Recombinant:Article Title: Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-a-tubulin (clone DM1A) Calbiochem Cat#:CP06; RRID:AB_212802 Rabbit monoclonal anti-BMAL1 (clone D2L7G) Cell Signaling Cat#:14020; RRID:AB_2728705 Rabbit monoclonal anti-CLOCK (clone D45B10) Cell Signaling Cat#:5157; RRID:AB_10695411 Mouse monoclonal anti-PBRM1 (clone E6N2K) Cell Signaling Cat#:81832 Rabbit monoclonal anti-PBRM1 (E9X2Z) Cell Signaling Cat#: 89123 Rabbit monoclonal anti-Rev-Erba (E1Y6D) Cell Signaling Cat#: 13418 Rabbit polyclonal anti-ADIRF Atlas HPA026810; RRID: AB_2672003 Rabbit monoclonal anti-BRG1 (D1Q7F) Cell Signaling Cat#: 49360; RRID:AB_2728743 Rabbit monoclonal anti-HIF-2a (D9E3) Cell Signaling Cat#: 7096; RRID:AB_10898028 BrdU Monoclonal Antibody (BU20A), APC eBiosciences 17-5071-42; RRID: AB_11040534 goat anti-rabbit alexa fluor 488 Invitrogen A-11008 Chemicals, peptides, and recombinant proteins Beetle luciferin, potassium salt Promega E1602 Dexamethasone Sigma D4902 CAS 50-02-2 Dulbecco’s MEM (DMEM) high glucose Corning MT10-013-CV RPMI-1640 Corning 10-040 Fetal bovine serum HyClone, Gemini Bioproducts SH30910.03 High-vacuum silicone grease Dow Corning/Sigma Z273554 G418 sulfate Corning MT30-234-CR Hygromycin B solution Corning 30-240-CR Puromycin dihydrochloride Gibco A1113803 TaqMan Reverse transcription kit Invitrogen N8080234 iScript reverse transcription supermix Bio-Rad 1708841 Phusion High-Fidelity PCR Kit Thermo Fisher Scientific F553L Mammalian protein extraction reagent (M-PER) Thermo Scientific PI78501 Lipofectamine 3000 transfection reagent Invitrogen L3000008 Lipofectamine RNAiMAX transfection reagent Invitrogen 13778150 NaCl, 5M solution Invitrogen AM9759; CAS 7647-14- 5 Bd 7AAD Staining Solution BD 559925 Formal-Fixx Thermo Fisher Scientific 6764254 Hepes, pH 7.5 Sigma NA MgCl2 Invitrogen AM9530G EDTA Invitrogen 15575-038 EGTA RPI Research Products International Corp E14100-50.0 DTT Bio-Rad 1610610 Protease inhibitor cocktail Promega G6521 Phosphatase inhibitor Sigma P5726 Phosphatase inhibitor Sigma P0044 Glucose Sigma G8769 Sodium Bicarbonate Gibco 25080094 Penicillin-Streptomycin USBiological D9812-05 (Continued on next page) e1 Cell Reports 41, 111514, October 18, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER L-Glutamine Lonza BEBP17-605E Duolink in situ mounting medium with DAPI Sigma DUO82040-5ml biotin labeling mix Roche 11685597910 T7 polymerase Promega P2075 Tris-HCL pH 7 Invitrogen 15567-027 tRNA Life Technologies AM7119 IGEPAL (NP-40 substitute) Sigma CA-630,18896 PierceTM Streptavidin Agarose Thermo Fisher Scientific 20353 Urea Thermo Fisher Scientific BP169-500 Critical commercial assays RNeasy plus mini kit Qiagen 74134 DC protein assay kit II Bio-Rad 5000112 Power SYBRTM Green PCR Master Mix Thermo Fisher 436870 Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit Millipore Sigma 17-700 SimpleChIP(R) Enzymatic Chromatin IP Kit (Magnetic Beads) Cell Signaling 9003S PierceTM Magnetic RNA-Protein Pull-Down Kit Thermo Fisher Scientific 20164 MEGAscriptTM T7 Transcription Kit Invitrogen AM1334 Phusion High-Fidelity PCR Master Mix with HF Buffer Thermo Fisher Scientific F531L pCR 2.1-TOPO TA Thermo Fisher Scientific 451641 OpalTM 620 Reagent Pack Akoya Biosciences FP1495001KT RNA-Protein Co-Detection Ancillary Kit Advanced Cell Diagnostics 323180 RNAscope Intro Pack for Multiplex Fluorescent Reagent Kit v2-Hs Advanced Cell Diagnostics 323135 Pierce RNA 30 End desthiobiotinylation kit Thermo Fisher Scientific 20163 SuperScriptTM III First-Strand Synthesis System Invitrogen 18080051 CellTiter-Glo Reagent Promega G7571 Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit for Illumina Lexogen Cat. No. 015 Deposited data Quant-seq This paper GSE199825 Proteomics This paper MSV000090286 ChIP-seq This paper GSE199825 Experimental models: Cell lines Human: U2OS Laboratory of Roger Greenberg ATCC HTB-96 NA Human: U2OS Arntl::dLUC Laboratory of John Hogenesch NA Human: U2OS PX458 sgSCR This study NA Human: U2OS PX458 sgADIRF-AS1 clone 1 This study NA Human: U2OS PX458 sgADIRF-AS1 clone 2 This study NA Human: U2OS sgSCR Laboratory of Amita Sehgal NA Human: U2OS sgBMAL1 Laboratoryof Amita Sehgal NA Human: U2OS ADIRF-AS1::dLUC This study NA Human: 786O Laboratory of Celeste Simon NA Human: 769P Laboratory of Celeste Simon NA (Continued on next page) Cell Reports 41, 111514, October 18, 2022 e2 Article ll OPEN ACCESS
