Virus:Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat#1725035 iTaq SYBR green master mix BIO-RAD Cat1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Recombinant:Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat#1725035 iTaq SYBR green master mix BIO-RAD Cat1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Article Title: Identification of Pax protein inhibitors that suppress target gene expression and cancer cell proliferation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Cadherin-6 Cho et al., 1998 N/A Rabbit Pax2 Dressler and Douglass, 1992 N/A Rabbit PTIP Lechner et al., (2000) N/A Rabbit Pax8 Proteintech Cat#10336-1-AP Rabbit Beta-Actin Sigma-Aldrich Cat#A2066 Rabbit phospho-Histone H3 (Ser10) Millipore Cat#06-570 Rabbit Histone H3 Abcam Cat#ab1791 Rabbit phospho-MAPK Family Sampler kit Cell Signaling Technologies Cat#9910T Rabbit MAPK Family Sampler kit Cell Signaling Technologies Cat#9926 Rabbit Histone H3K4me3 Abcam Cat#ab8580 RNA Polymerase II CTD Abcam Cat#ab5408 Chemicals, peptides, and recombinant proteins BG-1 (CCG-191845) ChemDiv/Molport PubChem ID 124738812 BG-2 (CCG-130202) ChemDiv/Molport 124682279 BG-3 (CCG-191087) ChemDiv/Molport 124738112 Critical commercial assays Steady-Glo Promega Cat#E2520 CellTiter-Glo Promega Cat#G7572 iTaq SYBR Green master mix Bio-Rad Cat1725121 Experimental models: Cell lines PRS4-Luc (HEK293) Patel, et al. 2012 N/A BRE-Luc (HEK293) Bradford, et al. 2019 N/A Human Renal Carcinoma Gnarra and Dressler 1995 N/A Human Ovarian Carcinoma SKOV3 ATCC HTB-77 Mouse IMCD3 ATCC CRL-2123 Oligonucleotides See Table S1 N/A Recombinant DNA CMV-Pax2b mouse Grimley and Dressler, 2018 N/A CMV-Pax2C63Y mouse Grimley and Dressler, 2018 N/A CMV-Luc Grimley and Dressler, 2018 N/A Software and algorithms Instant JChem 17.20.0 ChemAxon, Boston, MA https://chemaxon.com/products/instant-jchem Prism 8.4.2 GraphPad Software, San Diego, CA https://www.graphpad.com/scientific-software/prism/ MScreen (Jacob et al., 2012) https://mscreen.lsi.umich.edu/ ImageJ 2.0.0 (Schindelin et al., 2012) https://imagej.net/software/fiji/ ..
cDNA Synthesis:Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat#1725035 iTaq SYBR green master mix BIO-RAD Cat1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
SYBR Green Assay:Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat#1725035 iTaq SYBR green master mix BIO-RAD Cat1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Article Title: Identification of Pax protein inhibitors that suppress target gene expression and cancer cell proliferation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Cadherin-6 Cho et al., 1998 N/A Rabbit Pax2 Dressler and Douglass, 1992 N/A Rabbit PTIP Lechner et al., (2000) N/A Rabbit Pax8 Proteintech Cat#10336-1-AP Rabbit Beta-Actin Sigma-Aldrich Cat#A2066 Rabbit phospho-Histone H3 (Ser10) Millipore Cat#06-570 Rabbit Histone H3 Abcam Cat#ab1791 Rabbit phospho-MAPK Family Sampler kit Cell Signaling Technologies Cat#9910T Rabbit MAPK Family Sampler kit Cell Signaling Technologies Cat#9926 Rabbit Histone H3K4me3 Abcam Cat#ab8580 RNA Polymerase II CTD Abcam Cat#ab5408 Chemicals, peptides, and recombinant proteins BG-1 (CCG-191845) ChemDiv/Molport PubChem ID 124738812 BG-2 (CCG-130202) ChemDiv/Molport 124682279 BG-3 (CCG-191087) ChemDiv/Molport 124738112 Critical commercial assays Steady-Glo Promega Cat#E2520 CellTiter-Glo Promega Cat#G7572 iTaq SYBR Green master mix Bio-Rad Cat1725121 Experimental models: Cell lines PRS4-Luc (HEK293) Patel, et al. 2012 N/A BRE-Luc (HEK293) Bradford, et al. 2019 N/A Human Renal Carcinoma Gnarra and Dressler 1995 N/A Human Ovarian Carcinoma SKOV3 ATCC HTB-77 Mouse IMCD3 ATCC CRL-2123 Oligonucleotides See Table S1 N/A Recombinant DNA CMV-Pax2b mouse Grimley and Dressler, 2018 N/A CMV-Pax2C63Y mouse Grimley and Dressler, 2018 N/A CMV-Luc Grimley and Dressler, 2018 N/A Software and algorithms Instant JChem 17.20.0 ChemAxon, Boston, MA https://chemaxon.com/products/instant-jchem Prism 8.4.2 GraphPad Software, San Diego, CA https://www.graphpad.com/scientific-software/prism/ MScreen (Jacob et al., 2012) https://mscreen.lsi.umich.edu/ ImageJ 2.0.0 (Schindelin et al., 2012) https://imagej.net/software/fiji/ ..
