Awesome
JUMP-MOA
JUMP-MOA is list of compounds with diverse MOAs that fit on a single 384-well plate, with 4 replicates per compound.
There are 90 compounds from 47 distinct MOA classes. The recommended concentration for these compounds is 3 uM.
This resource was created through the JUMP-Cell Painting Consortium.
The MOA annotations were obtained from https://clue.io/repurposing.
The company Specs has assembled the compounds for purchase; for info contact tamara.baptist@specs.net
How does JUMP-MOA differ from JUMP-Target-Compound? JUMP-MOA and JUMP-Target-Compound are similar in goals: to allow testing whether a compound can "retrieve" (match) replicates of itself, and also whether it can retrieve compounds with the same annotated mechanism (though the mechanism annotations are imperfect).
- JUMP-Target is bigger in terms of the number of compounds with typically one replicate of each compound on the plate. Bigger is better for statistical confidence, but worse if someone wants to not “waste” so much effort/expense on controls; one would want to run 4 replicate plates for a retrieval test and keep in mind that plate position effects may confound this analysis (a given compound will always be in the same well position, which can inflate them matching each other, for technical variation reasons). JUMP-Target-Compound is what we recommend to be run with each batch of plates in large scale experiments (as controls) and is what was chosen for the JUMP consortium dataset.
- JUMP-MOA has 4 replicates of each compound internal to the plate and thus in different well positions, so it allows testing replicate retrieval that is unconfounded by plate position effects (where well positions especially at the edge of the plate look alike for technical variation reasons and not because of the effect of the compound). But it has only ~1/4 the number of compounds and mechanism classes.
Files
JUMP-MOA_compound_metadata.tsv
| Column | Description |
|---|---|
| broad_sample | Compound ID in Broad Institute's compound management database |
| pert_iname | Compound name |
| pubchem_cid | PubChem ID e.g. 72716071 |
| moa | Mechanism-of-action annotation, derived from Broad Drug Repurposing Hub and curated here |
| smiles | Simplified molecular-input line-entry system (SMILES) string |
| InChI | International Chemical Identifier corresponding to smiles |
| InChIKey | InChIKey generated from InChI |
smiles was standardized using JUMP-CP Standardizer.
See https://github.com/jump-cellpainting/JUMP-MOA/pull/13 for details about the standardization.
JUMP-MOA_compound_platemap.tsv
| Column | Description |
|---|---|
| well_position | Well position |
| broad_sample | Compound ID in Broad Institute's compound management database |
| solvent | Solvent (always DMSO) |
Plate layout
De-identified compounds
Eight of these compounds have been de-identified; they have broad_sample values of Compound1, Compound2, ..., Compound8.
If you are recreating this plate, we recommend replacing these de-identified compounds with their (non-de-identified) counterparts i.e. the other compound in the set with the same MOA:
| moa | replace_with | original |
|---|---|---|
| HMGCR inhibitor | delta-Tocotrienol | Compound1 |
| kinesin inhibitor | ispinesib | Compound2 |
| BCL inhibitor | ABT-737 | Compound3 |
| PARP inhibitor | veliparib | Compound4 |
| IGF-1 inhibitor | NVP-AEW541 | Compound5 |
| tricyclic antidepressant | dosulepin | Compound6 |
| FGFR inhibitor | BLU9931 | Compound7 |
| phosphodiesterase inhibitor | quazinone | Compound8 |
Broad internal notes
- Originally called CPJUMP-Stain1
- 90 compounds x 4 replicates
- Compound Request Number: CR-11516 - placed by Shantanu Singh - $2,950
- 3 milliMolar 10 uL total volume (5 uL dead volume)