Formulation:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: Used for co- culture at 12.5 pg/ml Other HLA- A24 Retrovirus Hsiue et al., 2021 N/A Retrovirus which introduces and HLA- A24 expression vector Other Luciferase lentivirus OriGene Cat #PS100071 Lentivirus that introduces luciferase into cells Chemical compound, drug 1% penicillin–streptomycin Thermo Fisher Scientific Cat #15140122 Other 4–15% Mini- PROTEAN TGX Precast Protein Gels Bio- Rad Cat #456- 1086 Used for western blotting Chemical compound, drug 5- Fluoruracil Sigma- Aldrich Cat #F6627 Other AMPure beads Beckman Coulter Cat #A63880 Used to purify DNA before sequencing Chemical compound, drug Cremaphor Sigma- Aldrich Cat #C5135 Chemical compound, drug DharmaFECT1 transfection reagent Horizon Cat #T- 2001- 02 Chemical compound, drug Dimethyl sulfoxide (DMSO) Sigma- Aldrich Cat #C6295 Chemical compound, drug DMEM medium Gibco Cat #11995065 Chemical compound, drug EMEM medium ATCC Cat #30- 2003 Chemical compound, drug Emetine Sigma- Aldrich Cat #7083- 71- 8 Chemical compound, drug EPITHELIAL CELL MEDIUM- Complete Kit Science Cell Research Cat #4101 Chemical compound, drug Fetal bovine serum (FBS) HyClone Cat #16777- 006 Chemical compound, drug Glycerol Sigma- Aldrich Cat #G5516 Chemical compound, drug KVS0001 This study N/A Novel small molecule targeting SMG1 kinase. .. See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq.
Saline:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: Used for co- culture at 12.5 pg/ml Other HLA- A24 Retrovirus Hsiue et al., 2021 N/A Retrovirus which introduces and HLA- A24 expression vector Other Luciferase lentivirus OriGene Cat #PS100071 Lentivirus that introduces luciferase into cells Chemical compound, drug 1% penicillin–streptomycin Thermo Fisher Scientific Cat #15140122 Other 4–15% Mini- PROTEAN TGX Precast Protein Gels Bio- Rad Cat #456- 1086 Used for western blotting Chemical compound, drug 5- Fluoruracil Sigma- Aldrich Cat #F6627 Other AMPure beads Beckman Coulter Cat #A63880 Used to purify DNA before sequencing Chemical compound, drug Cremaphor Sigma- Aldrich Cat #C5135 Chemical compound, drug DharmaFECT1 transfection reagent Horizon Cat #T- 2001- 02 Chemical compound, drug Dimethyl sulfoxide (DMSO) Sigma- Aldrich Cat #C6295 Chemical compound, drug DMEM medium Gibco Cat #11995065 Chemical compound, drug EMEM medium ATCC Cat #30- 2003 Chemical compound, drug Emetine Sigma- Aldrich Cat #7083- 71- 8 Chemical compound, drug EPITHELIAL CELL MEDIUM- Complete Kit Science Cell Research Cat #4101 Chemical compound, drug Fetal bovine serum (FBS) HyClone Cat #16777- 006 Chemical compound, drug Glycerol Sigma- Aldrich Cat #G5516 Chemical compound, drug KVS0001 This study N/A Novel small molecule targeting SMG1 kinase. .. See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq.
Polymerase Chain Reaction:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: Used for co- culture at 12.5 pg/ml Other HLA- A24 Retrovirus Hsiue et al., 2021 N/A Retrovirus which introduces and HLA- A24 expression vector Other Luciferase lentivirus OriGene Cat #PS100071 Lentivirus that introduces luciferase into cells Chemical compound, drug 1% penicillin–streptomycin Thermo Fisher Scientific Cat #15140122 Other 4–15% Mini- PROTEAN TGX Precast Protein Gels Bio- Rad Cat #456- 1086 Used for western blotting Chemical compound, drug 5- Fluoruracil Sigma- Aldrich Cat #F6627 Other AMPure beads Beckman Coulter Cat #A63880 Used to purify DNA before sequencing Chemical compound, drug Cremaphor Sigma- Aldrich Cat #C5135 Chemical compound, drug DharmaFECT1 transfection reagent Horizon Cat #T- 2001- 02 Chemical compound, drug Dimethyl sulfoxide (DMSO) Sigma- Aldrich Cat #C6295 Chemical compound, drug DMEM medium Gibco Cat #11995065 Chemical compound, drug EMEM medium ATCC Cat #30- 2003 Chemical compound, drug Emetine Sigma- Aldrich Cat #7083- 71- 8 Chemical compound, drug EPITHELIAL CELL MEDIUM- Complete Kit Science Cell Research Cat #4101 Chemical compound, drug Fetal bovine serum (FBS) HyClone Cat #16777- 006 Chemical compound, drug Glycerol Sigma- Aldrich Cat #G5516 Chemical compound, drug KVS0001 This study N/A Novel small molecule targeting SMG1 kinase. .. See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq.
