Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)

Version 1.4
Clark T; Parker J; Al Manir S; Axelsson U; Ballllosero Navarro F; Chinn B; Churas CP; Dailamy A; Doctor Y; Fall J; Forget A; Gao J; Hansen JN; Hu M; Johannesson A; Khaliq H; Lee YH; Lenkiewicz J; Levinson MA; Marquez C; Metallo C; Muralidharan M; Nourreddine S; Niestroy J; Obernier K; Pan E; Polacco B; Pratt D; Qian G; Schaffer L; Sigaeva A; Thaker S; Zhang Y; Bélisle-Pipon JC; Brandt C; Chen JY; Ding Y; Fodeh S; Krogan N; Lundberg E; Mali P; Payne-Foster P; Ratcliffe S; Ravitsky V; Sali A; Schulz W; Ideker T, 2025, "Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)", https://doi.org/10.18130/V3/B35XWX, University of Virginia Dataverse, V1
Learn about Data Citation Standards.
    The dataset is too large to download. Please select the files you need from the files table.
Contact Owner Share
Dataset Metrics
341 Downloads
Dataset 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)
Subject Medicine, Health and Life Sciences
Keyword 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
Related Publication References: 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
License/Data Use Agreement

CC BY-NC-SA 4.0

Table
Tree
Filter by
1 to 6 of 6 Files
ro-crate-metadata.json
CRISPR Perturbation Cell Atlas/JSON - 31.1 KB
Published Mar 3, 2025
44 Downloads
MD5: cbdb263b1c099396d75e16f00a79a818
This dataset represents an expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J human induced pluripotent stem cells (hiPSCs) mapping transcriptional and fitness phenotypes associated with 11,739 targeted genes, as part of the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org) Functional Genomics Grand Challenge, a component of the U.S. National Institute of Health’s (NIH) Bridge2AI program. We validated these findings via phenotypic, protein-interaction, and metabolic tracing assays.
ro-crate-metadata.json
CRISPR Perturbation RNA Sequences - Raw Sequences/JSON - 1000.1 KB
Published Mar 3, 2025
28 Downloads
MD5: 1cafefa32a897998e3e2ba0a29a3ef5c
This dataset represents raw sequence data from an expressed genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J human induced pluripotent stem cells (hiPSCs) mapping transcriptional and fitness phenotypes associated with 11,739 targeted genes, as part of the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org) Functional Genomics Grand Challenge, a component of the U.S. National Institute of Health’s (NIH) Bridge2AI program.
cm4ai-v0.6-beta-if-images-paclitaxel.zip
Protein Localization Subcellular Images/ZIP Archive - 2.6 GB
Published Mar 3, 2025
101 Downloads
MD5: 9422486c80bc9e1d35b2fbbc72a5f043
This data set displays the spatial localization of 563 proteins of interest in cells of the breast cancer cell line MDA-MB-468 treated with paclitaxel as imaged by immunofluorescence-based staining (ICC-IF) and confocal microscopy in the Lundberg Lab at Stanford University, as part of the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org) project. Nuclei were stained with DAPI (blue channel); endoplasmic reticulum with a calreticulin antibody (yellow channel); microtubules with tubulin antibody (red channel); and antibody against protein of interest (green channel).
Preview "Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip"
cm4ai-v0.6-beta-if-images-untreated.zip
Protein Localization Subcellular Images/ZIP Archive - 3.2 GB
Published Mar 3, 2025
76 Downloads
MD5: 0b4d129f5fbc3bb7f7ea564cd032cef7
This data set displays the spatial localization of 563 proteins of interest in untreated cells of the breast cancer cell line MDA-MB-468 as imaged by immunofluorescence-based staining (ICC-IF) and confocal microscopy in the Lundberg Lab at Stanford University, as part of the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org) project. Nuclei were stained with DAPI (blue channel); endoplasmic reticulum with a calreticulin antibody (yellow channel); microtubules with tubulin antibody (red channel); and antibody against protein of interest (green channel).
Preview "Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip"
cm4ai-v0.6-beta-if-images-vorinostat.zip
Protein Localization Subcellular Images/ZIP Archive - 2.8 GB
Published Mar 3, 2025
65 Downloads
MD5: ac577109a41a9806978461157b777d52
This data set displays the spatial localization of 563 proteins of interest in cells of the breast cancer cell line MDA-MB-468 treated with vorinostat as imaged by immunofluorescence-based staining (ICC-IF) and confocal microscopy in the Lundberg Lab at Stanford University, as part of the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org) project. Nuclei were stained with DAPI (blue channel); endoplasmic reticulum with a calreticulin antibody (yellow channel); microtubules with tubulin antibody (red channel); and antibody against protein of interest (green channel).
Preview "Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip"
ro-crate-metadata.json
Protein-protein Interaction SEC-MS/JSON - 2.9 KB
Published Mar 3, 2025
27 Downloads
MD5: cb67e7749b15ce87b9042a9feba9d032
This dataset was generated by size exclusion chromatography-mass spectroscopy (SEC-MS) on undifferentiated KOLF2.1J human induced pluripotent stem cells (hiPSCs), in the Nevan Krogan laboratory at the University of California San Francisco, as part of the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org) Functional Genomics Grand Challenge, a component of the U.S. National Institute of Health’s (NIH) Bridge2AI program. The data will be uploaded to Pride when available.
Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Enable access request
You must enable request access or add terms of access to restrict file access.
Save Changes
Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.
Edit Retention Period

