The JUMP-Target set of perturbations comprises three lists of perturbations
JUMP-Target-Compound– a list of compounds with diverse targets.JUMP-Target-ORF– a list of ORF sequences corresponding to genes that are targets of compounds fromJUMP-Target-Compound.JUMP-Target-CRISPR– a list of sgRNA sequences corresponding to genes that are targets of compounds fromJUMP-Target-Compound.
Both JUMP-Target-ORF and JUMP-Target-CRISPR have sgRNAs and ORFs corresponding to a set of 160 genes, each of which are targets of compounds in JUMP-Target-Compound. JUMP-Target-ORF has perturbations for an additional set of 15 genes that serve as negative controls (below).
Each of the 3 lists fit on a single 384-well plate; the suggested plate layouts are provided (below).
The target annotations were obtained from https://clue.io/repurposing.
This resource was created through the JUMP-Cell Painting Consortium.
Table of contents generated with markdown-toc
There are 306 compounds in total, of which 46 are included as controls serving different goals
poscon_orf: compounds that correlate strongly with (overexpressed) genes in previous Cell Painting experiments. There are 6 such compounds, and their corresponding genes are included inJUMP-Target-ORFandJUMP-Target-CRISPRposcon_cp: compounds with a strong association with the genes that they target, according to ChemicalProbes.org. There are 26 such compounds, and their corresponding genes are included inJUMP-Target-ORFandJUMP-Target-CRISPR.poscon_diverse: pairs of compounds that are strongly correlated to each other, and weakly correlated to otherposcon_diversepairs, in previous Cell Painting experiments. There are 7 such pairs, so 14 compounds in total.negcon: DMSO is the negative control.
The recommended concentration for these compounds is 5 uM.
There are
- n=2 replicate wells for each of 14
poscon_diversecompounds - n=64 DMSO wells
- n=1 well for the remaining compounds
JUMP-Target_compound_metadata.tsv
| Column | Description |
|---|---|
| InChIKey | International Chemical Identifier |
| pert_iname | Compound name |
| pubchem_cid | PubChem ID e.g. 72716071 |
| target | Gene target |
| pert_type | Perturbation type – trt: treatment, control: one of the 3 controls |
| control_type | Control type – poscon_orf, poscon_cp, or poscon_diverse |
| smiles | Simplified molecular-input line-entry system (SMILES) string |
JUMP-Target_compound_platemap.tsv
| Column | Description |
|---|---|
| well_position | Well position |
| broad_sample | Compound ID in Broad Institute's compound management database |
| solvent | Solvent (always DMSO) |
- 306 compounds
- Compound Request Number: CR-12417 - placed by Niranj Chandrasekaran - $10,404
- 5 milliMolar 13.75 uL total volume (5 uL dead volume)
There are 335 sgRNAs (corresponding to 175 genes) in total, of which 88 sgRNAs are included as controls serving different goals
poscon_orf: the corresponding genes targets of theposcon_orfcompounds. Total: 3 genes x 2 sgRNAs per gene (except for one gene which has a single sgRNA) = 5 sgRNAs.poscon_cp: the corresponding genes targets of theposcon_cpcompounds. Total: 13 genes x 2 sgRNAs per gene (except for one gene which has a single sgRNA) = 25 sgRNAs.poscon_diverse: the corresponding genes targets of theposcon_diversecompounds. Total: 14 genes x 2 sgRNAs per gene = 28 sgRNAs.negcon: 30 unique sgRNAs that serve as negative controls because they are either non-targeting (NO_SITE) or target intergenic region (ONE_INTERGENIC_SITE).negconsgRNAs have an additional annotation e.g.NO_SITE (5 zeros). The number of zeros indicates how deep into the "threat matrix" a particular sgRNA makes it before a single match is found. An sgRNAnegconwith higher number of zeros is less likely to have off-target effects and therefore may be a better negative control.
There are
- n=2 replicate wells for each of
negcons, as well as for 1poscon_cpsgRNA, 1poscon_orfsgRNA, and 13 other sgRNAs - n=1 well for each remaining sgRNAs
- n=4 empty wells
JUMP-Target_crispr_metadata.tsv
| Column | Description |
|---|---|
| broad_sample | sgRNA id in Broad Institute's Genetic Perturbation Platform database |
| gene | Gene targeted by the sgRNA |
| pert_type | Perturbation type – trt: treatment, control: one of the 4 controls |
| control_type | Control type – negcon, poscon_orf, poscon_cp, or poscon_diverse |
| target_sequence | sgRNA sequence |
| negcon_control_type | Negative control type – NO_SITE or ONE_INTERGENIC_SITE |
JUMP-Target_crispr_platemap.tsv
| Column | Description |
|---|---|
| well_position | Well position |
| broad_sample | sgRNA id in Broad Institute's Genetic Perturbation Platform database |
There are 175 ORFs (corresponding to 175 genes) in total, of which 45 ORFs (corresponding to 45 genes) are included as controls serving different goals
All genes have a single corresponding ORF
poscon_orf: the corresponding genes targets of theposcon_orfcompounds. Total: 3 genes.poscon_cp: the corresponding genes targets of theposcon_cpcompounds. Total: 13 genes.poscon_diverse: the corresponding genes targets of theposcon_diversecompounds. Total: 14 genes.negcon: genes that have had weak signatures in previous Cell Painting overexpression experiments. Total: 15 genes.
There are
- n=2 replicate wells for each of the 30 poscons
- n=4 replicate wells for each of the 15 negcons
- n=1 well for each remaining sgRNAs
- n=4 empty wells
| Column | Description |
|---|---|
| broad_sample | ORF id in Broad Institute's Genetic Perturbation Platform database |
| gene | Gene overexpressed by the ORF |
| pert_type | Perturbation type – trt: treatment, control: one of the 4 controls |
| control_type | Control type – negcon, poscon_orf, poscon_cp, or poscon_diverse |
| Column | Description |
|---|---|
| well_position | Well position |
| broad_sample | ORF id in Broad Institute's Genetic Perturbation Platform database |