Skip to content

Latest commit

 

History

History
245 lines (184 loc) · 19.4 KB

README.md

File metadata and controls

245 lines (184 loc) · 19.4 KB
Raw

JUMP-Target

The JUMP-Target set of perturbations comprises three lists of perturbations

  1. JUMP-Target-Compound – a list of compounds with diverse targets. See also JUMP-MOA for a similar compound set.
  2. JUMP-Target-ORF – a list of ORF sequences corresponding to genes that are targets of compounds from JUMP-Target-Compound.
  3. JUMP-Target-CRISPR – a list of sgRNA sequences corresponding to genes that are targets of compounds from JUMP-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.

Versioning

  • There's a single version for the JUMP-Target-CRISPR and JUMP-Target-ORF plates (JUMP-Target-1-CRISPR and JUMP-Target-1-ORF respectively)
  • There are two versions of JUMP-Target-Compound (JUMP-Target-1-Compound and JUMP-Target-2-Compound). Both have the same set of compounds, but have different broad_sample IDs and different layouts. JUMP-Target-2-Compound is used in the production of the JUMP dataset. We recommend using this layout because it will remove layout as a potential confounder when matching against the JUMP dataset. While the broad_sample IDs differ between versions, the compounds can be matched between versions using their InChIKey values, which remain identical for the same compound.

JUMP-Target-Compound

There are 301 compounds in total, of which 46 are included as controls serving different goals

  1. poscon_orf: compounds that correlate strongly with (overexpressed) genes in previous Cell Painting experiments. There are 6 such compounds, and their corresponding 3 genes are included in JUMP-Target-ORF and JUMP-Target-CRISPR
  2. poscon_cp: compounds with a strong association with the genes that they target, according to ChemicalProbes.org. There are 26 such compounds, and their corresponding 13 genes are included in JUMP-Target-ORF and JUMP-Target-CRISPR.
  3. poscon_diverse: pairs of compounds that are strongly correlated to each other, and weakly correlated to other poscon_diverse pairs, in previous Cell Painting experiments. There are 7 such pairs, so 14 compounds in total.
  4. 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_diverse compounds
  • n=64 DMSO wells
  • n=1 well for the remaining compounds

The company Specs has assembled the compounds for purchase; for info contact [email protected]

Files

JUMP-Target-1_compound_metadata.tsv JUMP-Target-2_compound_metadata.tsv

Column Description
pert_iname Compound name
pubchem_cid PubChem ID e.g. 72716071
target_list List of genes targeted by the compound
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
InChI International Chemical Identifier corresponding to smiles
InChIKey InChIKey generated from InChI

smiles was standardized using JUMP-CP Standardizer. See #34 for details about the standardization.

JUMP-Target-1_compound_platemap.tsv JUMP-Target-2_compound_platemap.tsv

Column Description
well_position Well position
broad_sample Compound ID in Broad Institute's compound management database
solvent Solvent (always DMSO)

Broad internal notes

  • 301 compounds
  • JUMP-Target-1_Compound:
    • Compound Request Number: CR-12417 - placed by Niranj Chandrasekaran - $10,404
    • 5 milliMolar 13.75 uL total volume (5 uL dead volume)
  • JUMP-Target-2_Compound:
    • Compound Request Number: CR-12908 - placed by Niranj Chandrasekaran - $???
    • 5 milliMolar 13.75 uL total volume (5 uL dead volume)
    • This plate was created because CDoT was unable to create plates with the same plate map as JUMP-Target-1 for the production experiments. Thus, the compounds in JUMP-Target-2 are identical to the compounds in JUMP-Target-1 but the plate maps are different. The broad sample IDs of some compounds are also different.
      • To map the compounds in JUMP-Target-1 to JUMP-Target-2 use InChIKey for "joining".

