Journal: Molecular cell

Article Title: Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene

doi: 10.1016/j.molcel.2017.11.004

Figure Lengend Snippet: (A) AMIGO2 expression levels detected by qRT-PCR in NHM and a panel of metastatic melanoma cell lines harboring distinct melanoma mutations. Data are normalized to GAPDH.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BRD2 Bethyl Laboratories A302-583A BRD4 Bethyl Laboratories A301-985A H3K4me1 Abcam ab8895 H3K4me3 Abcam ab1012 H3K27ac Abcam ab177178 H3K27me3 EMD 07-449 MED1 Bethyl Laboratories A300-793A macroH2A2 Bernstein Laboratory, ISMMS in house macroH2A1 Abcam ab37264 CTCF EMD 07-729 FOSL2 Santa Cruz SC-604 TEAD4 Santa Cruz SC-101184 HSP90 Santa Cruz SC-13119 GAPDH Santa Cruz SC-32233 GFP Roche 11814460001 LAMIN B1 Santa Cruz SC-6217 ALCAM Abcam ab109215 L1CAM Abcam ab20148 NRP2 Santa Cruz SC-13117 NRP1 Abcam ab81321 TUBULIN Sigma T9026 FOXM1 Cell Signaling Technology 5436 Casp3 Cell Signaling Technology 9662 PARP Cell Signaling Technology 9542 AMIGO2 (for IHC) Abnova H00347902-B01P Lot# F8271 RRID:AB_1672842 AMIGO2 (for IF and WB) R&D systems AF2080 PTK7 (N-terminal) (for WB) R&D systems AF4499 PTK7 (C-terminal) (for IF and WB) Cell Signaling 11926 Secondary rabbit anti goat (for AMIGO2 detection on WB) Sigma A5420 HRP-conjugated ACTIN Sigma A3854 Biological Samples Melanoma and normal skin tissue microarray Biomax ME208 Nevus tissue microarray IMCG, NYU MT032808 Patient derived short term cultures Osman Laboratory, NYU de Miera et al., 2012 NHM (this paper) Bernstein Laboratory, ISMMS NHM1-5 Chemicals, Peptides, and Recombinant Proteins GFP Trap-A beads Chromotek gta-10 BET inhibitor JQ1 Bradner Laboratory; Agreement # {"type":"entrez-nucleotide","attrs":{"text":"A09608","term_id":"490581","term_text":"A09608"}} A09608 N/A BET inhibitor I-BET762 Apex Bio 501014747 IGEPAL Sigma I-8896 Micrococcal Nuclease Affymetrix 70196Y Dynabeads Protein A Immunoprécipitation kit Invitrogen 10006D Magna ChIP Protein A+G Magnetic beads Millipore 16-663 DSG Pierce (ThermoFisher) 20593 Critical Commercial Assays Click- Click-IT EdU Pacific Blue Flow Cytometry Assay Kit ThermoFisher {"type":"entrez-nucleotide","attrs":{"text":"C10636","term_id":"1535707","term_text":"C10636"}} C10636 Caspase Activity assay MBL Int.

