Recombinant:Article Title: Proteome-wide copy-number estimation from transcriptomics.
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Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models AC16 cells (H. sapiens) Davidson et al, 2005 – AC16-CXADR cells (H. sapiens) Shah et al, 2017 – B2B1-iLuc cells (H. sapiens) Wang et al, 2023 – B2B1-iNUP37 cells (H. sapiens) Wang et al, 2023 – B2B1-ishLuc cells (H. sapiens) Wang et al, 2023 – B2B1-ishNUP37 cells (H. sapiens) Wang et al, 2023 – BT20 (H. sapiens) ATCC Cat # HTB-19 CAMA1 cells (H. sapiens) ATCC Cat # HTB-21 Coxsackievirus B3, Kandolf strain Laboratory of Bruce McManus Genbank # M33854 HCC1395 (H. sapiens) ATCC Cat # CRL-2324 HCC38 (H. sapiens) ATCC Cat # CRL-2314 HEK293T/17 cells (H. sapiens) ATCC Cat # CRL-11268 K562 (H. sapiens) ATCC Cat # CCL-243 MCF7 cells (H. sapiens) ATCC Cat # HTB-22 T47D cells (H. sapiens) ATCC Cat # HTB-133 ZR751 cells (H. sapiens) ATCC Cat # CRL-1500 Recombinant DNA pEN_TTmiRc2 Addgene #25752 pEN_TT 3xFLAG-NUP37 (H. sapiens) Addgene #192299 pEN_TT CXADR-V5 (H. sapiens) Addgene (this study) #220358 pEN_TT DNM1L-V5 (H. sapiens) Addgene (this study) #220359 pEN_TT luciferase-V5 (P. pyralis) Addgene (this study) #220360 pLX304 CXADR-V5 (H. sapiens) Addgene #82723 pSLIK 3xFLAG-luciferase neo (P. pyralis) Addgene #98392 pSLIK 3xFLAG-NUP37 neo (H. sapiens) Addgene (this study) #220361 pSLIK CXADR-V5 hygro (H. sapiens) Addgene (this study) #220362 pSLIK DNM1L-V5 neo (H. sapiens) Addgene (this study) #220363 pSLIK hygro Addgene #25737 pSLIK luciferase-V5 neo (P. pyralis) Addgene (this study) #220364 pSLIK neo Addgene #25735 pSuperior.retro.neo GFP shDNM1L (H. sapiens) Addgene #220356 pSuperior.retro.neo GFP shScramble Addgene #220357 tet pLKO.1-shLuc puro (P. pyralis) Addgene #136587 tet pLKO.1-shNUP37 v1 puro (H. sapiens) Addgene #192343 Antibodies Beta-actin (AC-15) Mouse mAb Invitrogen Cat # AM4302 CAR (D3W3G) Rabbit mAb Cell Signaling Technology Cat # 16984 CDK4 (D9G3E) Rabbit mAb Cell Signaling Technology Cat # 12790 DRP1 (EPR19274) Recombinant Rabbit mAb Abcam Cat # ab184247 FLAG (M2) Mouse mAb Sigma Cat # F1804 GRB2 (C-23) Rabbit Polyclonal Ab Santa Cruz Biotechnology Cat # sc-255 NUP37 (N-13) Rabbit Polyclonal Ab Santa Cruz Biotechnology Cat # sc-109348 p38 (C-20) Rabbit Polyclonal Ab Santa Cruz Biotechnology Cat # sc-535 © The Author(s) Molecular Systems Biology 11 D ow nloaded from https://w w w .em bopress.org on O ctober 5, 2024 from IP 2403:3800:3283:ee5:b148:687:1f91:5d52. .. Reagent/resource Reference or source Identifier or catalog number α-Tubulin Chicken Polyclonal Ab Abcam Cat # ab89984 α-Tubulin Chicken Polyclonal Ab LSBio Cat # LS-C108486 SERPINB6 Rabbit Polyclonal Ab Proteintech Cat # 14962-1-AP Vinculin (V284) Mouse mAb Millipore Sigma Cat # 05-386 V5 Chicken Polyclonal Ab Bethyl Laboratories Cat # A190-118A V5 (SV5-Pk1) Mouse mAb Invitrogen Cat # R960-25 VP1 (31A2) Mouse mAb Mediagnost Cat # M47 Goat anti-rabbit Jackson ImmunoResearch Cat # 111-005-144 Goat anti-mouse Jackson ImmunoResearch Cat # 115-005-146 IRDye 800CW-conjugated donkey anti-goat LI-COR Cat # 926-32214 IRDye 680LT-conjugated donkey anti-chicken LI-COR Cat # 926-68028 IRDye 800CW-conjugated goat anti-rabbit LI-COR Cat # 926-32211 IRDye 680LT-conjugated goat anti-rabbit LI-COR Cat # 926-68021 IRDye 800CW-conjugated goat anti-mouse LI-COR Cat # 926-32210 IRDye 680LT-conjugated goat anti-mouse LI-COR Cat # 926-68020 