Reverse Transcription:Article Title: Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-a-tubulin (clone DM1A) Calbiochem Cat#:CP06; RRID:AB_212802 Rabbit monoclonal anti-BMAL1 (clone D2L7G) Cell Signaling Cat#:14020; RRID:AB_2728705 Rabbit monoclonal anti-CLOCK (clone D45B10) Cell Signaling Cat#:5157; RRID:AB_10695411 Mouse monoclonal anti-PBRM1 (clone E6N2K) Cell Signaling Cat#:81832 Rabbit monoclonal anti-PBRM1 (E9X2Z) Cell Signaling Cat#: 89123 Rabbit monoclonal anti-Rev-Erba (E1Y6D) Cell Signaling Cat#: 13418 Rabbit polyclonal anti-ADIRF Atlas HPA026810; RRID: AB_2672003 Rabbit monoclonal anti-BRG1 (D1Q7F) Cell Signaling Cat#: 49360; RRID:AB_2728743 Rabbit monoclonal anti-HIF-2a (D9E3) Cell Signaling Cat#: 7096; RRID:AB_10898028 BrdU Monoclonal Antibody (BU20A), APC eBiosciences 17-5071-42; RRID: AB_11040534 goat anti-rabbit alexa fluor 488 Invitrogen A-11008 Chemicals, peptides, and recombinant proteins Beetle luciferin, potassium salt Promega E1602 Dexamethasone Sigma D4902 CAS 50-02-2 Dulbecco’s MEM (DMEM) high glucose Corning MT10-013-CV RPMI-1640 Corning 10-040 Fetal bovine serum HyClone, Gemini Bioproducts SH30910.03 High-vacuum silicone grease Dow Corning/Sigma Z273554 G418 sulfate Corning MT30-234-CR Hygromycin B solution Corning 30-240-CR Puromycin dihydrochloride Gibco A1113803 TaqMan Reverse transcription kit Invitrogen N8080234 iScript reverse transcription supermix Bio-Rad 1708841 Phusion High-Fidelity PCR Kit Thermo Fisher Scientific F553L Mammalian protein extraction reagent (M-PER) Thermo Scientific PI78501 Lipofectamine 3000 transfection reagent Invitrogen L3000008 Lipofectamine RNAiMAX transfection reagent Invitrogen 13778150 NaCl, 5M solution Invitrogen AM9759; CAS 7647-14- 5 Bd 7AAD Staining Solution BD 559925 Formal-Fixx Thermo Fisher Scientific 6764254 Hepes, pH 7.5 Sigma NA MgCl2 Invitrogen AM9530G EDTA Invitrogen 15575-038 EGTA RPI Research Products International Corp E14100-50.0 DTT Bio-Rad 1610610 Protease inhibitor cocktail Promega G6521 Phosphatase inhibitor Sigma P5726 Phosphatase inhibitor Sigma P0044 Glucose Sigma G8769 Sodium Bicarbonate Gibco 25080094 Penicillin-Streptomycin USBiological D9812-05 (Continued on next page) e1 Cell Reports 41, 111514, October 18, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER L-Glutamine Lonza BEBP17-605E Duolink in situ mounting medium with DAPI Sigma DUO82040-5ml biotin labeling mix Roche 11685597910 T7 polymerase Promega P2075 Tris-HCL pH 7 Invitrogen 15567-027 tRNA Life Technologies AM7119 IGEPAL (NP-40 substitute) Sigma CA-630,18896 PierceTM Streptavidin Agarose Thermo Fisher Scientific 20353 Urea Thermo Fisher Scientific BP169-500 Critical commercial assays RNeasy plus mini kit Qiagen 74134 DC protein assay kit II Bio-Rad 5000112 Power SYBRTM Green PCR Master Mix Thermo Fisher 436870 Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit Millipore Sigma 17-700 SimpleChIP(R) Enzymatic Chromatin IP Kit (Magnetic Beads) Cell Signaling 9003S PierceTM Magnetic RNA-Protein Pull-Down Kit Thermo Fisher Scientific 20164 MEGAscriptTM T7 Transcription Kit Invitrogen AM1334 Phusion High-Fidelity PCR Master Mix with HF Buffer Thermo Fisher Scientific F531L pCR 2.1-TOPO TA Thermo Fisher Scientific 451641 OpalTM 620 Reagent Pack Akoya Biosciences FP1495001KT RNA-Protein Co-Detection Ancillary Kit Advanced Cell Diagnostics 323180 RNAscope