On this page, you can find an overview of the information we collected
from the JUMP-CP Consortium’s communications on the JUMP-CP data.
The JUMP-CP Consortium website contains info on the Consortium and its partners.
JUMP-CP Github page contains info on the actual data and processing, as shared by the Consortium.
Cell Painting - Assay Development
An overview of the recent Cell Painting protocols can be found on GitHub.
The optimized Cell Painting assay protocol (2022, BioRxiv preprint) was used for the final JUMP-CP dataset released starting Nov. 1st 2022.
The Pilot dataset was generated using v2.5 of the protocol.
The original Cell Painting assay protocol was published in 2016.
The Broad Institute's Cell Painting Wiki contains further information, tips & tricks.
PerkinElmer PhenoVue Kits, containing the six fluorescent probes for Cell Painting, can be purchased here.
Specs offers a number of compound sets, containing combinations of the compounds in the JUMP library. More information can be found on the Specs website. Until the end of the year, a set of the JUMP-CP Pilot Set (10ul/10mMol per compound) will be complementary with new StratoMineR subscriptions.
Image Analysis in CellProfiler
The updated CellProfiler pipelines for the final JUMP-CP dataset are on GitHub.
A different set of CellProfiler pipelines were used for the JUMP-CP pilot data. This is a previous version, which appears to have only been used for the Pilot data, as published in this preprint.
An overview of the JUMP-CP Datasets can be found here on GitHub.
The final JUMP-CP dataset (images & numeric data) can be found in AWS, including information on the license and citation. A large portion is available at the moment, but the entire dataset is expected to be complete by the end of 2022. The Consortium recommends to wait until the data upload and QC are complete before performing any analysis on the data.
The JUMP-CP Pilot dataset can be found on GitHub.
In addition to that, the Pilot data is also pre-loaded in StratoMineR, where it can be accessed by any user. Register for a free StratoMineR trial to start exploring it.
Please note that Core Life Analytics is not a JUMP-CP Consortium partner.
We are following the developments closely, as we see the obvious potential of this resource, but we also see the challenges that scientists face in accessing and leveraging it. We hope to contribute to making the dataset more accessible to anyone who is interested. This document was last updated on: 2022-10-27