The selected file or files have already been published. Contact an administrator to change the retention period date or reason of the file or files.
Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Continue
Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.
Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired or the files can only be transferred via Globus.

You may request access to any restricted file(s) by clicking the Request Access button.

Ineligible Files Selected

The selected file(s) may not be transferred because you have not been granted access or the file(s) have a retention period that has expired or the files are not Globus accessible.

You may request access to any restricted file(s) by clicking the Request Access button.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 1.9 GB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired.

Click Continue to download the files you have access to download.

Ineligible Files Selected

Some file(s) cannot be transferred. (They are restricted, embargoed, with an expired retention period, or not Globus accessible.)

Click Continue to transfer the elligible files.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Preview URL

You can create a Preview URL to copy and share with others who will not need a repository account to review this unpublished dataset version. Once the dataset is published or if the URL is disabled, the URL will no longer work and will point to a "Page not found" page. Only one Preview URL can be active for a single draft dataset.

To cite this data in publications, use the dataset's persistent ID instead of this URL. For more information about the Preview URL feature, please refer to the User Guide.

General Preview

Create a URL that others can use to review this draft dataset version before it is published. They will be able to access all files in the dataset and see all metadata, including metadata that may identify the dataset's authors.

Anonymous Preview

Create a URL that others can use to access an anonymized view of this unpublished dataset version. Metadata that could identify the dataset's author will not be displayed. (See Tool Tip for the list of withheld metadata fields.) Non-identifying metadata will be visible.

The dataset's files are not changed and users of the Anonymous Preview URL will be able to access them. Users of the Anonymous Preview URL will not be able to see the name of the Dataverse that this dataset is in but will be able to see the name of the repository, which might expose the dataset authors' identities.

To verify that all identifying information has been removed or anonymized, it is recommended that you logout and review the dataset as as it would be seen by an Anonymous Preview URL user. See User Guide for more information.

You won't be able to create an Anonymous Preview URL once a version of this dataset has been published.

Unpublished Dataset Preview URL

Are you sure you want to disable the Preview URL? If you have shared the Preview URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? This is permanent and the selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? This is permanent an it will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details
 
Version:
Last Updated:
Version:
Last Updated:
Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

  You need to Log In to request access.

Dataset Terms

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

CC BY-NC-SA 4.0

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

https://dataverse.lib.virginia.edu/api/access/datafile/

Compute Batch
Clear Batch
Dataset Persistent Identifier Change Compute Batch
Compute Batch
Submit for Review

You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Publish Dataset

This dataset cannot be published until Cell Maps for Artificial Intelligence is published by its administrator.

Publish Dataset

This dataset cannot be published until Cell Maps for Artificial Intelligence and School of Medicine are published.

Return to Author

Return this dataset to contributor for modification. The reason for return entered below will be sent by email to the author.

Curation Status History
StatusDateAssigner
No records found.
Add/Edit a Version Note
Styled Citation