Western Blot:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: Used for co- culture at 12.5 pg/ml Other HLA- A24 Retrovirus Hsiue et al., 2021 N/A Retrovirus which introduces and HLA- A24 expression vector Other Luciferase lentivirus OriGene Cat #PS100071 Lentivirus that introduces luciferase into cells Chemical compound, drug 1% penicillin–streptomycin Thermo Fisher Scientific Cat #15140122 Other 4–15% Mini- PROTEAN TGX Precast Protein Gels Bio- Rad Cat #456- 1086 Used for western blotting Chemical compound, drug 5- Fluoruracil Sigma- Aldrich Cat #F6627 Other AMPure beads Beckman Coulter Cat #A63880 Used to purify DNA before sequencing Chemical compound, drug Cremaphor Sigma- Aldrich Cat #C5135 Chemical compound, drug DharmaFECT1 transfection reagent Horizon Cat #T- 2001- 02 Chemical compound, drug Dimethyl sulfoxide (DMSO) Sigma- Aldrich Cat #C6295 Chemical compound, drug DMEM medium Gibco Cat #11995065 Chemical compound, drug EMEM medium ATCC Cat #30- 2003 Chemical compound, drug Emetine Sigma- Aldrich Cat #7083- 71- 8 Chemical compound, drug EPITHELIAL CELL MEDIUM- Complete Kit Science Cell Research Cat #4101 Chemical compound, drug Fetal bovine serum (FBS) HyClone Cat #16777- 006 Chemical compound, drug Glycerol Sigma- Aldrich Cat #G5516 Chemical compound, drug KVS0001 This study N/A Novel small molecule targeting SMG1 kinase. .. See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq.
Gene Expression:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: Used for co- culture at 12.5 pg/ml Other HLA- A24 Retrovirus Hsiue et al., 2021 N/A Retrovirus which introduces and HLA- A24 expression vector Other Luciferase lentivirus OriGene Cat #PS100071 Lentivirus that introduces luciferase into cells Chemical compound, drug 1% penicillin–streptomycin Thermo Fisher Scientific Cat #15140122 Other 4–15% Mini- PROTEAN TGX Precast Protein Gels Bio- Rad Cat #456- 1086 Used for western blotting Chemical compound, drug 5- Fluoruracil Sigma- Aldrich Cat #F6627 Other AMPure beads Beckman Coulter Cat #A63880 Used to purify DNA before sequencing Chemical compound, drug Cremaphor Sigma- Aldrich Cat #C5135 Chemical compound, drug DharmaFECT1 transfection reagent Horizon Cat #T- 2001- 02 Chemical compound, drug Dimethyl sulfoxide (DMSO) Sigma- Aldrich Cat #C6295 Chemical compound, drug DMEM medium Gibco Cat #11995065 Chemical compound, drug EMEM medium ATCC Cat #30- 2003 Chemical compound, drug Emetine Sigma- Aldrich Cat #7083- 71- 8 Chemical compound, drug EPITHELIAL CELL MEDIUM- Complete Kit Science Cell Research Cat #4101 Chemical compound, drug Fetal bovine serum (FBS) HyClone Cat #16777- 006 Chemical compound, drug Glycerol Sigma- Aldrich Cat #G5516 Chemical compound, drug KVS0001 This study N/A Novel small molecule targeting SMG1 kinase. .. See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq.