Intro Pack for Multiplex Fluorescent Reagent Kit v2-Hs Advanced Cell Diagnostics 323135 Pierce RNA 30 End desthiobiotinylation kit Thermo Fisher Scientific 20163 SuperScriptTM III First-Strand Synthesis System Invitrogen 18080051 CellTiter-Glo Reagent Promega G7571 Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit for Illumina Lexogen Cat. No. 015 Deposited data Quant-seq This paper GSE199825 Proteomics This paper MSV000090286 ChIP-seq This paper GSE199825 Experimental models: Cell lines Human: U2OS Laboratory of Roger Greenberg ATCC HTB-96 NA Human: U2OS Arntl::dLUC Laboratory of John Hogenesch NA Human: U2OS PX458 sgSCR This study NA Human: U2OS PX458 sgADIRF-AS1 clone 1 This study NA Human: U2OS PX458 sgADIRF-AS1 clone 2 This study NA Human: U2OS sgSCR Laboratory of Amita Sehgal NA Human: U2OS sgBMAL1 Laboratoryof Amita Sehgal NA Human: U2OS ADIRF-AS1::dLUC This study NA Human: 786O Laboratory of Celeste Simon NA Human: 769P Laboratory of Celeste Simon NA (Continued on next page) Cell Reports 41, 111514, October 18, 2022 e2 Article ll OPEN ACCESS
Polymerase Chain Reaction:Article Title: Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-a-tubulin (clone DM1A) Calbiochem Cat#:CP06; RRID:AB_212802 Rabbit monoclonal anti-BMAL1 (clone D2L7G) Cell Signaling Cat#:14020; RRID:AB_2728705 Rabbit monoclonal anti-CLOCK (clone D45B10) Cell Signaling Cat#:5157; RRID:AB_10695411 Mouse monoclonal anti-PBRM1 (clone E6N2K) Cell Signaling Cat#:81832 Rabbit monoclonal anti-PBRM1 (E9X2Z) Cell Signaling Cat#: 89123 Rabbit monoclonal anti-Rev-Erba (E1Y6D) Cell Signaling Cat#: 13418 Rabbit polyclonal anti-ADIRF Atlas HPA026810; RRID: AB_2672003 Rabbit monoclonal anti-BRG1 (D1Q7F) Cell Signaling Cat#: 49360; RRID:AB_2728743 Rabbit monoclonal anti-HIF-2a (D9E3) Cell Signaling Cat#: 7096; RRID:AB_10898028 BrdU Monoclonal Antibody (BU20A), APC eBiosciences 17-5071-42; RRID: AB_11040534 goat anti-rabbit alexa fluor 488 Invitrogen A-11008 Chemicals, peptides, and recombinant proteins Beetle luciferin, potassium salt Promega E1602 Dexamethasone Sigma D4902 CAS 50-02-2 Dulbecco’s MEM (DMEM) high glucose Corning MT10-013-CV RPMI-1640 Corning 10-040 Fetal bovine serum HyClone, Gemini Bioproducts SH30910.03 High-vacuum silicone grease Dow Corning/Sigma Z273554 G418 sulfate Corning MT30-234-CR Hygromycin B solution Corning 30-240-CR Puromycin dihydrochloride Gibco A1113803 TaqMan Reverse transcription kit Invitrogen N8080234 iScript reverse transcription supermix Bio-Rad 1708841 Phusion High-Fidelity PCR Kit Thermo Fisher Scientific F553L Mammalian protein extraction reagent (M-PER) Thermo Scientific PI78501 Lipofectamine 3000 transfection reagent Invitrogen L3000008 Lipofectamine RNAiMAX transfection reagent Invitrogen 13778150 NaCl, 5M solution Invitrogen AM9759; CAS 7647-14- 5 Bd 7AAD Staining Solution BD 559925 Formal-Fixx Thermo Fisher Scientific 6764254 Hepes, pH 7.5 Sigma NA MgCl2 Invitrogen AM9530G EDTA Invitrogen 15575-038 EGTA RPI Research Products International Corp E14100-50.0 DTT Bio-Rad 1610610 Protease inhibitor cocktail Promega G6521 Phosphatase inhibitor Sigma P5726 Phosphatase inhibitor Sigma P0044 Glucose Sigma G8769 Sodium Bicarbonate Gibco 25080094 Penicillin-Streptomycin USBiological D9812-05 (Continued on next page) e1 Cell Reports 41, 111514, October 18, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER L-Glutamine Lonza BEBP17-605E Duolink in situ mounting medium with DAPI Sigma DUO82040-5ml biotin labeling mix Roche 11685597910 T7 polymerase Promega P2075 Tris-HCL pH 7 Invitrogen 15567-027 tRNA Life Technologies AM7119 IGEPAL (NP-40 substitute) Sigma CA-630,18896 PierceTM Streptavidin Agarose Thermo Fisher Scientific 20353 Urea Thermo Fisher Scientific BP169-500 Critical commercial assays RNeasy plus mini kit Qiagen 74134 DC protein assay kit II Bio-Rad 5000112 Power SYBRTM Green PCR Master Mix Thermo Fisher 436870 Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit Millipore Sigma 17-700 SimpleChIP(R) Enzymatic Chromatin IP Kit (Magnetic Beads) Cell Signaling 9003S PierceTM Magnetic RNA-Protein Pull-Down Kit Thermo Fisher Scientific 20164 MEGAscriptTM T7 Transcription Kit Invitrogen AM1334 Phusion High-Fidelity PCR Master Mix with HF Buffer Thermo Fisher Scientific F531L pCR 2.1-TOPO TA Thermo Fisher Scientific 451641 OpalTM 620 Reagent Pack Akoya Biosciences FP1495001KT RNA-Protein Co-Detection Ancillary Kit Advanced Cell Diagnostics 323180 RNAscope Intro Pack for Multiplex Fluorescent Reagent Kit v2-Hs Advanced Cell Diagnostics 323135 Pierce RNA 30 End desthiobiotinylation kit Thermo Fisher Scientific 20163 SuperScriptTM III First-Strand Synthesis System Invitrogen 18080051 CellTiter-Glo Reagent Promega G7571 Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit for Illumina Lexogen Cat. No. 015 Deposited data Quant-seq This paper GSE199825 Proteomics This paper MSV000090286 ChIP-seq This paper GSE199825 Experimental models: Cell lines Human: U2OS Laboratory of Roger Greenberg ATCC HTB-96 NA Human: U2OS Arntl::dLUC Laboratory of John Hogenesch NA Human: U2OS PX458 sgSCR This study NA Human: U2OS PX458 sgADIRF-AS1 clone 1 This study NA Human: U2OS PX458 sgADIRF-AS1 clone 2 This study NA Human: U2OS sgSCR Laboratory of Amita Sehgal NA Human: U2OS sgBMAL1 Laboratoryof Amita Sehgal NA Human: U2OS ADIRF-AS1::dLUC This study NA Human: 786O Laboratory of Celeste Simon NA Human: 769P Laboratory of Celeste Simon NA (Continued on next page) Cell Reports 41, 111514, October 18, 2022 e2 Article ll OPEN ACCESS
Protein Extraction:Article Title: Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-a-tubulin (clone DM1A) Calbiochem Cat#:CP06; RRID:AB_212802 Rabbit monoclonal anti-BMAL1 (clone D2L7G) Cell Signaling Cat#:14020; RRID:AB_2728705 Rabbit monoclonal anti-CLOCK (clone D45B10) Cell Signaling Cat#:5157; RRID:AB_10695411 Mouse monoclonal anti-PBRM1 (clone E6N2K) Cell Signaling Cat#:81832 Rabbit monoclonal anti-PBRM1 (E9X2Z) Cell Signaling Cat#: 89123 Rabbit monoclonal anti-Rev-Erba (E1Y6D) Cell Signaling Cat#: 13418 Rabbit polyclonal anti-ADIRF Atlas HPA026810; RRID: AB_2672003 Rabbit monoclonal anti-BRG1 (D1Q7F) Cell Signaling Cat#: 49360; RRID:AB_2728743 Rabbit monoclonal anti-HIF-2a (D9E3) Cell Signaling Cat#: 7096; RRID:AB_10898028 BrdU Monoclonal Antibody (BU20A), APC eBiosciences 17-5071-42; RRID: AB_11040534 goat anti-rabbit alexa fluor 488 Invitrogen A-11008 Chemicals, peptides, and recombinant proteins Beetle luciferin, potassium salt Promega E1602 Dexamethasone Sigma D4902 CAS 50-02-2 Dulbecco’s MEM (DMEM) high glucose Corning MT10-013-CV RPMI-1640 Corning 10-040 Fetal bovine serum HyClone, Gemini Bioproducts SH30910.03 High-vacuum silicone grease Dow Corning/Sigma Z273554 G418 sulfate Corning MT30-234-CR Hygromycin B solution Corning 30-240-CR Puromycin dihydrochloride Gibco A1113803 TaqMan Reverse transcription kit Invitrogen N8080234 iScript reverse transcription supermix Bio-Rad 1708841 Phusion High-Fidelity PCR Kit Thermo Fisher Scientific F553L Mammalian protein extraction reagent (M-PER) Thermo Scientific PI78501 Lipofectamine 3000 transfection reagent Invitrogen L3000008 Lipofectamine RNAiMAX transfection reagent Invitrogen 13778150 NaCl, 5M solution Invitrogen AM9759; CAS 7647-14- 5 Bd 7AAD Staining Solution BD 559925 Formal-Fixx Thermo Fisher Scientific 6764254 Hepes, pH 7.5 Sigma NA MgCl2 Invitrogen AM9530G EDTA Invitrogen 15575-038 EGTA RPI Research Products International Corp E14100-50.0 DTT Bio-Rad 1610610 Protease inhibitor cocktail Promega G6521 Phosphatase inhibitor Sigma P5726 Phosphatase inhibitor Sigma P0044 Glucose Sigma G8769 Sodium Bicarbonate Gibco 25080094 Penicillin-Streptomycin USBiological D9812-05 (Continued on next page) e1 Cell Reports 41, 111514, October 18, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER