# dataverse 10.18130 V3 F3TD5R tab versions d4d

Datasheet for Dataset - Human Readable Format

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## Motivation

Why was the dataset created?

Purposes

- Name
    Purpose
  Response
    AI-ready datasets to support research in functional genomics, including training and evaluating AI models for cell architecture and process analysis.

Funders

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

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## Composition

What do the instances represent?

Instances

Data Type | Instance Type | Name | Representation
--- | --- | --- | ---
Raw reads available via SRA; processed matrices may be provided in linked repositories. | scRNA-seq cells and perturbation targets | CRISPRi perturb-seq (scRNA-seq) in KOLF2.1J iPSCs | Single-cell transcriptional profiles following CRISPRi perturbations in undifferentiated KOLF2.1J iP...
Mass spectrometry raw/processed files in external MassIVE repositories. | Protein complexes and interactome fractions across cell types and conditions | SEC-MS proteomics | Protein-protein interaction and complex profiling by size exclusion chromatography followed by mass ...
Image archives (ZIP) containing multi-channel IF images across treatments (untreated, paclitaxel, vo... | Images and associated acquisition/analysis metadata | Immunofluorescence (IF) imaging in MDA-MB-468 cells | Confocal microscopy images of protein localization with multiple channels (DAPI, ER, microtubules, p...

Distribution Formats
Distribution Dates
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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 Beta Data Release of Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org), the Functional Genomics Grand Challenge in the NIH Bridge2AI program. The release includes: CRISPRi perturb-seq data in undifferentiated KOLF2.1J iPSCs; size exclusion chromatography mass spectrometry (SEC-MS) data in undifferentiated KOLF2.1J iPSCs, iPSC-derived NPCs, neurons, cardiomyocytes, and treated and untreated MDA-MB-468 breast cancer cells; and immunofluorescence (IF) images in MDA-MB-468 breast cancer cells with and without chemotherapy (vorinostat and paclitaxel). Human subjects: No. De-identified samples: Yes. FDA regulated: No. Some datasets are under temporary pre-publication embargo. Computed cell maps are not included in this release.
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
- 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

Language
en
Created By

- CM4AI Project Team
- Clark T
- Parker J
- Ideker T
- Lundberg E
- Krogan N
- Mali P
- Sali A
- Schulz W
- Brandt C
- Fodeh S
- Levinson MA
- Ratcliffe S
- Nourreddine S
- Pratt D
- Schaffer L
- Obernier K
- Bélisle-Pipon JC

Status
bibo:draft
Addressing Gaps
Creators

Role | Name | ORCID | Affiliation
--- | --- | --- | ---
Principal Investigator | Trey Ideker | 0000-0002-1708-8454 | University of California San Diego

External Resources

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

Collection Mechanisms

- Name
    Data Collection Mechanisms
  Description
    - CRISPRi perturb-seq using scRNA-seq
    - Size exclusion chromatography followed by mass spectrometry (SEC-MS)
    - Immunofluorescence-based staining (ICC-IF) and confocal microscopy

Data Collectors

- Name
    Data Collectors
  Description
    - University of California San Diego
    - University of California San Francisco
    - Stanford University
    - University of Virginia

Collection Timeframes

- Name
    Data Collection/Creation Timeframe
  Description
    - Data Creation Date
        2025-02-27
    - Release Finalized As Of
        2025-06-30
    - Dataset Published
        2025-07-01
    - Additional Image Archives Published
        2025-10-22

Ethical Reviews

- Name
    Data Governance & 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 Bélisle-Pipon (jean-christophe_belisle-pipon@sfu.ca)