Real-time Polymerase Chain Reaction:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: Used for co- culture at 12.5 pg/ml Other HLA- A24 Retrovirus Hsiue et al., 2021 N/A Retrovirus which introduces and HLA- A24 expression vector Other Luciferase lentivirus OriGene Cat #PS100071 Lentivirus that introduces luciferase into cells Chemical compound, drug 1% penicillin–streptomycin Thermo Fisher Scientific Cat #15140122 Other 4–15% Mini- PROTEAN TGX Precast Protein Gels Bio- Rad Cat #456- 1086 Used for western blotting Chemical compound, drug 5- Fluoruracil Sigma- Aldrich Cat #F6627 Other AMPure beads Beckman Coulter Cat #A63880 Used to purify DNA before sequencing Chemical compound, drug Cremaphor Sigma- Aldrich Cat #C5135 Chemical compound, drug DharmaFECT1 transfection reagent Horizon Cat #T- 2001- 02 Chemical compound, drug Dimethyl sulfoxide (DMSO) Sigma- Aldrich Cat #C6295 Chemical compound, drug DMEM medium Gibco Cat #11995065 Chemical compound, drug EMEM medium ATCC Cat #30- 2003 Chemical compound, drug Emetine Sigma- Aldrich Cat #7083- 71- 8 Chemical compound, drug EPITHELIAL CELL MEDIUM- Complete Kit Science Cell Research Cat #4101 Chemical compound, drug Fetal bovine serum (FBS) HyClone Cat #16777- 006 Chemical compound, drug Glycerol Sigma- Aldrich Cat #G5516 Chemical compound, drug KVS0001 This study N/A Novel small molecule targeting SMG1 kinase. .. See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq.
Protease Inhibitor:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: Used for co- culture at 12.5 pg/ml Other HLA- A24 Retrovirus Hsiue et al., 2021 N/A Retrovirus which introduces and HLA- A24 expression vector Other Luciferase lentivirus OriGene Cat #PS100071 Lentivirus that introduces luciferase into cells Chemical compound, drug 1% penicillin–streptomycin Thermo Fisher Scientific Cat #15140122 Other 4–15% Mini- PROTEAN TGX Precast Protein Gels Bio- Rad Cat #456- 1086 Used for western blotting Chemical compound, drug 5- Fluoruracil Sigma- Aldrich Cat #F6627 Other AMPure beads Beckman Coulter Cat #A63880 Used to purify DNA before sequencing Chemical compound, drug Cremaphor Sigma- Aldrich Cat #C5135 Chemical compound, drug DharmaFECT1 transfection reagent Horizon Cat #T- 2001- 02 Chemical compound, drug Dimethyl sulfoxide (DMSO) Sigma- Aldrich Cat #C6295 Chemical compound, drug DMEM medium Gibco Cat #11995065 Chemical compound, drug EMEM medium ATCC Cat #30- 2003 Chemical compound, drug Emetine Sigma- Aldrich Cat #7083- 71- 8 Chemical compound, drug EPITHELIAL CELL MEDIUM- Complete Kit Science Cell Research Cat #4101 Chemical compound, drug Fetal bovine serum (FBS) HyClone Cat #16777- 006 Chemical compound, drug Glycerol Sigma- Aldrich Cat #G5516 Chemical compound, drug KVS0001 This study N/A Novel small molecule targeting SMG1 kinase. .. See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq.
Recombinant:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: Used for co- culture at 12.5 pg/ml Other HLA- A24 Retrovirus Hsiue et al., 2021 N/A Retrovirus which introduces and HLA- A24 expression vector Other Luciferase lentivirus OriGene Cat #PS100071 Lentivirus that introduces luciferase into cells Chemical compound, drug 1% penicillin–streptomycin Thermo Fisher Scientific Cat #15140122 Other 4–15% Mini- PROTEAN TGX Precast Protein Gels Bio- Rad Cat #456- 1086 Used for western blotting Chemical compound, drug 5- Fluoruracil Sigma- Aldrich Cat #F6627 Other AMPure beads Beckman Coulter Cat #A63880 Used to purify DNA before sequencing Chemical compound, drug Cremaphor Sigma- Aldrich Cat #C5135 Chemical compound, drug DharmaFECT1 transfection reagent Horizon Cat #T- 2001- 02 Chemical compound, drug Dimethyl sulfoxide (DMSO) Sigma- Aldrich Cat #C6295 Chemical compound, drug DMEM medium Gibco Cat #11995065 Chemical compound, drug EMEM medium ATCC Cat #30- 2003 Chemical compound, drug Emetine Sigma- Aldrich Cat #7083- 71- 8 Chemical compound, drug EPITHELIAL CELL MEDIUM- Complete Kit Science Cell Research Cat #4101 Chemical compound, drug Fetal bovine serum (FBS) HyClone Cat #16777- 006 Chemical compound, drug Glycerol Sigma- Aldrich Cat #G5516 Chemical compound, drug KVS0001 This study N/A Novel small molecule targeting SMG1 kinase. .. See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq.
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