Cloning:Article Title: Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms.
Article Snippet: U2OS ATCC HTB-96 (Continued on next page) Molecular Cell 85, 1445–1466.e1–e13, April 3, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Yeast Yɑ1867 Reece-Hoyes et al.60 N/A Yeast Y1Has2 Reece-Hoyes et al.60 N/A Yeast Y8800 Luck et al.61 N/A Yeast Y8930 Luck et al.61 N/A Oligonucleotides Primers used for cloning Data S1 N/A Primer used for PBMs Integrated DNA Technologies Agilent Primer1 Recombinant DNA pDONR223 Rual et al.128 N/A pDEST-P4P1R ThermoFisher N/A pMW#2 Addgene 13349 pMW#3 Addgene 13350 pGADT7-GW Addgene 61702 pDEST-AD2m Reece Hoyes et al.60 N/A pGL4.23[luc2/minP]-GW Fuxman Bass et al.4 N/A pEZY3-VP160 Santoso et al.129 N/A pGL4.74[hRluc/TK] Promega E6921 pEZY3-DB Lu et al.130 N/A Gateway pDEST15 Vector Thermo Fisher Scientific 11802014 pt7CFE1-NHis-GST-CHA [Gateway compatible] Thermo Fisher Scientific 88871 pDEST-N2H-N1 Addgene 125547 pDEST-N2H-N2 Addgene 125548 pDEST-N2H-F1 Addgene 125551 pDEST-N2H-F2 Addgene 125552 pDEST-DB Luck et al.61 N/A pDEST-AD-CYH2 Luck et al.61 N/A pcDNA3.1-ccdB-EGFP Gift from Taipale Lab N/A N-term GST pDEST 27 Invitrogen 11812013 Software and algorithms kallisto Bray et al.131 pachterlab.github.io/kallisto HMMER v3.3 Eddy69 hmmer.org AlphaFold v2.3.1 Jumper et al.55 https://github.com/google-deepmind/alphafold upbm v0.99.0 Kock et al.71 github.com/pkimes/upbm GENRE Mariani et al.132 github.com/BulykLab/MEDEA GSEApy v1.1.3 Fang et al.133 gseapy.readthedocs.io Mathematica-based image analysis interface Riback et al.106 N/A STAR v2.4.0 Dobin et al.134 github.com/alexdobin/STAR AltAnalyze v2.1.4 Emig et al.135 and Li et al.136 http://altanalyze.org/ Other Custom tRNA Mix New England BioLabs N6842Z XT Reducing Agent 20X 1610792 BioRad 1610792 XT Sample Buffer 4X BioRad 1610791 BlueStain 2 Protein Ladder, 5-245kDa GoldBio P008 GST Glutathione S-Transferase Thermo Fisher Scientific 20237 Tween 20 Sigma-Aldrich P1379 XT MES Running Buffer 20X BioRad 1610789 RPI Dry Milk Powder Research Products International M17200 (Continued on next page) e2 Molecular Cell 85, 1445–1466.e1–e13, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Phosphate Buffered Saline 10X PBS for Western Blots and IP Sigma-Aldrich P7059 1-Step Transfer Buffer Thermo Scientific 84731 Thermo Sequenase Cycle Sequencing Kit [Discontinued] Thermo Fisher Scientific 785001KT Cytiva Thermo Sequenase Reaction Buffer 10X Cytiva Life Sciences E790000Y Cytiva Thermo Sequenase DNA Polymerase (with Thermoplasma acidophilum Inorganic Pyrophosphatase (TAP)) Cytiva Life Sciences E790000Y Deoxynucleotide (dNTP) Solution Set, 100mM New England BioLabs N0446S Amersham CyDye Fluorescent Nucleotides Cy3-dUTP Cytiva Life Sciences PA53022 Triton X-100 Sigma-Aldrich T9284 Nonfat Dried Milk Bovine Sigma-Aldrich M7409 Deoxyribonucleic acid, single stranded from salmon testes Sigma-Aldrich D7656 Molecular Grade Bovine Serum Albumin New England BioLabs B9200 KOD HotStart Polymerase Novagen 71086 BP Clonase Life Technologies 11791043 Spectinomycin Sigma Aldrich S4014-5G 3-AMINO-1 2 4-TRIAZOLE >=95% (TLC) Sigma Aldrich A8056-100g CYCLOHEXIMIDE FROM MICROBIAL SOURCE Sigma Aldrich C7698-5G 96-well, flat bottom, cell culture microplate Greiner 655083 Axygen Oasis Robotic Tips Fisher Scientific 14-222-223 Corning Untreated 245mm Square BioAssay Dishes Fisher Scientific 07-200-600 96WL R-BTM PLT TCT W/LP 100/CS Fisher Scientific 07 200 720A PEI MAX 40000 Polysciences Inc 24765 SWIM primer Life Technologies Custom Furimazine Pasteur Institute Custom FuGENE HD Transfection Reagent Promega E2311 Lipofectamine 3000 Transfection Reagent Invitrogen L3000001 CHAPS Detergent Thermo Fisher 28299 Unstained protein ladder Thermo Fisher 84786 Bolt Sample Reducing Agent Thermo Fisher B0004 Bolt MOPS SDS Running Buffer Thermo Fisher B0001
Recombinant:Article Title: Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms.