Techniques: Expressing, Quantitative RT-PCR

Journal: Molecular cell

Article Title: Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene

doi: 10.1016/j.molcel.2017.11.004

Figure Lengend Snippet: (A) Relative growth curves of 501MEL and SKmel147 cells stably transduced with non-targeting scrambled control shRNA (shSCR) and two AMIGO2 shRNAs (shA2 #1 and #2). Values are normalized to seeding control (n = 3).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BRD2 Bethyl Laboratories A302-583A BRD4 Bethyl Laboratories A301-985A H3K4me1 Abcam ab8895 H3K4me3 Abcam ab1012 H3K27ac Abcam ab177178 H3K27me3 EMD 07-449 MED1 Bethyl Laboratories A300-793A macroH2A2 Bernstein Laboratory, ISMMS in house macroH2A1 Abcam ab37264 CTCF EMD 07-729 FOSL2 Santa Cruz SC-604 TEAD4 Santa Cruz SC-101184 HSP90 Santa Cruz SC-13119 GAPDH Santa Cruz SC-32233 GFP Roche 11814460001 LAMIN B1 Santa Cruz SC-6217 ALCAM Abcam ab109215 L1CAM Abcam ab20148 NRP2 Santa Cruz SC-13117 NRP1 Abcam ab81321 TUBULIN Sigma T9026 FOXM1 Cell Signaling Technology 5436 Casp3 Cell Signaling Technology 9662 PARP Cell Signaling Technology 9542 AMIGO2 (for IHC) Abnova H00347902-B01P Lot# F8271 RRID:AB_1672842 AMIGO2 (for IF and WB) R&D systems AF2080 PTK7 (N-terminal) (for WB) R&D systems AF4499 PTK7 (C-terminal) (for IF and WB) Cell Signaling 11926 Secondary rabbit anti goat (for AMIGO2 detection on WB) Sigma A5420 HRP-conjugated ACTIN Sigma A3854 Biological Samples Melanoma and normal skin tissue microarray Biomax ME208 Nevus tissue microarray IMCG, NYU MT032808 Patient derived short term cultures Osman Laboratory, NYU de Miera et al., 2012 NHM (this paper) Bernstein Laboratory, ISMMS NHM1-5 Chemicals, Peptides, and Recombinant Proteins GFP Trap-A beads Chromotek gta-10 BET inhibitor JQ1 Bradner Laboratory; Agreement # {"type":"entrez-nucleotide","attrs":{"text":"A09608","term_id":"490581","term_text":"A09608"}} A09608 N/A BET inhibitor I-BET762 Apex Bio 501014747 IGEPAL Sigma I-8896 Micrococcal Nuclease Affymetrix 70196Y Dynabeads Protein A Immunoprécipitation kit Invitrogen 10006D Magna ChIP Protein A+G Magnetic beads Millipore 16-663 DSG Pierce (ThermoFisher) 20593 Critical Commercial Assays Click- Click-IT EdU Pacific Blue Flow Cytometry Assay Kit ThermoFisher {"type":"entrez-nucleotide","attrs":{"text":"C10636","term_id":"1535707","term_text":"C10636"}} C10636 Caspase Activity assay MBL Int.

Techniques: Stable Transfection, Transduction, shRNA

Journal: Molecular cell

Article Title: Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene

doi: 10.1016/j.molcel.2017.11.004

Figure Lengend Snippet: (A) Immunofluorescence of SKmel147 cells stably expressing AMIGO2-GFP (green), stained with AMIGO2 antibody (red) and Hoechst 33342 (blue). Scale bar, 20 μm.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BRD2 Bethyl Laboratories A302-583A BRD4 Bethyl Laboratories A301-985A H3K4me1 Abcam ab8895 H3K4me3 Abcam ab1012 H3K27ac Abcam ab177178 H3K27me3 EMD 07-449 MED1 Bethyl Laboratories A300-793A macroH2A2 Bernstein Laboratory, ISMMS in house macroH2A1 Abcam ab37264 CTCF EMD 07-729 FOSL2 Santa Cruz SC-604 TEAD4 Santa Cruz SC-101184 HSP90 Santa Cruz SC-13119 GAPDH Santa Cruz SC-32233 GFP Roche 11814460001 LAMIN B1 Santa Cruz SC-6217 ALCAM Abcam ab109215 L1CAM Abcam ab20148 NRP2 Santa Cruz SC-13117 NRP1 Abcam ab81321 TUBULIN Sigma T9026 FOXM1 Cell Signaling Technology 5436 Casp3 Cell Signaling Technology 9662 PARP Cell Signaling Technology 9542 AMIGO2 (for IHC) Abnova H00347902-B01P Lot# F8271 RRID:AB_1672842 AMIGO2 (for IF and WB) R&D systems AF2080 PTK7 (N-terminal) (for WB) R&D systems AF4499 PTK7 (C-terminal) (for IF and WB) Cell Signaling 11926 Secondary rabbit anti goat (for AMIGO2 detection on WB) Sigma A5420 HRP-conjugated ACTIN Sigma A3854 Biological Samples Melanoma and normal skin tissue microarray Biomax ME208 Nevus tissue microarray IMCG, NYU MT032808 Patient derived short term cultures Osman Laboratory, NYU de Miera et al., 2012 NHM (this paper) Bernstein Laboratory, ISMMS NHM1-5 Chemicals, Peptides, and Recombinant Proteins GFP Trap-A beads Chromotek gta-10 BET inhibitor JQ1 Bradner Laboratory; Agreement # {"type":"entrez-nucleotide","attrs":{"text":"A09608","term_id":"490581","term_text":"A09608"}} A09608 N/A BET inhibitor I-BET762 Apex Bio 501014747 IGEPAL Sigma I-8896 Micrococcal Nuclease Affymetrix 70196Y Dynabeads Protein A Immunoprécipitation kit Invitrogen 10006D Magna ChIP Protein A+G Magnetic beads Millipore 16-663 DSG Pierce (ThermoFisher) 20593 Critical Commercial Assays Click- Click-IT EdU Pacific Blue Flow Cytometry Assay Kit ThermoFisher {"type":"entrez-nucleotide","attrs":{"text":"C10636","term_id":"1535707","term_text":"C10636"}} C10636 Caspase Activity assay MBL Int.