L-Glutamine Lonza BEBP17-605E Duolink in situ mounting medium with DAPI Sigma DUO82040-5ml biotin labeling mix Roche 11685597910 T7 polymerase Promega P2075 Tris-HCL pH 7 Invitrogen 15567-027 tRNA Life Technologies AM7119 IGEPAL (NP-40 substitute) Sigma CA-630,18896 PierceTM Streptavidin Agarose Thermo Fisher Scientific 20353 Urea Thermo Fisher Scientific BP169-500 Critical commercial assays RNeasy plus mini kit Qiagen 74134 DC protein assay kit II Bio-Rad 5000112 Power SYBRTM Green PCR Master Mix Thermo Fisher 436870 Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit Millipore Sigma 17-700 SimpleChIP(R) Enzymatic Chromatin IP Kit (Magnetic Beads) Cell Signaling 9003S PierceTM Magnetic RNA-Protein Pull-Down Kit Thermo Fisher Scientific 20164 MEGAscriptTM T7 Transcription Kit Invitrogen AM1334 Phusion High-Fidelity PCR Master Mix with HF Buffer Thermo Fisher Scientific F531L pCR 2.1-TOPO TA Thermo Fisher Scientific 451641 OpalTM 620 Reagent Pack Akoya Biosciences FP1495001KT RNA-Protein Co-Detection Ancillary Kit Advanced Cell Diagnostics 323180 RNAscope Intro Pack for Multiplex Fluorescent Reagent Kit v2-Hs Advanced Cell Diagnostics 323135 Pierce RNA 30 End desthiobiotinylation kit Thermo Fisher Scientific 20163 SuperScriptTM III First-Strand Synthesis System Invitrogen 18080051 CellTiter-Glo Reagent Promega G7571 Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit for Illumina Lexogen Cat. No. 015 Deposited data Quant-seq This paper GSE199825 Proteomics This paper MSV000090286 ChIP-seq This paper GSE199825 Experimental models: Cell lines Human: U2OS Laboratory of Roger Greenberg ATCC HTB-96 NA Human: U2OS Arntl::dLUC Laboratory of John Hogenesch NA Human: U2OS PX458 sgSCR This study NA Human: U2OS PX458 sgADIRF-AS1 clone 1 This study NA Human: U2OS PX458 sgADIRF-AS1 clone 2 This study NA Human: U2OS sgSCR Laboratory of Amita Sehgal NA Human: U2OS sgBMAL1 Laboratoryof Amita Sehgal NA Human: U2OS ADIRF-AS1::dLUC This study NA Human: 786O Laboratory of Celeste Simon NA Human: 769P Laboratory of Celeste Simon NA (Continued on next page) Cell Reports 41, 111514, October 18, 2022 e2 Article ll OPEN ACCESS
Transfection:Article Title: Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-a-tubulin (clone DM1A) Calbiochem Cat#:CP06; RRID:AB_212802 Rabbit monoclonal anti-BMAL1 (clone D2L7G) Cell Signaling Cat#:14020; RRID:AB_2728705 Rabbit monoclonal anti-CLOCK (clone D45B10) Cell Signaling Cat#:5157; RRID:AB_10695411 Mouse monoclonal anti-PBRM1 (clone E6N2K) Cell Signaling Cat#:81832 Rabbit monoclonal anti-PBRM1 (E9X2Z) Cell Signaling Cat#: 89123 Rabbit monoclonal anti-Rev-Erba (E1Y6D) Cell Signaling Cat#: 13418 Rabbit polyclonal anti-ADIRF Atlas HPA026810; RRID: AB_2672003 Rabbit monoclonal anti-BRG1 (D1Q7F) Cell Signaling Cat#: 49360; RRID:AB_2728743 Rabbit monoclonal anti-HIF-2a (D9E3) Cell Signaling Cat#: 7096; RRID:AB_10898028 BrdU Monoclonal Antibody (BU20A), APC eBiosciences 17-5071-42; RRID: AB_11040534 goat anti-rabbit alexa fluor 488 Invitrogen A-11008 Chemicals, peptides, and recombinant proteins Beetle luciferin, potassium salt Promega E1602 Dexamethasone Sigma D4902 CAS 50-02-2 Dulbecco’s MEM (DMEM) high glucose Corning MT10-013-CV RPMI-1640 Corning 10-040 Fetal bovine serum HyClone, Gemini Bioproducts SH30910.03 High-vacuum silicone grease Dow Corning/Sigma Z273554 G418 sulfate Corning MT30-234-CR Hygromycin B solution Corning 30-240-CR Puromycin dihydrochloride Gibco A1113803 TaqMan Reverse transcription kit Invitrogen N8080234 iScript reverse transcription supermix Bio-Rad 1708841 Phusion High-Fidelity PCR Kit Thermo Fisher Scientific F553L Mammalian protein extraction reagent (M-PER) Thermo Scientific PI78501 Lipofectamine 3000 transfection reagent Invitrogen L3000008 Lipofectamine RNAiMAX transfection reagent Invitrogen 13778150 NaCl, 5M solution Invitrogen AM9759; CAS 7647-14- 5 Bd 7AAD Staining