Article Snippet: U2OS ATCC HTB-96 (Continued on next page) Molecular Cell 85, 1445–1466.e1–e13, April 3, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Yeast Yɑ1867 Reece-Hoyes et al.60 N/A Yeast Y1Has2 Reece-Hoyes et al.60 N/A Yeast Y8800 Luck et al.61 N/A Yeast Y8930 Luck et al.61 N/A Oligonucleotides Primers used for cloning Data S1 N/A Primer used for PBMs Integrated DNA Technologies Agilent Primer1 Recombinant DNA pDONR223 Rual et al.128 N/A pDEST-P4P1R ThermoFisher N/A pMW#2 Addgene 13349 pMW#3 Addgene 13350 pGADT7-GW Addgene 61702 pDEST-AD2m Reece Hoyes et al.60 N/A pGL4.23[luc2/minP]-GW Fuxman Bass et al.4 N/A pEZY3-VP160 Santoso et al.129 N/A pGL4.74[hRluc/TK] Promega E6921 pEZY3-DB Lu et al.130 N/A Gateway pDEST15 Vector Thermo Fisher Scientific 11802014 pt7CFE1-NHis-GST-CHA [Gateway compatible] Thermo Fisher Scientific 88871 pDEST-N2H-N1 Addgene 125547 pDEST-N2H-N2 Addgene 125548 pDEST-N2H-F1 Addgene 125551 pDEST-N2H-F2 Addgene 125552 pDEST-DB Luck et al.61 N/A pDEST-AD-CYH2 Luck et al.61 N/A pcDNA3.1-ccdB-EGFP Gift from Taipale Lab N/A N-term GST pDEST 27 Invitrogen 11812013 Software and algorithms kallisto Bray et al.131 pachterlab.github.io/kallisto HMMER v3.3 Eddy69 hmmer.org AlphaFold v2.3.1 Jumper et al.55 https://github.com/google-deepmind/alphafold upbm v0.99.0 Kock et al.71 github.com/pkimes/upbm GENRE Mariani et al.132 github.com/BulykLab/MEDEA GSEApy v1.1.3 Fang et al.133 gseapy.readthedocs.io Mathematica-based image analysis interface Riback et al.106 N/A STAR v2.4.0 Dobin et al.134 github.com/alexdobin/STAR AltAnalyze v2.1.4 Emig et al.135 and Li et al.136 http://altanalyze.org/ Other Custom tRNA Mix New England BioLabs N6842Z XT Reducing Agent 20X 1610792 BioRad 1610792 XT Sample Buffer 4X BioRad 1610791 BlueStain 2 Protein Ladder, 5-245kDa GoldBio P008 GST Glutathione S-Transferase Thermo Fisher Scientific 20237 Tween 20 Sigma-Aldrich P1379 XT MES Running Buffer 20X BioRad 1610789 RPI Dry Milk Powder Research Products International M17200 (Continued on next page) e2 Molecular Cell 85, 1445–1466.e1–e13, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Phosphate Buffered Saline 10X PBS for Western Blots and IP Sigma-Aldrich P7059 1-Step Transfer Buffer Thermo Scientific 84731 Thermo Sequenase Cycle Sequencing Kit [Discontinued] Thermo Fisher Scientific 785001KT Cytiva Thermo Sequenase Reaction Buffer 10X Cytiva Life Sciences E790000Y Cytiva Thermo Sequenase DNA Polymerase (with Thermoplasma acidophilum Inorganic Pyrophosphatase (TAP)) Cytiva Life Sciences E790000Y Deoxynucleotide (dNTP) Solution