Techniques: Immunofluorescence, Stable Transfection, Expressing, Staining

Journal: Molecular cell

Article Title: Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene

doi: 10.1016/j.molcel.2017.11.004

Figure Lengend Snippet: (A) Capture of the UCSC genome browser (GRCh37/hg19) showing 800 kb region on human chromosome 12 (y axis = reads per kilobase per million reads). Ensembl genes (blue) and AMIGO2 SEs (red) are shown at the top. Putative TAD/LAD domain is shown at the bottom.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BRD2 Bethyl Laboratories A302-583A BRD4 Bethyl Laboratories A301-985A H3K4me1 Abcam ab8895 H3K4me3 Abcam ab1012 H3K27ac Abcam ab177178 H3K27me3 EMD 07-449 MED1 Bethyl Laboratories A300-793A macroH2A2 Bernstein Laboratory, ISMMS in house macroH2A1 Abcam ab37264 CTCF EMD 07-729 FOSL2 Santa Cruz SC-604 TEAD4 Santa Cruz SC-101184 HSP90 Santa Cruz SC-13119 GAPDH Santa Cruz SC-32233 GFP Roche 11814460001 LAMIN B1 Santa Cruz SC-6217 ALCAM Abcam ab109215 L1CAM Abcam ab20148 NRP2 Santa Cruz SC-13117 NRP1 Abcam ab81321 TUBULIN Sigma T9026 FOXM1 Cell Signaling Technology 5436 Casp3 Cell Signaling Technology 9662 PARP Cell Signaling Technology 9542 AMIGO2 (for IHC) Abnova H00347902-B01P Lot# F8271 RRID:AB_1672842 AMIGO2 (for IF and WB) R&D systems AF2080 PTK7 (N-terminal) (for WB) R&D systems AF4499 PTK7 (C-terminal) (for IF and WB) Cell Signaling 11926 Secondary rabbit anti goat (for AMIGO2 detection on WB) Sigma A5420 HRP-conjugated ACTIN Sigma A3854 Biological Samples Melanoma and normal skin tissue microarray Biomax ME208 Nevus tissue microarray IMCG, NYU MT032808 Patient derived short term cultures Osman Laboratory, NYU de Miera et al., 2012 NHM (this paper) Bernstein Laboratory, ISMMS NHM1-5 Chemicals, Peptides, and Recombinant Proteins GFP Trap-A beads Chromotek gta-10 BET inhibitor JQ1 Bradner Laboratory; Agreement # {"type":"entrez-nucleotide","attrs":{"text":"A09608","term_id":"490581","term_text":"A09608"}} A09608 N/A BET inhibitor I-BET762 Apex Bio 501014747 IGEPAL Sigma I-8896 Micrococcal Nuclease Affymetrix 70196Y Dynabeads Protein A Immunoprécipitation kit Invitrogen 10006D Magna ChIP Protein A+G Magnetic beads Millipore 16-663 DSG Pierce (ThermoFisher) 20593 Critical Commercial Assays Click- Click-IT EdU Pacific Blue Flow Cytometry Assay Kit ThermoFisher {"type":"entrez-nucleotide","attrs":{"text":"C10636","term_id":"1535707","term_text":"C10636"}} C10636 Caspase Activity assay MBL Int.

Techniques:

