Capsules:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
Polymerase Chain Reaction:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
Purification:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
Gel Extraction:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
cDNA Synthesis:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
RNA HS Assay:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
Plasmid Preparation:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
BIA-KA:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
DNA Sequencing:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
Multiple Displacement Amplification:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
Chromatin Immunoprecipitation:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
Recombinant:Article Title: Systematic characterization of mutations altering protein degradation in human cancers.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Nuclease-Free Water Ambion Cat#AM9938 Pierce Homobifunctional Cross Linkers Life Technologies Cat#20593 2-Mercaptoethanol Sigma Aldrich Cat#M6250-10ML Dynabeads Protein A Thermo Fisher Scientific Cat#10004D Dynabeads Protein G Thermo Fisher Scientific Cat#10002D EDTA Sigma Aldrich Cat#E8008-100ML Protease/Phosphatase Inhibitor Cocktail (100X) Cell Signaling Technology Cat#5872S Quick-Load 1 kb Plus DNA Ladder New England Biolabs Cat#N0469S LB Broth Mp Biomedicals Cat#244610 L-Broth Agar Large Capsules Mp Biomedicals Cat#MP 113001236 RIPA buffer Invitrogen Cat#R0278 Pierce 16% Formaldehyde (w/v), Methanol-free Life Technologies Cat#28906 Opti-MEM I Reduced Serum Medium, no phenol red Thermo Fisher Scientific Cat#11058021 Cycloheximide powder Cell Signaling Technology Cat2112 Critical commercial assays QIAprep Spin Miniprep Kit QIAGEN Cat#27106 RNeasy Plus Mini Kit QIAGEN Cat#74134 QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick gel extraction kit QIAGEN Cat#28704 Gibson Assembly Master Mix New England Biolabs Cat#E2611L iScript cDNA Synthesis Kit Bio-Rad Laboratories Cat#1708891 SsoAdvanced Univ SYBR Grn Suprmx Bio-Rad Laboratories Cat#1725272 Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q32854 Qubit RNA HS Assay Kit Thermo Fisher Scientific Cat#Q32855 GenElute HP Plasmid Maxiprep Kit Sigma-Aldrich Cat#NA0410-1KT Ampure xp Beckman Coulter Cat#A63881 BCA Assay Kit Thermo Fisher Scientific Cat#23225 SMARTer ThruPLEX DNA-Seq Kit Takara Bio Cat#R400675 Experimental models: cell lines Human: HEK293FT Thermo Fisher Scientific Cat#R70007 Human: MDA-MB-231 American Type Culture Collection Cat#ATCC-HTB-26 Human: CAL27 Ravi Uppaluri lab N/A Human: CAL33 Ravi Uppaluri lab N/A Deposited data GATA3 ChIP-Seq This paper GSE162003 Original gel images This paper https://doi.org/10.17632/kgfzbpv2w4.1 Oligonucleotides Primers for PCR, see Table S5 Invitrogen N/A Recombinant DNA hWIP1-FLAG Addgene RRID:Addgene_28105 pHAGE-GATA3 Addgene RRID:Addgene_116747 lentiCRISPR v2 puro Addgene RRID:Addgene_98290 pMD2.G Addgene RRID:Addgene_12259 psPAX2 Addgene RRID:Addgene_12260 pHAGE-CMV-DsRed-IRES-GFP Koren et al., 2018 N/A pHAGE-SFFV-GFP-IRES-DsRed Timms et al., 2019 N/A pLenti-EF1a-PGK-Puro Kai Wucherpfennig lab N/A pLenti-EF1a-GATA3-WT This paper N/A (Continued on next page) e2 Molecular Cell 81, 1292–1308.e1–e11, March 18, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER pLenti-EF1a-GATA3-A442M This paper N/A pLenti-EF1a-GATA3-G444E This paper N/A pLenti-EF1a-GATA3-H400 This paper N/A pLenti-EF1a-GATA3-WT-Fg This paper N/A pLenti-EF1a-GATA3-A442M-Fg This paper N/A pLenti-EF1a-GATA3-G444E-Fg This paper N/A pLenti-EF1a-GATA3-H400-Fg This paper N/A pLenti-EF1a-PPM1D-WT This paper N/A pLenti-EF1a-PPM1D-V604Q This paper N/A pLenti-EF1a-PPM1D-C605W This paper N/A pLenti-EF1a-PPM1D-L450 This paper N/A pLenti-EF1a-PPM1D-WT-HA This paper N/A pLenti-EF1a-PPM1D-V604Q-HA This paper N/A pLenti-EF1a-PPM1D-C605W-HA This paper N/A pLenti-EF1a-PPM1D-L450-HA This paper N/A Software and algorithms GraphPad Prism 7 GraphPad Software https://www.graphpad.com DeepDegron This Paper https://github.com/ctokheim/deepDegron Transcription factor inference This Paper https://github.com/ctokheim/tf_association Other Corning Filter System (0.45um) Corning Life Sciences Cat#431096 milliTUBE 1 ml AFA Fiber Covaris Inc. Cat#520130 NITROCEL MEMB 0.45um Bio-Rad Laboratories Cat#1620115 Multiplate 96-Well PCR Plates Bio-Rad Laboratories Cat#MLL9601 QUBIT ASSAY TUBES SET Life Technologies Cat#Q32856 Microseal ‘B’ Adhesive Seals Bio-Rad Laboratories Cat#MSB-1001
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