Set, 100mM New England BioLabs N0446S Amersham CyDye Fluorescent Nucleotides Cy3-dUTP Cytiva Life Sciences PA53022 Triton X-100 Sigma-Aldrich T9284 Nonfat Dried Milk Bovine Sigma-Aldrich M7409 Deoxyribonucleic acid, single stranded from salmon testes Sigma-Aldrich D7656 Molecular Grade Bovine Serum Albumin New England BioLabs B9200 KOD HotStart Polymerase Novagen 71086 BP Clonase Life Technologies 11791043 Spectinomycin Sigma Aldrich S4014-5G 3-AMINO-1 2 4-TRIAZOLE >=95% (TLC) Sigma Aldrich A8056-100g CYCLOHEXIMIDE FROM MICROBIAL SOURCE Sigma Aldrich C7698-5G 96-well, flat bottom, cell culture microplate Greiner 655083 Axygen Oasis Robotic Tips Fisher Scientific 14-222-223 Corning Untreated 245mm Square BioAssay Dishes Fisher Scientific 07-200-600 96WL R-BTM PLT TCT W/LP 100/CS Fisher Scientific 07 200 720A PEI MAX 40000 Polysciences Inc 24765 SWIM primer Life Technologies Custom Furimazine Pasteur Institute Custom FuGENE HD Transfection Reagent Promega E2311 Lipofectamine 3000 Transfection Reagent Invitrogen L3000001 CHAPS Detergent Thermo Fisher 28299 Unstained protein ladder Thermo Fisher 84786 Bolt Sample Reducing Agent Thermo Fisher B0004 Bolt MOPS SDS Running Buffer Thermo Fisher B0001
Software:Article Title: Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms.
Article Snippet: U2OS ATCC HTB-96 (Continued on next page) Molecular Cell 85, 1445–1466.e1–e13, April 3, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Yeast Yɑ1867 Reece-Hoyes et al.60 N/A Yeast Y1Has2 Reece-Hoyes et al.60 N/A Yeast Y8800 Luck et al.61 N/A Yeast Y8930 Luck et al.61 N/A Oligonucleotides Primers used for cloning Data S1 N/A Primer used for PBMs Integrated DNA Technologies Agilent Primer1 Recombinant DNA pDONR223 Rual et al.128 N/A pDEST-P4P1R ThermoFisher N/A pMW#2 Addgene 13349 pMW#3 Addgene 13350 pGADT7-GW Addgene 61702 pDEST-AD2m Reece Hoyes et al.60 N/A pGL4.23[luc2/minP]-GW Fuxman Bass et al.4 N/A pEZY3-VP160 Santoso et al.129 N/A pGL4.74[hRluc/TK] Promega E6921 pEZY3-DB Lu et al.130 N/A Gateway pDEST15 Vector Thermo Fisher Scientific 11802014 pt7CFE1-NHis-GST-CHA [Gateway compatible] Thermo Fisher Scientific 88871 pDEST-N2H-N1 Addgene 125547 pDEST-N2H-N2 Addgene 125548 pDEST-N2H-F1 Addgene 125551 pDEST-N2H-F2 Addgene 125552 pDEST-DB Luck et al.61 N/A pDEST-AD-CYH2 Luck et al.61 N/A pcDNA3.1-ccdB-EGFP Gift from Taipale Lab N/A N-term GST pDEST 27 Invitrogen 11812013 Software and algorithms kallisto Bray et al.131 pachterlab.github.io/kallisto HMMER v3.3 Eddy69 hmmer.org AlphaFold v2.3.1 Jumper et al.55 https://github.com/google-deepmind/alphafold