Solution BD 559925 Formal-Fixx Thermo Fisher Scientific 6764254 Hepes, pH 7.5 Sigma NA MgCl2 Invitrogen AM9530G EDTA Invitrogen 15575-038 EGTA RPI Research Products International Corp E14100-50.0 DTT Bio-Rad 1610610 Protease inhibitor cocktail Promega G6521 Phosphatase inhibitor Sigma P5726 Phosphatase inhibitor Sigma P0044 Glucose Sigma G8769 Sodium Bicarbonate Gibco 25080094 Penicillin-Streptomycin USBiological D9812-05 (Continued on next page) e1 Cell Reports 41, 111514, October 18, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER L-Glutamine Lonza BEBP17-605E Duolink in situ mounting medium with DAPI Sigma DUO82040-5ml biotin labeling mix Roche 11685597910 T7 polymerase Promega P2075 Tris-HCL pH 7 Invitrogen 15567-027 tRNA Life Technologies AM7119 IGEPAL (NP-40 substitute) Sigma CA-630,18896 PierceTM Streptavidin Agarose Thermo Fisher Scientific 20353 Urea Thermo Fisher Scientific BP169-500 Critical commercial assays RNeasy plus mini kit Qiagen 74134 DC protein assay kit II Bio-Rad 5000112 Power SYBRTM Green PCR Master Mix Thermo Fisher 436870 Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit Millipore Sigma 17-700 SimpleChIP(R) Enzymatic Chromatin IP Kit (Magnetic Beads) Cell Signaling 9003S PierceTM Magnetic RNA-Protein Pull-Down Kit Thermo Fisher Scientific 20164 MEGAscriptTM T7 Transcription Kit Invitrogen AM1334 Phusion High-Fidelity PCR Master Mix with HF Buffer Thermo Fisher Scientific F531L pCR 2.1-TOPO TA Thermo Fisher Scientific 451641 OpalTM 620 Reagent Pack Akoya Biosciences FP1495001KT RNA-Protein Co-Detection Ancillary Kit Advanced Cell Diagnostics 323180 RNAscope Intro Pack for Multiplex Fluorescent Reagent Kit v2-Hs Advanced Cell Diagnostics 323135 Pierce RNA 30 End desthiobiotinylation kit Thermo Fisher Scientific 20163 SuperScriptTM III First-Strand Synthesis System Invitrogen 18080051 CellTiter-Glo Reagent Promega G7571 Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit for Illumina Lexogen Cat. No. 015 Deposited data Quant-seq This paper GSE199825 Proteomics This paper MSV000090286 ChIP-seq This paper GSE199825 Experimental models: Cell lines Human: U2OS Laboratory of Roger Greenberg ATCC HTB-96 NA Human: U2OS Arntl::dLUC Laboratory of John Hogenesch NA Human: U2OS PX458 sgSCR This study NA Human: U2OS PX458 sgADIRF-AS1 clone 1 This study NA Human: U2OS PX458 sgADIRF-AS1 clone 2 This study NA Human: U2OS sgSCR Laboratory of Amita Sehgal NA Human: U2OS sgBMAL1 Laboratoryof Amita Sehgal NA Human: U2OS ADIRF-AS1::dLUC This study NA Human: 786O Laboratory of Celeste Simon NA Human: 769P Laboratory of Celeste Simon NA (Continued on next page) Cell Reports 41, 111514, October 18, 2022 e2 Article ll OPEN ACCESS
Staining:Article Title: Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-a-tubulin (clone DM1A) Calbiochem Cat#:CP06; RRID:AB_212802 Rabbit monoclonal anti-BMAL1 (clone D2L7G) Cell Signaling Cat#:14020; RRID:AB_2728705 Rabbit monoclonal anti-CLOCK (clone D45B10) Cell Signaling Cat#:5157; RRID:AB_10695411 Mouse monoclonal anti-PBRM1 (clone E6N2K) Cell Signaling Cat#:81832 Rabbit monoclonal anti-PBRM1 (E9X2Z) Cell Signaling Cat#: 89123 Rabbit monoclonal anti-Rev-Erba (E1Y6D) Cell Signaling Cat#: 13418 Rabbit polyclonal anti-ADIRF Atlas HPA026810; RRID: AB_2672003 Rabbit monoclonal anti-BRG1 (D1Q7F) Cell Signaling Cat#: 49360; RRID:AB_2728743 Rabbit monoclonal anti-HIF-2a (D9E3) Cell Signaling Cat#: 7096; RRID:AB_10898028 BrdU Monoclonal Antibody (BU20A), APC eBiosciences 17-5071-42; RRID: AB_11040534 goat anti-rabbit alexa fluor 488 Invitrogen A-11008 Chemicals, peptides, and recombinant proteins Beetle luciferin, potassium salt Promega E1602 Dexamethasone Sigma D4902 CAS 50-02-2 Dulbecco’s MEM (DMEM) high glucose Corning MT10-013-CV RPMI-1640 Corning 10-040 Fetal bovine serum HyClone, Gemini Bioproducts SH30910.03 High-vacuum silicone grease Dow Corning/Sigma Z273554 G418 sulfate