JUMP-Target-CRISPR

There are 335 sgRNAs (corresponding to 175 genes) in total, of which 88 sgRNAs are included as controls serving different goals

  1. poscon_orf: the corresponding genes targets of the poscon_orf compounds. Total: 3 genes, where 2 genes have 2 sgRNAs each and 1 gene has 1 sgRNA = 5 sgRNAs total.
  2. poscon_cp: the corresponding genes targets of the poscon_cp compounds. Total: 13 genes, where 12 genes have 2 sgRNAs each and 1 gene has 1 sgRNA = 25 sgRNAs total.
  3. poscon_diverse: the corresponding genes targets of the poscon_diverse compounds. Total: 14 genes x 2 sgRNAs per gene = 28 sgRNAs.
  4. negcon: 30 unique sgRNAs that serve as negative controls because they are either non-targeting (NO_SITE) or target intergenic region (ONE_INTERGENIC_SITE). negcon sgRNAs 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 sgRNA negcon with higher number of zeros is less likely to have off-target effects and therefore may be a better negative control.

For the remaining treatment genes (non-controls):

  • 117 genes have 2 sgRNAs each
  • 13 genes have 1 sgRNA each

There are

  • n=2 replicate wells for each of negcons, as well as for 1 poscon_cp sgRNA, 1 poscon_orf sgRNA, and 13 other sgRNAs
  • n=1 well for each remaining sgRNAs
  • n=4 empty wells

Files

JUMP-Target-1_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-1_crispr_platemap.tsv

Column Description
well_position Well position
broad_sample sgRNA id in Broad Institute's Genetic Perturbation Platform database

JUMP-Target-ORF

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 and 130 genes are represented in duplicate on the plate.

All genes have a single corresponding ORF

  1. poscon_orf: the corresponding genes targets of the poscon_orf compounds. Total: 3 genes.
  2. poscon_cp: the corresponding genes targets of the poscon_cp compounds. Total: 13 genes.
  3. poscon_diverse: the corresponding genes targets of the poscon_diverse compounds. Total: 14 genes.
  4. 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=2 wells for each remaining ORF (130 of them)
  • n=4 empty wells
  • For a total of 384 wells

Files

JUMP-Target-1_orf_metadata.tsv

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

JUMP-Target-1_orf_platemap.tsv

Column Description
well_position Well position
broad_sample ORF id in Broad Institute's Genetic Perturbation Platform database

Compound and gene selection

The list of compounds were derived from Broad's Drug Repurposing Hub dataset, a curated and annotated collection of FDA-approved drugs, clinical trial drugs, and pre-clinical tool compounds. The genes perturbed by genetic perturbations were chosen because they are the annotated targets of the compounds. The Repurposing Hub compounds were filtered using the following criteria:

  1. The compounds should target genes that belong to diverse gene families. This is because the ideal methods would work well for many different biological pathways, not just a few that are well-characterized and/or easy to predict.
  2. Each gene should be targeted by at least two compounds so that gene-compound matching and compound-compound matching can both be performed using the dataset.
  3. The constraint that each compound should target only a single gene, was considered. However, this criterion is difficult to achieve due to polypharmacology, which is the property for compounds to bind and impact many different gene products in the cell; this is especially common for protein kinase inhibitors in the dataset. Instead, only the so-called “historical compounds” listed in the Chemical Probes Portal, comprising compounds that are known to be quite non-selective (or not sufficiently potent) compared with other available chemical probes, were filtered out.
  4. Three types of positive control compounds and the genes that they target were selected. (Compound positive controls, CRISPR positive controls, and ORF positive controls).
  5. To ensure that the compounds and genes selected were available for performing experiments, compounds that were unavailable for purchase from at least one of four compound vendors (Sigma, SelleckChem, Tocris, and MedChemEx) and genes for which genetic reagents were unavailable from Broad's GPP portal were filtered out.
  6. Compounds that belong to DEA's list of controlled substances or OPCW's list of chemical weapons precursors were also excluded.

