# dataverse 10.18130 V3 B35XWX tab versions d4d

Datasheet for Dataset - Human Readable Format

🎯

## Motivation

Why was the dataset created?

Purposes

- Name
    CM4AI goal
  Response
    Provide AI-ready datasets and provenance for mapping human cell architecture from disease-relevant cell lines, enabling machine learning and AI research on genomics, proteomics, and imaging modalities.

Funders

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

📊

## Composition

What do the instances represent?

Instances

Counts | Data Type | Instance Type | Label | Name | Representation
--- | --- | --- | --- | --- | ---
11739 | Raw sequencing reads and processed gene-expression/fitness features (per RO-Crate packages). | Single cells; gene perturbations | Transcriptional and fitness phenotypes per targeted gene perturbation. | CRISPRi perturb-seq in KOLF2.1J hiPSCs | Single-cell transcriptomes and fitness phenotypes from CRISPRi perturbations in undifferentiated KOL...
563 | Multi-channel immunofluorescence images under untreated and drug-treated conditions (vorinostat, pac... | Cell images; protein localization | Protein-of-interest localization patterns across conditions. | Protein localization IF imaging in MDA-MB-468 | Immunofluorescence confocal microscopy images with four channels (DAPI, ER/calreticulin, tubulin, pr...
| Mass spectrometry intensity profiles indicative of protein complex size distributions. | Proteins; chromatographic fractions |  | Protein-protein interaction SEC-MS | Size exclusion chromatography–mass spectrometry profiles from undifferentiated KOLF2.1J iPSCs and iP...

Subpopulations

- Identification
    - Undifferentiated KOLF2.1J human iPSCs and iPSC-derived NPCs, neurons, and cardiomyocytes.
    - MDA-MB-468 breast cancer cells (untreated and treated with vorinostat or paclitaxel).
  Distribution
    - Multiple experimental conditions including presence/absence of chemotherapy.

Distribution Formats

- Description
    - RO-Crate JSON metadata packages.
    - ZIP archives for imaging data distributions.
  Used Software

    Name | URL
    --- | ---
    RO-Crate | https://www.researchobject.org/ro-crate/
    FAIRSCAPE | https://fairscape.net

Distribution Dates

- Description
    - 2025-03-03 (publication date on Dataverse).

🔍

## Collection Process

How was the data acquired?

ID *
doi:10.18130/V3/B35XWX
Name
Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
Title
Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)
Description
This dataset is the March 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 and iPSC-derived NPCs, neurons, and cardiomyocytes; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel). CM4AI output data are packaged with provenance graphs and rich metadata as AI-ready datasets in RO-Crate format using the FAIRSCAPE framework. Data presented here will be augmented regularly through the end of the project. CM4AI is a collaboration of UCSD, UCSF, Stanford, UVA, Yale, UA Birmingham, Simon Fraser University, and the Hastings Center. This data is Copyright (c) 2025 The Regents of the University of California except where otherwise noted. Spatial proteomics raw image data is copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University. Dataset licensed for reuse under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license (https://creativecommons.org/licenses/by-nc-sa/4.0/). Attribution is required to the copyright holders and the authors. Any publications referencing this data or derived products should cite the Related Publication below, as well as directly citing this data collection (2025-03-04). (2025-03-07)
Language
en
Publisher
https://dataverse.lib.virginia.edu
Issued
2025-03-03
Page
https://doi.org/10.18130/V3/B35XWX
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

Created On
2025-02-27
Conforms To
https://w3id.org/ro/crate
Is Tabular
no
Addressing Gaps

- Name
    AI-ready cell maps
  Response
    Create standardized, provenance-rich, FAIR AI-ready datasets to accelerate AI methods for functional genomics and cell architecture mapping.

Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Trey Ideker | - | Cell Maps for Artificial Intelligence (CM4AI)
Principal Investigator | Emma Lundberg | - | Stanford University
Principal Investigator | Nevan Krogan | - | University of California San Francisco

Acquisition Methods

1. Description
     - Data acquired via high-throughput scRNAseq (perturb-seq), confocal fluorescence microscopy (IF), and SEC-MS proteomics.
   Was Directly Observed
     True
   Was Reported By Subjects
     False
   Was Inferred Derived
     partial
   Was Validated Verified
     not specified

Collection Mechanisms

- Description
    - Hardware and instruments include sequencing platforms for scRNAseq, confocal microscopes for IF imaging, and mass spectrometers for SEC-MS; datasets packaged as RO-Crates using the FAIRSCAPE framework.

