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jump-cellpainting / JUMP-Target

Lists and 384-well plate maps of compounds and genetic perturbations designed to assess connectivity in profiling assays
MIT License
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Document positive controls used in JUMP production #22

Open shntnu opened 3 years ago

shntnu commented 3 years ago

This might move to a new repo, but documenting here for now. Copied from https://github.com/jump-cellpainting/normalization/issues/3#issuecomment-822494683

Poscons

Here are the recommended poscons, together with all the metadata we have about them (including SMILES – scroll right to see it)

The final concentration should be 5uM, and not 10uM (which is the concentration for the rest of the JUMP compounds).

Metadata_broad_sample Metadata_pert_iname Metadata_InChIKey Metadata_pubchem_cid Metadata_target Metadata_pert_type Metadata_control_type Metadata_smiles
BRD-K21728777-001-02-3 AMG900 IVUGFMLRJOCGAS-UHFFFAOYSA-N 24856041 AURKB control poscon_cp Cc1csc(c1)-c1nnc(Nc2ccc(Oc3ncccc3-c3ccnc(N)n3)cc2)c2ccccc12
BRD-K28132190-001-02-0 NVS-PAK1-1 OINGHOPGNMYCAB-INIZCTEOSA-N 122187564 PAK1 control poscon_cp CC(C)NC(=O)N1CCC@@HNC1=Nc2cc(F)ccc2N(CC(F)F)c2ccc(Cl)cc12
BRD-K38775274-001-22-1 dexamethasone UREBDLICKHMUKA-CXSFZGCWSA-N 5743 ANXA1 trt NA C[C@@H]1C[C@H]2[C@@H]3CCC4=CC(=O)C=C[C@]4(C)[C@@]3(F)C@@HC[C@]2(C)[C@@]1(O)C(=O)CO
BRD-K47557313-001-02-7 LY2109761 IHLVSLOZUHKNMQ-UHFFFAOYSA-N 11655119 TGFBR1 trt NA C(CN1CCOCC1)Oc1ccc2c(ccnc2c1)-c1c(nn2CCCc12)-c1ccccn1
BRD-K58550667-001-08-7 FK-866 KPBNHDGDUADAGP-VAWYXSNFSA-N 6914657 NAMPT control poscon_diverse O=C(NCCCCC1CCN(CC1)C(=O)c1ccccc1)\C=C\c1cccnc1
BRD-K59632282-052-03-1 quinidine LOUPRKONTZGTKE-LHHVKLHASA-N 441074 KCNK1 trt NA COc1ccc2nccc(C@H[C@H]3C[C@@H]4CC[N@]3C[C@@H]4C=C)c2c1
BRD-K89517477-001-01-4 TC-S-7004 CQKBSRPVZZLCJE-UHFFFAOYSA-N 57523919 DYRK1B control poscon_cp COc1ncc2cc(C(=O)Nc3cc(ccc3Cl)C(=O)NCc3cccc(Cl)c3)c(=O)[nH]c2n1
BRD-K91188791-001-17-5 aloxistatin SRVFFFJZQVENJC-IHRRRGAJSA-N 65663 CTSG trt NA CCOC(=O)[C@H]1O[C@@H]1C(=O)NC@@HC(=O)NCCC(C)C

Layout

384

Poscons on the outer columns, DMSO on the columns right next to them.

Metadata_pert_iname Metadata_poscon_id
aloxistatin C1
AMG900 C2
dexamethasone C3
FK-866 C4
LY2109761 C5
NVS-PAK1-1 C6
quinidine C7
TC-S-7004 C8

image

1586

Same as 384, but in 4 quadrants

image