upbm v0.99.0 Kock et al.71 github.com/pkimes/upbm GENRE Mariani et al.132 github.com/BulykLab/MEDEA GSEApy v1.1.3 Fang et al.133 gseapy.readthedocs.io Mathematica-based image analysis interface Riback et al.106 N/A STAR v2.4.0 Dobin et al.134 github.com/alexdobin/STAR AltAnalyze v2.1.4 Emig et al.135 and Li et al.136 http://altanalyze.org/ Other Custom tRNA Mix New England BioLabs N6842Z XT Reducing Agent 20X 1610792 BioRad 1610792 XT Sample Buffer 4X BioRad 1610791 BlueStain 2 Protein Ladder, 5-245kDa GoldBio P008 GST Glutathione S-Transferase Thermo Fisher Scientific 20237 Tween 20 Sigma-Aldrich P1379 XT MES Running Buffer 20X BioRad 1610789 RPI Dry Milk Powder Research Products International M17200 (Continued on next page) e2 Molecular Cell 85, 1445–1466.e1–e13, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Phosphate Buffered Saline 10X PBS for Western Blots and IP Sigma-Aldrich P7059 1-Step Transfer Buffer Thermo Scientific 84731 Thermo Sequenase Cycle Sequencing Kit [Discontinued] Thermo Fisher Scientific 785001KT Cytiva Thermo Sequenase Reaction Buffer 10X Cytiva Life Sciences E790000Y Cytiva Thermo Sequenase DNA Polymerase (with Thermoplasma acidophilum Inorganic Pyrophosphatase (TAP)) Cytiva Life Sciences E790000Y Deoxynucleotide (dNTP) Solution Set, 100mM New England BioLabs N0446S Amersham CyDye Fluorescent Nucleotides Cy3-dUTP Cytiva Life Sciences PA53022 Triton X-100 Sigma-Aldrich T9284 Nonfat Dried Milk Bovine Sigma-Aldrich M7409 Deoxyribonucleic acid, single stranded from salmon testes Sigma-Aldrich D7656 Molecular Grade Bovine Serum Albumin New England BioLabs B9200 KOD HotStart Polymerase Novagen 71086 BP Clonase Life Technologies 11791043 Spectinomycin Sigma Aldrich S4014-5G 3-AMINO-1 2 4-TRIAZOLE >=95% (TLC) Sigma Aldrich A8056-100g CYCLOHEXIMIDE FROM MICROBIAL SOURCE Sigma Aldrich C7698-5G 96-well, flat bottom, cell culture microplate Greiner 655083 Axygen Oasis Robotic Tips Fisher Scientific 14-222-223 Corning Untreated 245mm Square BioAssay Dishes Fisher Scientific 07-200-600 96WL R-BTM PLT TCT W/LP 100/CS Fisher Scientific 07 200 720A PEI MAX 40000 Polysciences Inc 24765 SWIM primer Life Technologies Custom Furimazine Pasteur Institute Custom FuGENE HD Transfection Reagent Promega E2311 Lipofectamine 3000 Transfection Reagent Invitrogen L3000001 CHAPS Detergent Thermo Fisher 28299 Unstained protein ladder Thermo Fisher 84786 Bolt Sample Reducing Agent Thermo Fisher B0004 Bolt MOPS SDS Running Buffer Thermo Fisher B0001
Milk:Article Title: Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms.