Oligonucleotides and other sequence-based reagents CXADR forward cloning primer This study gcgcACTAGTatggcgctcctgctgtgc CXADR reverse cloning primer This study gcgcCAATTGctacgtagaatcgagaccgaggag DNM1L forward cloning primer This study gcgcACTAGTatggaggcgctaattcctgt DNM1L reverse cloning primer This study gcgcGAATTCTCACGTAGAATCGAGACCGAGGAGAG GGTTAGGGATAGGCTTACCccaaagatgagtctcccggatt Luciferase forward cloning primer This study gcgcACTAGTatggaagacgccaaaaacat Luciferase reverse cloning primer This study gcgcGAATTCTCACGTAGAATCGAGACCGAGGAGA GGGTTAGGGATAGGCTTACCgatctttccgcccttcttgg Chemicals, enzymes and other reagents LR Clonase II ThermoFisher Scientific Cat # 11791020 Doxycycline Hyclate Sigma Cat # D9891 Software biomaRt v2.52.0 https://www.bioconductor.org/packages/ release/bioc/html/biomaRt.html ComplexHeatmap v2.12.1 https://bioconductor.org/packages/release/ bioc/html/ComplexHeatmap.html CPTAC breast CNA syn11328692 CPTAC breast RNA-seq syn11328694 DescTools v0.99.47 https://cran.r-project.org/web/packages/ DescTools/index.html ea-utils https://github.com/ExpressionAnalysis/ea-utils ggplot2 v3.4.0 https://ggplot2.tidyverse.org/ glmnet v4.1-6 https://cran.r-project.org/web/packages/ glmnet/index.html HISAT2 v2.1.0 http://daehwankimlab.github.io/hisat2/ HTSeq v2.0.2 https://pypi.org/project/HTSeq/ inflection v1.3.6 https://cran.r-project.org/web/packages/ inflection/index.html M3C v1.18.0 https://www.bioconductor.org/packages/ release/bioc/html/M3C.html MATLAB R2022a https://www.mathworks.com/products/ matlab.html 12 Molecular Systems Biology © The Author(s) D ow nloaded from https://w w w .em bopress.org on O ctober 5, 2024 from IP 2403:3800:3283:ee5:b148:687:1f91:5d52.
Luciferase:Article Title: Proteome-wide copy-number estimation from transcriptomics.
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Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models AC16 cells (H. sapiens) Davidson et al, 2005 – AC16-CXADR cells (H. sapiens) Shah et al, 2017 – B2B1-iLuc cells (H. sapiens) Wang et al, 2023 – B2B1-iNUP37 cells (H. sapiens) Wang et al, 2023 – B2B1-ishLuc cells (H. sapiens) Wang et al, 2023 – B2B1-ishNUP37 cells (H. sapiens) Wang et al, 2023 – BT20 (H. sapiens) ATCC Cat # HTB-19 CAMA1 cells (H. sapiens) ATCC Cat # HTB-21 Coxsackievirus B3, Kandolf strain Laboratory of Bruce McManus Genbank # M33854 HCC1395 (H. sapiens) ATCC Cat # CRL-2324 HCC38 (H. sapiens) ATCC Cat # CRL-2314 HEK293T/17 cells (H. sapiens) ATCC Cat # CRL-11268 K562 (H. sapiens) ATCC Cat # CCL-243 MCF7 cells (H. sapiens) ATCC Cat # HTB-22 T47D cells (H. sapiens) ATCC Cat # HTB-133 ZR751 cells (H. sapiens) ATCC Cat # CRL-1500 Recombinant DNA pEN_TTmiRc2 Addgene #25752 pEN_TT 3xFLAG-NUP37 (H. sapiens) Addgene #192299 pEN_TT CXADR-V5 (H. sapiens) Addgene (this study) #220358 pEN_TT DNM1L-V5 (H. sapiens) Addgene (this study) #220359 pEN_TT luciferase-V5 (P. pyralis) Addgene (this study) #220360 pLX304 CXADR-V5 (H. sapiens) Addgene #82723 pSLIK 3xFLAG-luciferase neo (P. pyralis) Addgene #98392 pSLIK 3xFLAG-NUP37 neo (H. sapiens) Addgene (this study) #220361 pSLIK CXADR-V5 hygro (H. sapiens) Addgene (this study) #220362 pSLIK DNM1L-V5 neo (H. sapiens) Addgene (this study) #220363 pSLIK hygro Addgene #25737 pSLIK luciferase-V5 neo (P. pyralis) Addgene (this study) #220364 pSLIK neo Addgene #25735 pSuperior.retro.neo GFP shDNM1L (H. sapiens) Addgene #220356 pSuperior.retro.neo GFP shScramble Addgene #220357 tet