Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| gene | ||||
| BRCA associated protein-1 (human) | BAP1 | Entrez Gene NCBI | Gene ID: 8314 | |
| Additional sex combs like 1 (human) | ASXL1 | Entrez Gene NCBI | Gene ID: 171023 | |
| strain, strain background | ||||
| NOD.CB17-Prkdcscid/NcrCrl | NOD SCID mice | Charles River Laboratories, UK | RRID:IMSR_CRL:394 | |
| cell line | ||||
| Early passage mesotheliomacell cultures | 7T, 8T, 45, 19, 14T, 23T, 40, 36, 26, 12T, 3T, 52, 2, 30, 15, 35, 24, 43, 34, 50T, 33T, 18, 53T, 38 |
MesobanK, Mesothelioma UK |
www.mesobank.com
Mesothelioma Tissue Bank, Papworth Hospital NHS Trust, UK |
|
| NCI-H2373 | H2373 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_A533 | |
| NCI-H2803 | H2803 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_U997 | |
| NCI-H2452 | H2452 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_1553 | |
| NCI-H2722 | H2722 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_U994 | |
| NCI-H2369 | H2369 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_A532 | |
| NCI-H2795 | H2795 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_U996 | |
| NCI-H2869 | H2869 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_V001 | |
| NCI-H2591 | H2591 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_A543 | |
| MPP 89 | MPP-89 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_1427 | |
| NCI-H2810 | H2810 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_U999 | |
| NCI-H2818 | H2818 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_V000 | |
| NCI-H513 | H513 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_A570 | |
| NCI-H2595 | H2595 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_A545 | |
| NCI-H2461 | H2461 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_A536 | |
| NCI-H2731 | H2731 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_U995 | |
| NCI-H2804 | H2804 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_U998 | |
| NCI-H28 | H28 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_1555 | |
| NCI-H226 | H226 | Szlosarek lab, Barts Cancer Institute, UK | RRID:CVCL_1544 | |
| MDA-MB-231 | MDAMB-231 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_0062 | |
| Caki-1 | Caki-1 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_0234 | |
| BB65 | BB65 | Wellcome Trust Sanger Institute, UK | RRID:CVCL_1078 | |
| antibody | ||||
| BAP1 (C-4) mouse mAb | anti-BAP1 | Santa Cruz Biotechnology, Santa Cruz, CA | Cat# sc-28383 RRID:AB_626723 | 1:500 in milk; 1:50 for flow cytometry |
| Caspase-8 (1C12) mouse mAb | anti-caspase 8 | Cell Signaling Technology, Danvers, MA | Cat# 9746 RRID:AB_2275120 | 1:1000 in BSA |
| FLIP (7F10) mouse mAb | anti c-FLIP | Enzo Life Sciences, Farmingdale, NY | Cat# ALX-804-961-0100 RRID:AB_2713915 | 1:1000 in milk |
| c-IAP1 (D5G9) rabbit mAb | anti-cIAP1 | Cell Signaling Technology,Danvers, MA | Cat# 7065S RRID:AB_10890862 | 1:1000 in BSA |
| c-IAP2 (58C7) rabbit mAb | anti-cIAP2 | Cell Signaling Technology, Danvers, MA |
Cat# 3130S RRID:AB_10693298 | 1:1000 in BSA |
| FADD rabbit pAb | anti-FADD | Cell Signaling Technology, Danvers MA |
Cat# 2782 RRID:AB_2100484 | 1:1000 in BSA |
| XIAP (3B6) rabbit mAb | anti-XIAP | Cell Signaling Technology, Danvers, MA |
Cat# 2045 RRID:AB_2214866 | 1:1000 in milk |
| survivin rabbit pAb | anti-survivin | Cell Signaling Technology, Danvers, MA |
Cat# 2803 RRID:AB_490807 | 1:1000 in BSA |
| α-Tubulin (11H10) Rabbit mAb | anti-α-tubulin | Cell Signaling Technology, Danvers, MA |
#2125 | 1:2000 in milk |
| Ubiquityl-Histone H2A (Lys119) (D27C4) XPRabbit mAb | anti-H2AK119Ub | Cell Signaling Technology, Danvers, MA |
Cat# 8240P RRID:AB_10891618 | 1:2000 in BSA |
| Histone H2A (D6O3A) Rabbit mAb | anti-H2A | Cell Signaling Technology, Danvers, MA |
Cat# 12349 RRID:AB_2687875 | 1:1000 in BSA |