Corning MT30-234-CR Hygromycin B solution Corning 30-240-CR Puromycin dihydrochloride Gibco A1113803 TaqMan Reverse transcription kit Invitrogen N8080234 iScript reverse transcription supermix Bio-Rad 1708841 Phusion High-Fidelity PCR Kit Thermo Fisher Scientific F553L Mammalian protein extraction reagent (M-PER) Thermo Scientific PI78501 Lipofectamine 3000 transfection reagent Invitrogen L3000008 Lipofectamine RNAiMAX transfection reagent Invitrogen 13778150 NaCl, 5M solution Invitrogen AM9759; CAS 7647-14- 5 Bd 7AAD Staining Solution BD 559925 Formal-Fixx Thermo Fisher Scientific 6764254 Hepes, pH 7.5 Sigma NA MgCl2 Invitrogen AM9530G EDTA Invitrogen 15575-038 EGTA RPI Research Products International Corp E14100-50.0 DTT Bio-Rad 1610610 Protease inhibitor cocktail Promega G6521 Phosphatase inhibitor Sigma P5726 Phosphatase inhibitor Sigma P0044 Glucose Sigma G8769 Sodium Bicarbonate Gibco 25080094 Penicillin-Streptomycin USBiological D9812-05 (Continued on next page) e1 Cell Reports 41, 111514, October 18, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER L-Glutamine Lonza BEBP17-605E Duolink in situ mounting medium with DAPI Sigma DUO82040-5ml biotin labeling mix Roche 11685597910 T7 polymerase Promega P2075 Tris-HCL pH 7 Invitrogen 15567-027 tRNA Life Technologies AM7119 IGEPAL (NP-40 substitute) Sigma CA-630,18896 PierceTM Streptavidin Agarose Thermo Fisher Scientific 20353 Urea Thermo Fisher Scientific BP169-500 Critical commercial assays RNeasy plus mini kit Qiagen 74134 DC protein assay kit II Bio-Rad 5000112 Power SYBRTM Green PCR Master Mix Thermo Fisher 436870 Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit Millipore Sigma 17-700 SimpleChIP(R) Enzymatic Chromatin IP Kit (Magnetic Beads) Cell Signaling 9003S PierceTM Magnetic RNA-Protein Pull-Down Kit Thermo Fisher Scientific 20164 MEGAscriptTM T7 Transcription Kit Invitrogen AM1334 Phusion High-Fidelity PCR Master Mix with HF Buffer Thermo Fisher Scientific F531L pCR 2.1-TOPO TA Thermo Fisher Scientific 451641 OpalTM 620 Reagent Pack Akoya Biosciences FP1495001KT RNA-Protein Co-Detection Ancillary Kit Advanced Cell Diagnostics 323180 RNAscope Intro Pack for Multiplex Fluorescent Reagent Kit v2-Hs Advanced Cell Diagnostics 323135 Pierce RNA 30 End desthiobiotinylation kit Thermo Fisher Scientific 20163 SuperScriptTM III First-Strand Synthesis System Invitrogen 18080051 CellTiter-Glo Reagent Promega G7571 Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit for Illumina Lexogen Cat. No. 015 Deposited data Quant-seq This paper GSE199825 Proteomics This paper MSV000090286 ChIP-seq This paper GSE199825 Experimental models: Cell lines Human: U2OS Laboratory of Roger Greenberg ATCC HTB-96 NA Human: U2OS Arntl::dLUC Laboratory of John Hogenesch NA Human: U2OS PX458 sgSCR This study NA Human: U2OS PX458 sgADIRF-AS1 clone 1 This study NA Human: U2OS PX458 sgADIRF-AS1 clone 2 This study NA Human: U2OS sgSCR Laboratory of Amita Sehgal NA Human: U2OS sgBMAL1 Laboratoryof Amita Sehgal NA Human: U2OS ADIRF-AS1::dLUC This study NA Human: 786O Laboratory of Celeste Simon NA Human: 769P Laboratory of Celeste Simon NA (Continued on next page) Cell Reports 41, 111514, October 18, 2022 e2 Article ll OPEN ACCESS
Protease Inhibitor:Article Title: Circadian lncRNA ADIRF-AS1 binds PBAF and regulates renal clear cell tumorigenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-a-tubulin (clone DM1A) Calbiochem Cat#:CP06; RRID:AB_212802 Rabbit monoclonal anti-BMAL1 (clone D2L7G) Cell Signaling Cat#:14020; RRID:AB_2728705 Rabbit monoclonal anti-CLOCK (clone D45B10) Cell Signaling Cat#:5157; RRID:AB_10695411 Mouse monoclonal anti-PBRM1 (clone E6N2K) Cell Signaling Cat#:81832 Rabbit monoclonal anti-PBRM1 (E9X2Z) Cell Signaling Cat#: 89123 Rabbit monoclonal anti-Rev-Erba (E1Y6D) Cell Signaling Cat#: 13418 Rabbit polyclonal anti-ADIRF Atlas HPA026810; RRID: AB_2672003 Rabbit