university Of Virginia) Orcid
    https://orcid.org/0000-0002-6644-8284
- Ravitsky V (university Of Montreal) Orcid
    https://orcid.org/0000-0002-7080-8801
- Sali A (university Of California San Diego) Orcid
    https://orcid.org/0000-0003-0435-6197
- Schulz W (yale University) Orcid
    https://orcid.org/0000-0002-2048-4028
- Ideker T (university Of California San Diego) Orcid
    https://orcid.org/0000-0002-1708-8454

Addressing Gaps

- Name
    Bridge2AI functional genomics gap
  Response
    Create standardized, AI-ready datasets integrating protein localization, protein-protein interactions, and perturb-seq in disease-relevant human cell lines.

Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Trey Ideker | - | -

External Resources

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

Confidential Elements

- Name
    Human subject status
  Description
    - Human Subjects
        No; data derived from commercially available de-identified human cell lines.

Content Warnings

- Name
    Prohibited clinical use
  Warnings
    - Not for clinical decision-making or patient care without appropriate regulatory oversight and approval.

Sensitive Elements

- Name
    Human-derived cell line data
  Description
    - Data are from de-identified, commercially available human cell lines; not linked to individuals.

Acquisition Methods

1. Name
     Laboratory acquisition
   Description
     - Data generated by participating CM4AI labs using standardized wet-lab and imaging protocols.
   Was Directly Observed
     Yes (imaging, mass spectrometry, sequencing)
   Was Reported By Subjects
     False
   Was Inferred Derived
     Partial (some analyses derived from raw measurements)
   Was Validated Verified
     Not specified in this release; provenance graphs provided for select components.

Collection Mechanisms

- Name
    Experimental modalities
  Description
    - Perturb-seq (CRISPRi-based scRNA-seq) in undifferentiated KOLF2.1J iPSCs.
    - Size exclusion chromatography mass spectrometry (SEC-MS) in iPSCs, NPCs, neurons, cardiomyocytes, and MDA-MB-468 (treated/untreated).
    - Immunofluorescence confocal microscopy (IF) imaging in MDA-MB-468 with multiplexed channels (DAPI, ER, tubulin, protein-of-interest).

Data Collectors

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Contributor | Participating labs | - | -

Collection Timeframes

- Name
    Release and creation dates
  Description
    - Data Creation Date
        2025-02-27; Dataset description updated 2025-06-30; Publication Date: 2025-07-01.

Ethical Reviews

- Name
    Data governance and ethics
  Description
    - Ethical Review Oversight
        Vardit Ravitsky (The Hastings Center) and Jean-Christophe Bélisle-Pipon (Simon Fraser University). Data Governance Committee contact: Jillian Parker (jillianparker@health.ucsd.edu). Human Subjects: No. De-identified Samples: Yes. FDA Regulated: No.

Preprocessing Strategies

- Name
    Provenance and pipelines
  Description
    - Modality-specific processing documented via RO-Crate metadata and provenance graph HTMLs for images and mass spectrometry subsets; computed cell maps are not included in this release.

Raw Sources

- Name
    Raw/primary data access
  Description
    - External raw or primary data can be accessed via linked repositories (NCBI SRA BioProject for perturb-seq; MassIVE for proteomics).

Maintainers

- Name
    Hosting and stewardship
  Description
    - Long-term preservation in the University of Virginia Dataverse with committed institutional support; CM4AI consortium to provide updates through November 2026.

Is Deidentified

Name
  De-identification status
Description
  - Yes—samples are de-identified and derived from commercially available human cell lines; no human subjects research.