Positive control compounds

Based on our experiments with the Target-1 compounds plates, we have identified a list of eight compounds (and also a subset of four compounds) with maximally diverse phenotypes.

pert_iname InChIKey Vendor URL clue.io URL
AMG900 IVUGFMLRJOCGAS-UHFFFAOYSA-N https://www.selleckchem.com/products/amg-900.html https://clue.io/repurposing-app?q=Name:AMG900
NVS-PAK1-1 OINGHOPGNMYCAB-INIZCTEOSA-N https://www.medchemexpress.com/NVS-PAK1-1.html https://clue.io/repurposing-app?q=Name:NVS-PAK1-1
dexamethasone UREBDLICKHMUKA-CXSFZGCWSA-N https://www.tocris.com/products/dexamethasone_1126 https://clue.io/repurposing-app?q=Name:dexamethasone
LY2109761 IHLVSLOZUHKNMQ-UHFFFAOYSA-N https://www.selleckchem.com/products/ly2109761.html https://clue.io/repurposing-app?q=Name:LY2109761
FK-866 KPBNHDGDUADAGP-VAWYXSNFSA-N https://www.selleckchem.com/products/apo866-fk866.html https://clue.io/repurposing-app?q=Name:FK-866
quinidine LOUPRKONTZGTKE-LHHVKLHASA-N https://www.medchemexpress.com/Quinidine.html https://clue.io/repurposing-app?q=Name:quinidine
TC-S-7004 CQKBSRPVZZLCJE-UHFFFAOYSA-N https://www.tocris.com/products/tc-s-7004_5088 https://clue.io/repurposing-app?q=Name:TC-S-7004
aloxistatin SRVFFFJZQVENJC-IHRRRGAJSA-N https://www.medchemexpress.com/Aloxistatin.html https://clue.io/repurposing-app?q=Name:aloxistatin

Compound names in bold is the subset of four compounds.

Layout

Our recommendation is to have at least four replicates of the eight (or four) compounds spread across the plate. If such a layout is not possible, then we recommend the following for a 384-well plate.

pert_iname well_position
AMG900 B1, J1, F24, N24
NVS-PAK1-1 F1, N1, B24, J24
dexamethasone C1, K1, G24, O24
LY2109761 E1, M1, A24, I24
FK-866 D1, L1, H24, P24
quinidine G1, O1, C24, K24
TC-S-7004 H1, P1, D24, L24
aloxistatin A1, I1, E24, M24

For a 1536-well plate, the layout is similar, but in four quadrants.

Control mappings

poscon_diverse

ID pair target_gene InChIKey broad_compound_id broad_orf_id broad_crispr_id_1 broad_crispr_id_2
poscon_diverse-pair0-1 0 RET XKFTZKGMDDZMJI BRD-K07881437-001-03-8 ccsbBroad304_14827 BRDN0001058343 BRDN0001058011
poscon_diverse-pair0-2 0 TUBB MTJHLONVHHPNSI BRD-K23363278-001-02-1 ccsbBroad304_05206 BRDN0001489809 BRDN0001488241
poscon_diverse-pair1-1 1 HSP90AA1 RVAQIUULWULRNW BRD-K38852836-001-04-9 ccsbBroad304_06412 BRDN0001488886 BRDN0001483257
poscon_diverse-pair1-2 1 PIK3CG CWHUFRVAEUJCEF BRD-K42191735-001-08-7 ccsbBroad304_14762 BRDN0001065162 BRDN0001065152
poscon_diverse-pair2-1 2 NAMPT KPBNHDGDUADAGP BRD-K58550667-001-08-7 ccsbBroad304_07557 BRDN0001484730 BRDN0001481327
poscon_diverse-pair2-2 2 AKT1 AFJRDFWMXUECEW BRD-K25412176-001-01-9 ccsbBroad304_14538 BRDN0001054985 BRDN0000562836
poscon_diverse-pair3-1 3 KRAS DHMTURDWPRKSOA BRD-K41599323-001-02-3 ccsbBroad304_16173 BRDN0001054815 BRDN0000563627
poscon_diverse-pair3-2 3 PAK4 AYCPARAPKDAOEN BRD-K37764012-001-03-3 ccsbBroad304_02392 BRDN0001145608 BRDN0001147629
poscon_diverse-pair4-1 4 DNMT3A NMUSYJAQQFHJEW BRD-K03406345-001-21-1 ccsbBroad304_00454 BRDN0001066838 BRDN0001066751
poscon_diverse-pair4-2 4 IMPDH1 WYWHKKSPHMUBEB BRD-K49350383-001-13-7 ccsbBroad304_06451 BRDN0001489452 BRDN0001488805
poscon_diverse-pair5-1 5 CDK7 HUXYBQXJVXOMKX BRD-K64800655-001-09-0 ccsbBroad304_00280 BRDN0001162216 BRDN0001147450
poscon_diverse-pair5-2 5 PLK1 XQVVPGYIWAGRNI BRD-K64890080-001-02-1 ccsbBroad304_14770 BRDN0001144995 BRDN0001054037
poscon_diverse-pair6-1 6 CHEK2 IAYGCINLNONXHY BRD-K86525559-001-07-8 ccsbBroad304_14989 BRDN0000585854 BRDN0001145610
poscon_diverse-pair6-2 6 GABRB2 ALBKMJDFBZVHAK BRD-K33882852-003-02-8 ccsbBroad304_00607 BRDN0001486784 BRDN0001482741