monoclonal anti-BRG1 (D1Q7F) Cell Signaling Cat#: 49360; RRID:AB_2728743 Rabbit monoclonal anti-HIF-2a (D9E3) Cell Signaling Cat#: 7096; RRID:AB_10898028 BrdU Monoclonal Antibody (BU20A), APC eBiosciences 17-5071-42; RRID: AB_11040534 goat anti-rabbit alexa fluor 488 Invitrogen A-11008 Chemicals, peptides, and recombinant proteins Beetle luciferin, potassium salt Promega E1602 Dexamethasone Sigma D4902 CAS 50-02-2 Dulbecco’s MEM (DMEM) high glucose Corning MT10-013-CV RPMI-1640 Corning 10-040 Fetal bovine serum HyClone, Gemini Bioproducts SH30910.03 High-vacuum silicone grease Dow Corning/Sigma Z273554 G418 sulfate Corning MT30-234-CR Hygromycin B solution Corning 30-240-CR Puromycin dihydrochloride Gibco A1113803 TaqMan Reverse transcription kit Invitrogen N8080234 iScript reverse transcription supermix Bio-Rad 1708841 Phusion High-Fidelity PCR Kit Thermo Fisher Scientific F553L Mammalian protein extraction reagent (M-PER) Thermo Scientific PI78501 Lipofectamine 3000 transfection reagent Invitrogen L3000008 Lipofectamine RNAiMAX transfection reagent Invitrogen 13778150 NaCl, 5M solution Invitrogen AM9759; CAS 7647-14- 5 Bd 7AAD Staining Solution BD 559925 Formal-Fixx Thermo Fisher Scientific 6764254 Hepes, pH 7.5 Sigma NA MgCl2 Invitrogen AM9530G EDTA Invitrogen 15575-038 EGTA RPI Research Products International Corp E14100-50.0 DTT Bio-Rad 1610610 Protease inhibitor cocktail Promega G6521 Phosphatase inhibitor Sigma P5726 Phosphatase inhibitor Sigma P0044 Glucose Sigma G8769 Sodium Bicarbonate Gibco 25080094 Penicillin-Streptomycin USBiological D9812-05 (Continued on next page) e1 Cell Reports 41, 111514, October 18, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER L-Glutamine Lonza BEBP17-605E Duolink in situ mounting medium with DAPI Sigma DUO82040-5ml biotin labeling mix Roche 11685597910 T7 polymerase Promega P2075 Tris-HCL pH 7 Invitrogen 15567-027 tRNA Life Technologies AM7119 IGEPAL (NP-40 substitute) Sigma CA-630,18896 PierceTM Streptavidin Agarose Thermo Fisher Scientific 20353 Urea Thermo Fisher Scientific BP169-500 Critical commercial assays RNeasy plus mini kit Qiagen 74134 DC protein assay kit II Bio-Rad 5000112 Power SYBRTM Green PCR Master Mix Thermo Fisher 436870 Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit Millipore Sigma 17-700 SimpleChIP(R) Enzymatic Chromatin IP Kit (Magnetic Beads) Cell Signaling 9003S PierceTM Magnetic RNA-Protein Pull-Down Kit Thermo Fisher Scientific 20164 MEGAscriptTM T7 Transcription Kit Invitrogen AM1334 Phusion High-Fidelity PCR Master Mix with HF Buffer Thermo Fisher Scientific F531L pCR 2.1-TOPO TA Thermo Fisher Scientific 451641 OpalTM 620 Reagent Pack Akoya Biosciences FP1495001KT RNA-Protein Co-Detection Ancillary Kit Advanced Cell Diagnostics 323180 RNAscope Intro Pack for Multiplex Fluorescent Reagent Kit v2-Hs Advanced Cell Diagnostics 323135 Pierce RNA 30 End desthiobiotinylation kit Thermo Fisher Scientific 20163 SuperScriptTM III First-Strand Synthesis System Invitrogen 18080051 CellTiter-Glo Reagent Promega G7571 Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit for Illumina Lexogen Cat. No. 015 Deposited data Quant-seq This paper GSE199825 Proteomics This paper MSV000090286 ChIP-seq This paper GSE199825 Experimental models: Cell lines Human: U2OS Laboratory of Roger Greenberg ATCC HTB-96 NA Human: U2OS Arntl::dLUC Laboratory of John Hogenesch NA Human: U2OS PX458 sgSCR This study NA Human: U2OS PX458 sgADIRF-AS1 clone 1 This study NA Human: U2OS PX458 sgADIRF-AS1 clone 2 This study NA Human: U2OS sgSCR Laboratory of Amita Sehgal NA Human: U2OS sgBMAL1 Laboratoryof Amita Sehgal NA Human: U2OS ADIRF-AS1::dLUC This study NA Human: 786O Laboratory of Celeste Simon NA Human: 769P Laboratory of Celeste Simon NA (Continued on next page) Cell Reports 41, 111514, October 18, 2022 e2 Article ll OPEN ACCESS
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