shntnu
commented
3 years ago We are sticking with the current JUMP-Target-Compound plate to the best of my knowledge, and likewise with the genetic perturbation plates, so we can consider this list final. Everything has been blocklisted and approved for public release.
Ultimately, our consortium aims to define some standards for the field. Having a standard set of genetic and chemical perturbations will allow normalizing data across sites and optimizing the assay or testing sensitivity and specificity under various conditions.
Genetic Perturbations: I discussed with Broad's Genetic Perturbation Platform. They generally are not allowed to distribute their genetic reagents to for-profit entities outside the Functional Genomic Consortium, and we agreed at the beginning of JUMP-Cell Painting that we would not request that. But, it is possible they could make an exception under very specific circumstances. If we have a single plate of controls that we want to make available (preferably 96 well, not 384 well - since virus production occurs in 96w format), this might be possible. But we should wait until the results of CPJUMP1 to see how reagents behave and decide what we want to include; they will not release multiple versions of the control plate. In other words, the set must be proven useful and then we can request permission to make the reagents available in some fashion. If we do trim to 96w format we would want choose one guide per gene (for those pairs that are consistent) and perhaps throw out genes that yield two different profiles across the 2 guides, and maybe also remove those that do not yield a signature (though that makes the plate not useful for testing new assays for sensitivity).
Small molecules: Here, our plan is just to share the identities and plate layout (information, not reagents) so all we need is the partner's permission, which depends in part on blocklisting. We could potentially contact a vendor and encourage them to offer the plate of compounds for sale to the public, for convenience. I'm not sure whether the CPJUMP-1 will definitely be the final layout recommended as this control plate, or if we may swap out some positive control compounds after CPJUMP-1 completes such that the recommended public control plate is actually different from CPJUMP-1.
In both cases, it seems we need to wait for CPJUMP-1 results to proceed on these.