pLKO.1-shLuc puro (P. pyralis) Addgene #136587 tet pLKO.1-shNUP37 v1 puro (H. sapiens) Addgene #192343 Antibodies Beta-actin (AC-15) Mouse mAb Invitrogen Cat # AM4302 CAR (D3W3G) Rabbit mAb Cell Signaling Technology Cat # 16984 CDK4 (D9G3E) Rabbit mAb Cell Signaling Technology Cat # 12790 DRP1 (EPR19274) Recombinant Rabbit mAb Abcam Cat # ab184247 FLAG (M2) Mouse mAb Sigma Cat # F1804 GRB2 (C-23) Rabbit Polyclonal Ab Santa Cruz Biotechnology Cat # sc-255 NUP37 (N-13) Rabbit Polyclonal Ab Santa Cruz Biotechnology Cat # sc-109348 p38 (C-20) Rabbit Polyclonal Ab Santa Cruz Biotechnology Cat # sc-535 © The Author(s) Molecular Systems Biology 11 D ow nloaded from https://w w w .em bopress.org on O ctober 5, 2024 from IP 2403:3800:3283:ee5:b148:687:1f91:5d52. .. Reagent/resource Reference or source Identifier or catalog number α-Tubulin Chicken Polyclonal Ab Abcam Cat # ab89984 α-Tubulin Chicken Polyclonal Ab LSBio Cat # LS-C108486 SERPINB6 Rabbit Polyclonal Ab Proteintech Cat # 14962-1-AP Vinculin (V284) Mouse mAb Millipore Sigma Cat # 05-386 V5 Chicken Polyclonal Ab Bethyl Laboratories Cat # A190-118A V5 (SV5-Pk1) Mouse mAb Invitrogen Cat # R960-25 VP1 (31A2) Mouse mAb Mediagnost Cat # M47 Goat anti-rabbit Jackson ImmunoResearch Cat # 111-005-144 Goat anti-mouse Jackson ImmunoResearch Cat # 115-005-146 IRDye 800CW-conjugated donkey anti-goat LI-COR Cat # 926-32214 IRDye 680LT-conjugated donkey anti-chicken LI-COR Cat # 926-68028 IRDye 800CW-conjugated goat anti-rabbit LI-COR Cat # 926-32211 IRDye 680LT-conjugated goat anti-rabbit LI-COR Cat # 926-68021 IRDye 800CW-conjugated goat anti-mouse LI-COR Cat # 926-32210 IRDye 680LT-conjugated goat anti-mouse LI-COR Cat # 926-68020 Oligonucleotides and other sequence-based reagents CXADR forward cloning primer This study gcgcACTAGTatggcgctcctgctgtgc CXADR reverse cloning primer This study gcgcCAATTGctacgtagaatcgagaccgaggag DNM1L forward cloning primer This study gcgcACTAGTatggaggcgctaattcctgt DNM1L reverse cloning primer This study gcgcGAATTCTCACGTAGAATCGAGACCGAGGAGAG GGTTAGGGATAGGCTTACCccaaagatgagtctcccggatt Luciferase forward cloning primer This study gcgcACTAGTatggaagacgccaaaaacat Luciferase reverse cloning primer This study gcgcGAATTCTCACGTAGAATCGAGACCGAGGAGA GGGTTAGGGATAGGCTTACCgatctttccgcccttcttgg Chemicals, enzymes and other reagents LR Clonase II ThermoFisher Scientific Cat # 11791020 Doxycycline Hyclate Sigma Cat # D9891 Software biomaRt v2.52.0 https://www.bioconductor.org/packages/ release/bioc/html/biomaRt.html ComplexHeatmap v2.12.1 https://bioconductor.org/packages/release/ bioc/html/ComplexHeatmap.html CPTAC breast CNA syn11328692 CPTAC breast RNA-seq syn11328694 DescTools v0.99.47 https://cran.r-project.org/web/packages/ DescTools/index.html ea-utils https://github.com/ExpressionAnalysis/ea-utils ggplot2 v3.4.0 https://ggplot2.tidyverse.org/ glmnet v4.1-6 https://cran.r-project.org/web/packages/ glmnet/index.html HISAT2 v2.1.0 http://daehwankimlab.github.io/hisat2/ HTSeq v2.0.2 https://pypi.org/project/HTSeq/ inflection v1.3.6 https://cran.r-project.org/web/packages/ inflection/index.html M3C v1.18.0 https://www.bioconductor.org/packages/ release/bioc/html/M3C.html MATLAB R2022a https://www.mathworks.com/products/ matlab.html 12 Molecular Systems Biology © The Author(s) D ow nloaded from https://w w w .em bopress.org on O ctober 5, 2024 from IP 2403:3800:3283:ee5:b148:687:1f91:5d52.
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