Article Snippet: U2OS ATCC HTB-96 (Continued on next page) Molecular Cell 85, 1445–1466.e1–e13, April 3, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains Yeast Yɑ1867 Reece-Hoyes et al.60 N/A Yeast Y1Has2 Reece-Hoyes et al.60 N/A Yeast Y8800 Luck et al.61 N/A Yeast Y8930 Luck et al.61 N/A Oligonucleotides Primers used for cloning Data S1 N/A Primer used for PBMs Integrated DNA Technologies Agilent Primer1 Recombinant DNA pDONR223 Rual et al.128 N/A pDEST-P4P1R ThermoFisher N/A pMW#2 Addgene 13349 pMW#3 Addgene 13350 pGADT7-GW Addgene 61702 pDEST-AD2m Reece Hoyes et al.60 N/A pGL4.23[luc2/minP]-GW Fuxman Bass et al.4 N/A pEZY3-VP160 Santoso et al.129 N/A pGL4.74[hRluc/TK] Promega E6921 pEZY3-DB Lu et al.130 N/A Gateway pDEST15 Vector Thermo Fisher Scientific 11802014 pt7CFE1-NHis-GST-CHA [Gateway compatible] Thermo Fisher Scientific 88871 pDEST-N2H-N1 Addgene 125547 pDEST-N2H-N2 Addgene 125548 pDEST-N2H-F1 Addgene 125551 pDEST-N2H-F2 Addgene 125552 pDEST-DB Luck et al.61 N/A pDEST-AD-CYH2 Luck et al.61 N/A pcDNA3.1-ccdB-EGFP Gift from Taipale Lab N/A N-term GST pDEST 27 Invitrogen 11812013 Software and algorithms kallisto Bray et al.131 pachterlab.github.io/kallisto HMMER v3.3 Eddy69 hmmer.org AlphaFold v2.3.1 Jumper et al.55 https://github.com/google-deepmind/alphafold upbm v0.99.0 Kock et al.71 github.com/pkimes/upbm GENRE Mariani et al.132 github.com/BulykLab/MEDEA GSEApy v1.1.3 Fang et al.133 gseapy.readthedocs.io Mathematica-based image analysis interface Riback et al.106 N/A STAR v2.4.0 Dobin et al.134 github.com/alexdobin/STAR AltAnalyze v2.1.4 Emig et al.135 and Li et al.136 http://altanalyze.org/ Other Custom tRNA Mix New England BioLabs N6842Z XT Reducing Agent 20X 1610792 BioRad 1610792 XT Sample Buffer 4X BioRad 1610791 BlueStain 2 Protein Ladder, 5-245kDa GoldBio P008 GST Glutathione S-Transferase Thermo Fisher Scientific 20237 Tween 20 Sigma-Aldrich P1379 XT MES Running Buffer 20X BioRad 1610789 RPI Dry Milk Powder Research Products International M17200 (Continued on next page) e2 Molecular Cell 85, 1445–1466.e1–e13, April 3, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Phosphate Buffered Saline 10X PBS for Western Blots and IP Sigma-Aldrich P7059 1-Step Transfer Buffer Thermo Scientific 84731 Thermo Sequenase Cycle Sequencing Kit [Discontinued] Thermo Fisher Scientific 785001KT Cytiva Thermo Sequenase Reaction Buffer 10X Cytiva Life Sciences E790000Y Cytiva Thermo Sequenase DNA Polymerase (with Thermoplasma acidophilum Inorganic Pyrophosphatase (TAP)) Cytiva Life Sciences E790000Y Deoxynucleotide (dNTP) Solution Set, 100mM New England BioLabs N0446S Amersham CyDye Fluorescent Nucleotides Cy3-dUTP Cytiva Life Sciences PA53022 Triton X-100 Sigma-Aldrich T9284 Nonfat Dried Milk Bovine Sigma-Aldrich M7409 Deoxyribonucleic acid, single stranded from salmon testes Sigma-Aldrich D7656 Molecular Grade Bovine Serum Albumin New England BioLabs B9200 KOD HotStart Polymerase Novagen 71086 BP Clonase Life Technologies 11791043 Spectinomycin Sigma Aldrich S4014-5G 3-AMINO-1 2 4-TRIAZOLE >=95% (TLC) Sigma Aldrich A8056-100g CYCLOHEXIMIDE FROM MICROBIAL SOURCE Sigma Aldrich C7698-5G 96-well, flat bottom, cell culture microplate Greiner 655083 Axygen Oasis Robotic Tips Fisher Scientific 14-222-223 Corning Untreated 245mm Square BioAssay Dishes Fisher Scientific 07-200-600 96WL R-BTM PLT TCT W/LP 100/CS Fisher Scientific 07 200 720A PEI MAX 40000 Polysciences Inc 24765 SWIM primer Life Technologies Custom Furimazine Pasteur Institute Custom FuGENE HD Transfection Reagent Promega E2311 Lipofectamine 3000 Transfection Reagent Invitrogen L3000001 CHAPS Detergent Thermo Fisher 28299 Unstained protein ladder Thermo Fisher 84786 Bolt Sample Reducing Agent Thermo Fisher B0004 Bolt MOPS SDS Running Buffer Thermo Fisher B0001
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