dataverse 10.18130 V3 F3TD5R tab versions d4d

Datasheet for Dataset - Human Readable Format

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Motivation

Why was the dataset created?

  • Name
    Purpose
    Response
    AI-ready datasets to support research in functional genomics, including training and evaluating AI models for cell architecture and process analysis.
GrantorGrant NameGrant Number
National Institutes of Health1OT2OD032742-011OT2OD032742-01
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Composition

What do the instances represent?

Data TypeInstance TypeNameRepresentation
Raw reads available via SRA; processed matrices may be provided in linked repositories.scRNA-seq cells and perturbation targetsCRISPRi perturb-seq (scRNA-seq) in KOLF2.1J iPSCsSingle-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 conditionsSEC-MS proteomicsProtein-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 metadataImmunofluorescence (IF) imaging in MDA-MB-468 cellsConfocal microscopy images of protein localization with multiple channels (DAPI, ER, microtubules, p...
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Collection Process

How was the data acquired?

doi:10.18130/V3/F3TD5R
CM4AI June 2025 Data Release (Beta)
Cell Maps for Artificial Intelligence - June 2025 Data Release (Beta)
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.
https://doi.org/10.18130/V3/F3TD5R
2025-07-01
2025-02-27
https://dataverse.lib.virginia.edu/
  • 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
en
  • 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
bibo:draft
RoleNameORCIDAffiliation
Principal InvestigatorTrey Ideker0000-0002-1708-8454University of California San Diego
  • 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
  • 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
  • Name
    Data Collectors
    Description
    • University of California San Diego
    • University of California San Francisco
    • Stanford University
    • University of Virginia
  • 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
  • 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)
Name
Deidentification
Description
  • Human Subjects
    False
  • De Identified Samples
    True
  • Fda Regulated
    False
DescriptionFormatIDIssuedMd5Media TypeNameTitle
HTML datasheet summarizing key release information.doi:10.18130/V3/F3TD5R#release-ro-crate-datasheet.html2025-07-01599c9ece9b88b3ce797b82463b4a1eb4text/htmlrelease-ro-crate-datasheet.htmlCM4AI Release HTML Datasheet
Release RO-Crate with pointers to sub RO-Crates.JSONdoi:10.18130/V3/F3TD5R#release-ro-crate-metadata.json2025-07-0199f9e00053bff3020fd9832a3a518bbbapplication/jsonrelease-ro-crate-metadata.jsonCM4AI 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.zip2025-10-22a98affcc05429650c6bb3906cd836d55application/zipcm4ai-ifimages-mda-mb-468-untreated.zipIF 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.zip2025-10-220d972b80744344ddeede516a0cf6e3d7application/zipcm4ai-ifimages-mda-mb-468-paclitaxel.zipIF 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.zip2025-10-22ad4e68ccc14b0f3349dad3321e7b81b2application/zipcm4ai-ifimages-mda-mb-468-vorinostat.zipIF 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.html2025-07-01e38e63e4c8dfc5808a5ffa2d7829fc38text/htmlImages-paclitaxel-provenance-graph.htmlIF images (paclitaxel) provenance graph
HTML provenance graph for untreated image workflow (download to view).doi:10.18130/V3/F3TD5R#Images-untreated-provenance-graph.html2025-07-011a3b510f74d3f8647e07c6559ce64ee8text/htmlImages-untreated-provenance-graph.htmlIF images (untreated) provenance graph
HTML provenance graph for vorinostat-treated image workflow (download to view).doi:10.18130/V3/F3TD5R#Images-vorinostat-provenance-graph.html2025-07-0158935fe4e254b31d33fed019f24c7668text/htmlImages-vorinostat-provenance-graph.htmlIF 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.html2025-07-01931ad9b552562024cb84ebe62d1f1838text/htmlmass-spec-cancer-cells-provenance-graph.htmlMass spec (cancer cells) provenance graph
RO-Crate metadata for mass spectrometry cancer cell subset.JSONdoi:10.18130/V3/F3TD5R#mass-spec-cancer-cells-ro-crate-metadata.json2025-07-013a7063bb391ea5e05a32ba5da5f4b2f8application/jsonmass-spec-cancer-cells-ro-crate-metadata.jsonMass spec (cancer cells) RO-Crate metadata
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Uses

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

NameResponse
TaskAI model training
TaskCellular process analysis
TaskAnalysis of cell architectural changes and interactions under disease, treatment, or genetic perturb...
  • 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
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Distribution

How will the dataset be distributed?

CC BY-NC-SA 4.0
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Maintenance

How will the dataset be maintained?

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