Data Collectors

- Description
    - Lundberg Lab at Stanford University (IF imaging).
    - Nevan Krogan Laboratory at UCSF (SEC-MS).
    - CM4AI collaboration across UCSD, UCSF, Stanford, UVA, Yale, UAB, Simon Fraser University, and the Hastings Center.

Collection Timeframes

- Description
    - Data creation date 2025-02-27; published 2025-03-03.

External Resources

1. External Resources
     - SEC-MS data will be uploaded to PRIDE when available.
   Future Guarantees
     - Not specified.
   Archival
     - Planned archival in PRIDE for proteomics data.
   Restrictions
     - Subject to repository terms and the dataset’s CC BY-NC-SA 4.0 license.

Is Deidentified

Description
  - No individually identifiable human data; experiments are on established human cell lines.

Maintainers

- Description
    - Point Of Contact
        Trey Ideker (University of California San Diego). Contact via Dataverse dataset page.

Subsets

Compression | Description | Format | Is Tabular | Issued | Md5 | Media Type | Name | Title
--- | --- | --- | --- | --- | --- | --- | --- | ---
| RO-Crate metadata for the expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated... | JSON | no | 2025-03-03 | cbdb263b1c099396d75e16f00a79a818 | application/json | CRISPR Perturbation Cell Atlas ro-crate-metadata.json | ro-crate-metadata.json
| RO-Crate metadata for raw sequence data from the CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs. | JSON | no | 2025-03-03 | 1cafefa32a897998e3e2ba0a29a3ef5c | application/json | CRISPR Perturbation RNA Sequences - Raw Sequences ro-crate-metadata.json | ro-crate-metadata.json
ZIP | Spatial localization of 563 proteins in MDA-MB-468 cells treated with paclitaxel imaged by ICC-IF an... |  | no | 2025-03-03 | 9422486c80bc9e1d35b2fbbc72a5f043 | application/zip | cm4ai-v0.6-beta-if-images-paclitaxel.zip | Protein Localization Subcellular Images (paclitaxel)
ZIP | Spatial localization of 563 proteins in untreated MDA-MB-468 cells imaged by ICC-IF and confocal mic... |  | no | 2025-03-03 | 0b4d129f5fbc3bb7f7ea564cd032cef7 | application/zip | cm4ai-v0.6-beta-if-images-untreated.zip | Protein Localization Subcellular Images (untreated)
ZIP | Spatial localization of 563 proteins in MDA-MB-468 cells treated with vorinostat imaged by ICC-IF an... |  | no | 2025-03-03 | ac577109a41a9806978461157b777d52 | application/zip | cm4ai-v0.6-beta-if-images-vorinostat.zip | Protein Localization Subcellular Images (vorinostat)
| RO-Crate metadata for SEC-MS dataset from undifferentiated KOLF2.1J hiPSCs (with additional iPSC-der... | JSON | no | 2025-03-03 | cb67e7749b15ce87b9042a9feba9d032 | application/json | Protein-protein Interaction SEC-MS ro-crate-metadata.json | ro-crate-metadata.json

🚀

## Uses

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

Tasks

- Name
    AI/ML analysis across modalities
  Response
    Analysis and model development using CRISPRi perturb-seq scRNAseq, SEC-MS protein interaction profiling, and immunofluorescence protein localization images.

License And Use Terms

Description
  - Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). Attribution required to the copyright holders and the authors.

Existing Uses

- Description
    - Related publications include bioRxiv preprints on CM4AI cell maps and the perturbation cell atlas (e.g., doi:10.1101/2024.05.21.589311; doi:10.1101/2024.11.03.621734).

📤

## Distribution

How will the dataset be distributed?

DOI
doi:10.18130/V3/B35XWX
License
CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/)
🔄

## Maintenance

How will the dataset be maintained?

Version
1.4
Last Updated On
2025-03-07
Updates

Description
  - Data will be augmented regularly through the end of the project; subsequent releases expected.

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