Is Deidentified

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

Ip Restrictions
Regulatory Restrictions
Maintainers
Resources

Description | Format | ID | Issued | Md5 | Media Type | Name | Title
--- | --- | --- | --- | --- | --- | --- | ---
HTML datasheet summarizing key release information. |  | doi:10.18130/V3/F3TD5R#release-ro-crate-datasheet.html | 2025-07-01 | 599c9ece9b88b3ce797b82463b4a1eb4 | text/html | release-ro-crate-datasheet.html | CM4AI Release HTML Datasheet
Release RO-Crate with pointers to sub RO-Crates. | JSON | doi:10.18130/V3/F3TD5R#release-ro-crate-metadata.json | 2025-07-01 | 99f9e00053bff3020fd9832a3a518bbb | application/json | release-ro-crate-metadata.json | CM4AI Release RO-Crate Metadata
Spatial localization of 464 proteins in MDA-MB-468 cells (untreated), imaged by ICC-IF and confocal ... |  | doi:10.18130/V3/F3TD5R#cm4ai-ifimages-mda-mb-468-untreated.zip | 2025-10-22 | a98affcc05429650c6bb3906cd836d55 | application/zip | cm4ai-ifimages-mda-mb-468-untreated.zip | IF images – MDA-MB-468, untreated
Spatial localization of 464 proteins in MDA-MB-468 cells treated with paclitaxel, imaged by ICC-IF a... |  | doi:10.18130/V3/F3TD5R#cm4ai-ifimages-mda-mb-468-paclitaxel.zip | 2025-10-22 | 0d972b80744344ddeede516a0cf6e3d7 | application/zip | cm4ai-ifimages-mda-mb-468-paclitaxel.zip | IF images – MDA-MB-468, paclitaxel-treated
Spatial localization of 464 proteins in MDA-MB-468 cells treated with vorinostat, imaged by ICC-IF a... |  | doi:10.18130/V3/F3TD5R#cm4ai-ifimages-mda-mb-468-vorinostat.zip | 2025-10-22 | ad4e68ccc14b0f3349dad3321e7b81b2 | application/zip | cm4ai-ifimages-mda-mb-468-vorinostat.zip | IF images – MDA-MB-468, vorinostat-treated
HTML provenance graph for paclitaxel-treated image workflow (download to view). |  | doi:10.18130/V3/F3TD5R#Images-paclitaxel-provenance-graph.html | 2025-07-01 | e38e63e4c8dfc5808a5ffa2d7829fc38 | text/html | Images-paclitaxel-provenance-graph.html | IF images (paclitaxel) provenance graph
HTML provenance graph for untreated image workflow (download to view). |  | doi:10.18130/V3/F3TD5R#Images-untreated-provenance-graph.html | 2025-07-01 | 1a3b510f74d3f8647e07c6559ce64ee8 | text/html | Images-untreated-provenance-graph.html | IF images (untreated) provenance graph
HTML provenance graph for vorinostat-treated image workflow (download to view). |  | doi:10.18130/V3/F3TD5R#Images-vorinostat-provenance-graph.html | 2025-07-01 | 58935fe4e254b31d33fed019f24c7668 | text/html | Images-vorinostat-provenance-graph.html | IF images (vorinostat) provenance graph
HTML provenance graph for SEC-MS cancer cell workflow (download to view). |  | doi:10.18130/V3/F3TD5R#mass-spec-cancer-cells-provenance-graph.html | 2025-07-01 | 931ad9b552562024cb84ebe62d1f1838 | text/html | mass-spec-cancer-cells-provenance-graph.html | Mass spec (cancer cells) provenance graph
RO-Crate metadata for mass spectrometry cancer cell subset. | JSON | doi:10.18130/V3/F3TD5R#mass-spec-cancer-cells-ro-crate-metadata.json | 2025-07-01 | 3a7063bb391ea5e05a32ba5da5f4b2f8 | application/json | mass-spec-cancer-cells-ro-crate-metadata.json | Mass spec (cancer cells) RO-Crate metadata

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## Uses

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

Tasks

Name | Response
--- | ---
Task | AI model training
Task | Cellular process analysis
Task | Analysis of cell architectural changes and interactions under disease, treatment, or genetic perturb...

Existing Uses

- Name
    Related Publications and Uses
  Description
    - Clark T, Parker J, Schaffer L, Obernier K, Al Manir S, Churas Cp, Dailamy A, Doctor Y, Forget A, Hansen Jn, Hu M, Lenkiewicz J, Levinson Ma, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle Pipon Jc, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T. 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, Doctor Y, Dailamy A, Forget A, Lee Yh, Chinn B, Khaliq H, Polacco B, Muralidharan M, Pan E, Zhang Y, Sigaeva A, Hansen Jn, Gao J, Parker Ja, Obernier K, Clark T, Chen Jy, Metallo C, Lundberg E, Ideker T, Krogan N, Mali P. 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

Other Tasks
Future Use Impacts
Discouraged Uses
License And Use Terms
Use Repository
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## Distribution

How will the dataset be distributed?

License
CC BY-NC-SA 4.0
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## Maintenance

How will the dataset be maintained?

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