Journal: Molecular cell

Article Title: Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene

doi: 10.1016/j.molcel.2017.11.004

Figure Lengend Snippet: (A) Schematic of AMIGO2 SE showing enhancers E1–E5 (B), deleted sequences for CRISPR-Cas9 editing (C), and DNA segments used for E3 lucif-erase assay (D).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BRD2 Bethyl Laboratories A302-583A BRD4 Bethyl Laboratories A301-985A H3K4me1 Abcam ab8895 H3K4me3 Abcam ab1012 H3K27ac Abcam ab177178 H3K27me3 EMD 07-449 MED1 Bethyl Laboratories A300-793A macroH2A2 Bernstein Laboratory, ISMMS in house macroH2A1 Abcam ab37264 CTCF EMD 07-729 FOSL2 Santa Cruz SC-604 TEAD4 Santa Cruz SC-101184 HSP90 Santa Cruz SC-13119 GAPDH Santa Cruz SC-32233 GFP Roche 11814460001 LAMIN B1 Santa Cruz SC-6217 ALCAM Abcam ab109215 L1CAM Abcam ab20148 NRP2 Santa Cruz SC-13117 NRP1 Abcam ab81321 TUBULIN Sigma T9026 FOXM1 Cell Signaling Technology 5436 Casp3 Cell Signaling Technology 9662 PARP Cell Signaling Technology 9542 AMIGO2 (for IHC) Abnova H00347902-B01P Lot# F8271 RRID:AB_1672842 AMIGO2 (for IF and WB) R&D systems AF2080 PTK7 (N-terminal) (for WB) R&D systems AF4499 PTK7 (C-terminal) (for IF and WB) Cell Signaling 11926 Secondary rabbit anti goat (for AMIGO2 detection on WB) Sigma A5420 HRP-conjugated ACTIN Sigma A3854 Biological Samples Melanoma and normal skin tissue microarray Biomax ME208 Nevus tissue microarray IMCG, NYU MT032808 Patient derived short term cultures Osman Laboratory, NYU de Miera et al., 2012 NHM (this paper) Bernstein Laboratory, ISMMS NHM1-5 Chemicals, Peptides, and Recombinant Proteins GFP Trap-A beads Chromotek gta-10 BET inhibitor JQ1 Bradner Laboratory; Agreement # {"type":"entrez-nucleotide","attrs":{"text":"A09608","term_id":"490581","term_text":"A09608"}} A09608 N/A BET inhibitor I-BET762 Apex Bio 501014747 IGEPAL Sigma I-8896 Micrococcal Nuclease Affymetrix 70196Y Dynabeads Protein A Immunoprécipitation kit Invitrogen 10006D Magna ChIP Protein A+G Magnetic beads Millipore 16-663 DSG Pierce (ThermoFisher) 20593 Critical Commercial Assays Click- Click-IT EdU Pacific Blue Flow Cytometry Assay Kit ThermoFisher {"type":"entrez-nucleotide","attrs":{"text":"C10636","term_id":"1535707","term_text":"C10636"}} C10636 Caspase Activity assay MBL Int.

Techniques: CRISPR

Journal: Molecular cell

Article Title: Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene

doi: 10.1016/j.molcel.2017.11.004

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BRD2 Bethyl Laboratories A302-583A BRD4 Bethyl Laboratories A301-985A H3K4me1 Abcam ab8895 H3K4me3 Abcam ab1012 H3K27ac Abcam ab177178 H3K27me3 EMD 07-449 MED1 Bethyl Laboratories A300-793A macroH2A2 Bernstein Laboratory, ISMMS in house macroH2A1 Abcam ab37264 CTCF EMD 07-729 FOSL2 Santa Cruz SC-604 TEAD4 Santa Cruz SC-101184 HSP90 Santa Cruz SC-13119 GAPDH Santa Cruz SC-32233 GFP Roche 11814460001 LAMIN B1 Santa Cruz SC-6217 ALCAM Abcam ab109215 L1CAM Abcam ab20148 NRP2 Santa Cruz SC-13117 NRP1 Abcam ab81321 TUBULIN Sigma T9026 FOXM1 Cell Signaling Technology 5436 Casp3 Cell Signaling Technology 9662 PARP Cell Signaling Technology 9542 AMIGO2 (for IHC) Abnova H00347902-B01P Lot# F8271 RRID:AB_1672842 AMIGO2 (for IF and WB) R&D systems AF2080 PTK7 (N-terminal) (for WB) R&D systems AF4499 PTK7 (C-terminal) (for IF and WB) Cell Signaling 11926 Secondary rabbit anti goat (for AMIGO2 detection on WB) Sigma A5420 HRP-conjugated ACTIN Sigma A3854 Biological Samples Melanoma and normal skin tissue microarray Biomax ME208 Nevus tissue microarray IMCG, NYU MT032808 Patient derived short term cultures Osman Laboratory, NYU de Miera et al., 2012 NHM (this paper) Bernstein Laboratory, ISMMS NHM1-5 Chemicals, Peptides, and Recombinant Proteins GFP Trap-A beads Chromotek gta-10 BET inhibitor JQ1 Bradner Laboratory; Agreement # {"type":"entrez-nucleotide","attrs":{"text":"A09608","term_id":"490581","term_text":"A09608"}} A09608 N/A BET inhibitor I-BET762 Apex Bio 501014747 IGEPAL Sigma I-8896 Micrococcal Nuclease Affymetrix 70196Y Dynabeads Protein A Immunoprécipitation kit Invitrogen 10006D Magna ChIP Protein A+G Magnetic beads Millipore 16-663 DSG Pierce (ThermoFisher) 20593 Critical Commercial Assays Click- Click-IT EdU Pacific Blue Flow Cytometry Assay Kit ThermoFisher {"type":"entrez-nucleotide","attrs":{"text":"C10636","term_id":"1535707","term_text":"C10636"}} C10636 Caspase Activity assay MBL Int.

Techniques: Microarray, Derivative Assay, Recombinant, Magnetic Beads, Flow Cytometry, Caspase Activity Assay, Blocking Assay, TA Cloning, Sequencing, RNA Sequencing Assay, Western Blot, Mass Spectrometry, Expressing, Software