Other poscons

ID target_gene broad_compound_id_1 broad_compound_id_2 broad_orf_id broad_crispr_id_1 broad_crispr_id_2
poscon_cp-00 AURKB BRD-K21728777-001-02-3 BRD-K55966568-001-09-6 ccsbBroad304_14932 BRDN0001054845 BRDN0000562944
poscon_cp-01 BRD4 BRD-K13094524-001-04-2 BRD-K12502280-001-11-4 ccsbBroad304_11738 BRDN0000733514 BRDN0001146786
poscon_cp-02 CLK1 BRD-K66430217-001-03-8 BRD-K97072811-001-11-4 ccsbBroad304_00326 BRDN0001147209 BRDN0001146512
poscon_cp-03 DYRK1B BRD-K89517477-001-01-4 BRD-K80935598-001-01-1 ccsbBroad304_14931 BRDN0001149482 BRDN0001149418
poscon_cp-04 ERBB2 BRD-K76908866-001-07-6 BRD-K61642990-001-01-0 ccsbBroad304_14631 BRDN0001148320 BRDN0000579738
poscon_cp-05 EZH2 BRD-K91535048-001-01-2 BRD-K26989966-001-04-3 ccsbBroad304_00526 BRDN0001057455
poscon_cp-06 FLT3 BRD-K90747162-001-01-4 BRD-K91283740-003-01-6 ccsbBroad304_14644 BRDN0001145324 BRDN0001149376
poscon_cp-07 HDAC3 BRD-K61688984-001-02-9 BRD-K61397605-001-01-8 ccsbBroad304_07311 BRDN0000582721 BRDN0000733096
poscon_cp-08 IGF1R BRD-K15179513-001-04-2 BRD-K24696047-001-02-3 ccsbBroad304_14671 BRDN0001065819 BRDN0001065728
poscon_cp-09 JAK1 BRD-K16803204-001-01-6 BRD-K53972329-001-01-3 ccsbBroad304_14679 BRDN0001065674 BRDN0001065858
poscon_cp-10 MET BRD-K73319509-001-08-0 BRD-K19477839-001-07-6 ccsbBroad304_14696 BRDN0000734703 BRDN0001065558
poscon_cp-11 PAK1 BRD-K19333160-001-01-3 BRD-K28132190-001-02-0 ccsbBroad304_01144 BRDN0001145958 BRDN0001147867
poscon_cp-12 USP1 BRD-K93942811-001-01-3 BRD-K81197548-003-01-4 ccsbBroad304_01760 BRDN0001487607 BRDN0001484218
poscon_orf-00 BRAF BRD-K73789395-001-09-9 BRD-K62810658-001-11-4 ccsbBroad304_16175 BRDN0001054801 BRDN0000562882
poscon_orf-01 CDK2 BRD-K50836978-001-03-3 BRD-K07762753-001-05-1 ccsbBroad304_14572 BRDN0001147786 BRDN0001148950
poscon_orf-02 MAPK14 BRD-K54330070-001-19-6 BRD-A37704979-001-12-3 ccsbBroad304_00371 BRDN0001148417