| Anti-mouse IgG, HRP-linked antibody | anti-mouse HRP | Cell Signaling Technology, Danvers, MA |
Cat# 7076 RRID:AB_330924 | 1:2000 in milk |
| Anti-rabbit IgG, HRP-linked antibody | anti-rabbit HRP | Cell Signaling Technology, Danvers, MA |
Cat# 7074 RRID:AB_2099233 | 1:2000 in milk |
| Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, AlexaFluor 488 | AlexaFluor 488-conjugated anti-mouse antibody | Thermo Fisher Scientific, UK | Cat# A-21202 RRID:AB_141607 | 1:200 for flow cytometry |
| Annexin V, AlexaFluor 647 conjugate | Annexin V AlexaFluor 647-conjugated antibody | Thermo Fisher Scientific, UK | Cat# A23204 RRID:AB_2341149 | 1:100 for flow cytometry |
| PE anti-human CD261 (DR4, TRAIL-R1) antibody | PE-conjugated antibody to DR4 | Biolegend, UK | Cat# 307205 RRID:AB_314669 | 1:100 for flow cytometry |
| PE anti-human CD262 (DR5, TRAIL-R2) antibody | PE-conjugated antibody to DR5 | Biolegend, UK | Cat# 307405 RRID:AB_314677 | 1:100 for flow cytometry |
| PE Mouse IgG1, κ Isotype Ctrl Antibody | PE isotype control antibody | Biolegend, UK | Cat# 400112 | 1:100 for flow cytometry |
| Goat anti-Rabbit IgG (H + L) Secondary Antibody, AlexaFluor 488 conjugate | AlexaFluor 488-conjugated anti-rabbit secondary antibody | Thermo Fisher Scientific, UK | Cat# R37116 RRID:AB_2556544 | 1:200 for flow cytometry |
| Anti-Cleaved PARP1 (E51) mAb | cleaved PARP primary antibody; anti-cleaved PARP | Abcam, UK | Cat# ab32064 RRID:AB_777102 | (1:6000) for immunohistochemistry |
| recombinant DNA reagent | ||||
| BAP1 (NM_004656) Human cDNA Clone | pCMV6-AC BAP1 plasmid | Origene, Rockville, MD | Cat# SC117256 | |
| pHIV-Luc-ZsGreen | ZS-green luciferase plasmid, pHIV-Luc-ZsGreen | Bryan Welm Lab, University of Utah, Addgene, Logan, UT | Cat# 39196 | |
| pCMVR8.74 | pCMV-dR8.74 | Thrasher lab, UCL, Addgene, UK |
Cat# 22036 | |
| pMD2.G | pMD2.G | Thrasher lab, UCL, Addgene, UK |
Cat# 12259 | |
| sequence based reagent | ||||
| BAP1 GIPZ Lentiviral shRNA | BAP1 shRNA | UCL RNAi Library (Dharmacon, Lafayett, CO) | V2LHS 41473 | |
| ASXL1 GIPZ Lentiviral shRNA | ASXL1 shRNA | UCL RNAi Library (Dharmacon, Lafayett, CO) | V2LHS 78829 | |
| ASXL2 GIPZ Lentiviral shRNA | ASXL2 shRNA | UCL RNAi Library (Dharmacon, Lafayette, CO) | V3LHS_313940 | |
| peptide, recombinant protein | ||||
| Recombinant Human sTRAIL | rTRAIL | Peprotech, UK | Cat# 310–04 | |
| commercial assay or kit | ||||
| Cell Proliferation Kit XTT | XTT reagent | Applichem, UK | A8088 | |
| Q5 Site-Directed Mutagenesis Kit | Site directed mutagenesis | New England Biolabs, Ipswich, MA | Cat# E0554 | |
| Rabbit specific HRP/DAB (ABC) Detection IHC Kit | rabbit-specific HRP/DAB (ABC) detection IHC kit | Abcam, UK | Cat# ab64261 | |
| chemical compound, drug | ||||
| MEDI3039 | MEDI3039 | MedImmune, UK | ||
| software, algorithm | ||||
| GraphPad Prism software | Graphpad Prism | GraphPad Software, CA, USA | ||
| CaVEMan algorithm | CaVEMan | https://github.com/cancerit/CaVEMan | ||
| Pindel algorithm | Pindel | https://github.com/genome/pindel | ||
| Predicting Integral Copy Numbers In Cancer algorithm | PICNIC | http://www.sanger.ac.uk/science/tools/picnic | ||
| FlowJo software | Flowjo | FlowJo LLC | ||
| Other | ||||
| RIPA buffer | RIPA | Sigma-Aldrich, St. Louis, MO | Cat# R0278 | |
| Syto™ 60 red fluorescent nucleic acid stain | Syto 60 | Thermo Fisher Scientific, UK | Cat# S11342 | |
| Thiazolyl Blue Tetrazolium Bromide (MTT) | MTT reagent | Sigma-Aldrich, St. Louis, MO | Cat# M2128 | |
| jetPEI DNA transfection reagent | jetPEI | Source Bioscience, UK | Cat# 101–10 | |
| Polybrene | Polybrene | Sigma-Aldrich, St Louis, MO | Cat# 107689 | 8 μg/ml |
| Hoechst 33342 Solution (20 mM) | Hoechst 33342 | Thermo Fisher Scientific, UK | Cat# 62249 | |
| 4’, 6-diamidino-2-phenylindole | DAPI | Sigma-Aldrich, St Louis, MO | Cat# D9542 | 200 μg/ml |