The JUMP-CP Consortium has generated a public Cell Painting dataset with morphological profiles of over 140,000 reference small molecules, CRISPRs and ORFs. What makes this dataset so powerful, besides its size, is the fact that it is standardized: the final dataset is generated using standardized protocols, which are publically available.
This reference dataset will allow scientists to use a data-driven approach to accelerate their drug discovery projects. This approach can help to determine a potential therapeutic’s mechanism of action, predict its activity or toxicity, and more. All based on imaging data. Making sure that your Cell Painting data is aligned and comparable, however, can be quite a challenge.
Leverage JUMP-CP for your research
Through various channels, the Consortium has shared information on the protocols and pipelines used to generate the different datasets. We have collected this information in one document, which you can find here.
JUMP-CP Pilot reference compounds
As discussed in last year's webinar, we have created a list of 19 compounds that gave reproducible, diverse phenotypes in the JUMP-CP Pilot dataset. Including these compounds as a reference can help you to compare and align your data to the JUMP-CP data. The Dutch company Specs offers these compounds as the JUMP-CP Pilot set.
Curious to learn if StratoMineR would be helpful your research? Please contact us, our scientists are happy to help.
What is Cell Painting?
Cell Painting (CP) is a high-content, image-based morphological profiling assay. For the assay, six fluorescent dyes are used, revealing up to eight cellular components or organelles. Combined with sophisticated image analysis tools, this approach allows the user to obtain detailed cellular profiles, consisting of hundreds or even thousands of morphological features —measures of intensity, size, shape, spatial relationships, amongst many others. The amount of detail in these morphological profiles makes this assay sensitive to subtle cellular changes, and therefore a valuable tool to assess cellular responses to drugs or genetic perturbations.
What is the JUMP-CP consortium?
The Joint Undertaking in Morphological Profiling (JUMP) Cell Painting (CP) consortium, spearheaded by the Broad Institute of MIT and Harvard, is a collaboration between non-profit and industry partners. The consortium’s aim is to create an unprecedented public Cell Painting dataset. For this purpose, the consortium developed a standardized Cell Painting protocol, which was used to obtain the phenotypic profiles of over one billion cells responding to over 140.000 small molecules and genetic perturbations. The dataset will be released starting Nov 1st,2022.
The consortium’s ultimate goal is “to make cell images as computable as genomes and transcriptomes".
Read more on the JUMP-CP website.