Subsets

Compression | Description | Format | ID | Is A | Issued | Md5 | Media Type | Name | Path | Title
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ZIP | Confocal IF images (DAPI, ER/calreticulin, tubulin, protein-of-interest) for 464 proteins in MDA-MB-... |  | cm4ai-ifimages-mda-mb-468-untreated | DataSubset | 2025-10-22 | a98affcc05429650c6bb3906cd836d55 | application/zip | IF images — MDA-MB-468 untreated | Images/cm4ai-ifimages-mda-mb-468-untreated.zip | Immunofluorescence images for 464 proteins — MDA-MB-468 untreated
ZIP | Confocal IF images for 464 proteins in MDA-MB-468 cells treated with paclitaxel. |  | cm4ai-ifimages-mda-mb-468-paclitaxel | DataSubset | 2025-10-22 | 0d972b80744344ddeede516a0cf6e3d7 | application/zip | IF images — MDA-MB-468 paclitaxel | Images/cm4ai-ifimages-mda-mb-468-paclitaxel.zip | Immunofluorescence images for 464 proteins — MDA-MB-468 paclitaxel
ZIP | Confocal IF images for 464 proteins in MDA-MB-468 cells treated with vorinostat. |  | cm4ai-ifimages-mda-mb-468-vorinostat | DataSubset | 2025-10-22 | ad4e68ccc14b0f3349dad3321e7b81b2 | application/zip | IF images — MDA-MB-468 vorinostat | Images/cm4ai-ifimages-mda-mb-468-vorinostat.zip | Immunofluorescence images for 464 proteins — MDA-MB-468 vorinostat
| HTML datasheet summarizing key release information. |  | release-ro-crate-datasheet | DataSubset | 2025-07-01 | 599c9ece9b88b3ce797b82463b4a1eb4 | text/html | Release datasheet (RO-Crate HTML) | release-ro-crate-datasheet.html | CM4AI release datasheet
| RO-Crate JSON-LD metadata describing the release and linking to modality crates. | JSON | release-ro-crate-metadata | DataSubset | 2025-07-01 | 99f9e00053bff3020fd9832a3a518bbb | application/json | Release RO-Crate metadata | release-ro-crate-metadata.json | RO-Crate metadata with pointers to sub-RO-Crates
| Provenance graph HTML for paclitaxel imaging subset (download to view properly). |  | images-paclitaxel-provenance-graph | DataSubset | 2025-07-01 | e38e63e4c8dfc5808a5ffa2d7829fc38 | text/html | IF images paclitaxel provenance graph | Images/paclitaxel/Images-paclitaxel-provenance-graph.html | Images paclitaxel provenance graph (HTML)
| Provenance graph HTML for untreated imaging subset (download to view properly). |  | images-untreated-provenance-graph | DataSubset | 2025-07-01 | 1a3b510f74d3f8647e07c6559ce64ee8 | text/html | IF images untreated provenance graph | Images/untreated/Images-untreated-provenance-graph.html | Images untreated provenance graph (HTML)
| Provenance graph HTML for vorinostat imaging subset (download to view properly). |  | images-vorinostat-provenance-graph | DataSubset | 2025-07-01 | 58935fe4e254b31d33fed019f24c7668 | text/html | IF images vorinostat provenance graph | Images/vorinostat/Images-vorinostat-provenance-graph.html | Images vorinostat provenance graph (HTML)
| RO-Crate JSON metadata describing mass spectrometry cancer cell subset. | JSON | mass-spec-cancer-cells-ro-crate | DataSubset | 2025-07-01 | 3a7063bb391ea5e05a32ba5da5f4b2f8 | application/json | Mass spec cancer cells RO-Crate metadata | mass-spec/cancer-cells/mass-spec-cancer-cells-ro-crate-metadata.json | Mass spectrometry (cancer cells) RO-Crate metadata

Third Party Sharing

Name
  Public distribution
Description
  Dataset is publicly distributed via University of Virginia Dataverse; raw/primary data are also hosted in external third-party repositories (NCBI SRA, MassIVE).

🚀

## Uses

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

Tasks

Name | Response
--- | ---
AI model training | Training and evaluation of AI/ML models on functional genomics modalities (scRNA-seq perturb-seq, SE...
Cellular process analysis | Analyze cell architectural changes and interactions under disease-relevant conditions, treatments, a...

Existing Uses

Description | Name
--- | ---
{'Clark T, Parker J, Schaffer L, Obernier K, 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'} | CM4AI preprints
{'Nourreddine S, Doctor Y, Dailamy A, Forget A, et al. A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS. bioRxiv. 2024 Nov 4;2024.11.03.621734. PMCID': 'PMC11580897 doi: https://doi.org/10.1101/2024.11.03.621734'} | Perturbation cell atlas

Other Tasks

- Name
    Additional potential uses
  Description
    - Benchmarking multimodal integration methods; evaluating treatment response signatures; mapping protein complexes and localization patterns.

Future Use Impacts

- Name
    Limitations and risk considerations
  Description
    - Interim Beta release; computed cell maps not yet included.
    - Modality protein target sets incompletely overlap; may affect integrative analyses.
    - Most suitable for bioinformatics analyses of individual datasets; domain expertise required.
    - Data derived from specific cell lines and conditions; may not represent biological diversity across populations.

Discouraged Uses

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

License And Use Terms

Name
  Dataverse license and norms
Description
  - CC BY-NC-SA 4.0. Community norms expect proper citation using the dataset citation provided on the dataset page.

📤

## Distribution

How will the dataset be distributed?

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

## Maintenance

How will the dataset be maintained?

Version
2.0
Updates

Name
  Update plan
Description
  - Dataset will be regularly updated and augmented through the end of the project in November 2026, with quarterly updates. Updates and preservation via University of Virginia Dataverse.

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