Single Cell:Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat#1725035 iTaq SYBR green master mix BIO-RAD Cat1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
RNA Sequencing:Article Title: Auxin-dependent post-translational regulation of MONOPTEROS in the Arabidopsis root.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Agrobacterium tumefaciens C58pMP90 strain Widely distributed N/A Agrobacterium tumefaciens GV3101 strain Widely distributed N/A Chemicals, peptides, and recombinant proteins Indole-3-acetic acid Merck Cat#87-51-4 Bortezomib Merck Cat#179324-69-7 MG-132 Merck Cat#133407-82-6 PYR-41 Merck Cat#418805-02-4 Dexamethasone Merck Cat#50-02-2 Propidium iodide Merck Cat#25535-16-4 Renaissance SR2200 Renaissance Chemicals SR2200 DMSO Merck Cat#67-68-5 MS medium Duchefa Biochemie Cat#M0221 Cycloheximide Merck Cat#66-81-9 Chloramphenicol Merck Cat#56-75-7 Glycerol Merck Cat#56-81-5 Critical commercial assays Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S GoTaq DNA Polymerase Promega Cat#M3001 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iScriptTM gDNA Clear cDNA Synthesis Kit BIO-RAD Cat#1725035 iTaq SYBR green master mix BIO-RAD Cat1725121 Deposited data mathematical modeling code Jupyter notebook This study Zenodo: https://doi.org/10.5281/ zenodo.7716649 RNA-SEQ raw reads This study NCBI: PRJNA1165180 Root single-cell RNA sequencing Ryu et al.41 N/A Root tissues transcriptomes Brady et al.70 N/A Experimental models: Organisms/strains Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Center (NASC) N/A Arabidopsis thaliana: pMP::MP:eGFP(mr) Schlereth et al.24 N/A Arabidopsis thaliana: pMP::MP:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pMP:MP-GFP(ct) This study N/A Arabidopsis thaliana: pARF6:ARF6:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: pARF8:ARF8:VENUS-2ApmTURQUOISE This study N/A Arabidopsis thaliana: R2D2 Liao et al.42 N/A Arabidopsis thaliana: GR:bdl Weijers et al.26 N/A Arabidopsis thaliana: pMP::MP Cucinotta et al.34 N/A Arabidopsis thaliana: pMP::MP11ir Cucinotta et al.34 N/A (Continued on next page) 16 Cell Reports 43, 115083, December 24, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers this study Table S6 Recombinant DNA pMP::MP:VENUS-2Ap-mTURQUOISE This study N/A pARF6:ARF6:VENUS-2Ap-mTURQUOISE This study N/A pARF8:ARF8:VENUS-2Ap-mTURQUOISE This study N/A pMP:MP-GFP(ct) This study N/A Software and algorithms LAS X Leica www.leica-microsystems.com NIS-Elements Nikon www.microscope.healthcare. nikon.com BioLogic LP software BIO-RAD www.bio-rad.com CFX Maestro BIO-RAD www.bio-rad.com Fiji Schindelin et al.76 N/A MorphoLibJ plugin Legland et al.77 N/A Trimmomatic (v.0.36) Bolger et al.78 N/A STAR (v2.7.10a) Dobin et al.79 N/A featureCounts (v2.0.1) Liao et al.80 N/A R (v4.3.3) The R Project for Statistical Computing https://www.r-project.org/ ShinyGo (v0.80) Ge et al.57 http://bioinformatics.sdstate. edu/go/ Deseq2 Love et al.81 N/A
Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Reverse Transcription:Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Labeling:Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Cloning:Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Expressing:Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Alternative Splicing:Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Plasmid Preparation:Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Software:Article Title: Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains Escherichia coli DH5a N/A N/A Agrobacterium tumefaciens GV3101 N/A N/A Chemicals, Peptides, and Recombinant Proteins Q5 High-Fidelity DNA Polymerase NEB Cat#M0491S Basta Herbicide BASF N/A GoTaq DNA Polymerase Promega Cat#M3001 Critical Commercial Assays NucleoSpin RNA Plant kit Macherey-Nagel Cat#740949.50 TURBOTM DNase ThermoFisher Scientific Cat#AM2238 ddPCRTM Supermix for Probes Bio-Rad Cat#186-3023 ImProm-IITM Reverse Transcription System Promega Cat#A3800 SuperScriptTM IV VILOTM Master Mix with ezDNaseTM ThermoFisher Scientific Cat#11766050 iTaq SYBR green master mix Bio-Rad Cat1725121 Cstm ddPCR FAM Assay 200R Bio-Rad Cat#10031276 Cstm ddPCR HEX Assay 200R Bio-Rad Cat#10031279 DIG RNA Labeling Kit (SP6/T7) Roche Cat#11175025910 Deposited Data RNA-seq Arabidopsis thaliana Col0 inflorescences this study NCBI Database: SRR12990564, https://www.ncbi. nlm.nih.gov/sra/SRR12990564N Experimental Models: Organisms/Strains Arabidopsis thaliana pTMO3::3xGFP 15 N/A Arabidopsis thaliana DRv2::ntdTomato 17 N/A Arabidopsis thaliana mpS319 31 N/A Arabidopsis thaliana arf5-1 32 N/A Arabidopsis thaliana DII-VENUS 16 N/A Arabidopsis thaliana pMP:MP11ir-GFP this study N/A Arabidopsis thaliana pMP:MP this study N/A Arabidopsis thaliana Col-0 The Nottingham Arabidopsis Stock Centre (NASC) N/A Arabidopsis thaliana pMP:MP-GFP 15 N/A Arabidopsis thaliana pTMO5::3xGFP 15 N/A Oligonucleotides Oligonucleotides for cloning and for expression analysis see Table S1 N/A Oligonucletides for detection of alternative splicing see Table S1 N/A Recombinant DNA Plasmid: pMP:MP11ir-GFP this study N/A Software and Algorithms LAS AF 2.2.0 Leica Microsystems Srl https://www.leica-microsystems.com/ QuantaSoftTM Bio-Rad https://www.bio-rad.com/en-it/SearchResults? ..
Article Title: Identification of Pax protein inhibitors that suppress target gene expression and cancer cell proliferation.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit Cadherin-6 Cho et al., 1998 N/A Rabbit Pax2 Dressler and Douglass, 1992 N/A Rabbit PTIP Lechner et al., (2000) N/A Rabbit Pax8 Proteintech Cat#10336-1-AP Rabbit Beta-Actin Sigma-Aldrich Cat#A2066 Rabbit phospho-Histone H3 (Ser10) Millipore Cat#06-570 Rabbit Histone H3 Abcam Cat#ab1791 Rabbit phospho-MAPK Family Sampler kit Cell Signaling Technologies Cat#9910T Rabbit MAPK Family Sampler kit Cell Signaling Technologies Cat#9926 Rabbit Histone H3K4me3 Abcam Cat#ab8580 RNA Polymerase II CTD Abcam Cat#ab5408 Chemicals, peptides, and recombinant proteins BG-1 (CCG-191845) ChemDiv/Molport PubChem ID 124738812 BG-2 (CCG-130202) ChemDiv/Molport 124682279 BG-3 (CCG-191087) ChemDiv/Molport 124738112 Critical commercial assays Steady-Glo Promega Cat#E2520 CellTiter-Glo Promega Cat#G7572 iTaq SYBR Green master mix Bio-Rad Cat1725121 Experimental models: Cell lines PRS4-Luc (HEK293) Patel, et al. 2012 N/A BRE-Luc (HEK293) Bradford, et al. 2019 N/A Human Renal Carcinoma Gnarra and Dressler 1995 N/A Human Ovarian Carcinoma SKOV3 ATCC HTB-77 Mouse IMCD3 ATCC CRL-2123 Oligonucleotides See Table S1 N/A Recombinant DNA CMV-Pax2b mouse Grimley and Dressler, 2018 N/A CMV-Pax2C63Y mouse Grimley and Dressler, 2018 N/A CMV-Luc Grimley and Dressler, 2018 N/A Software and algorithms Instant JChem 17.20.0 ChemAxon, Boston, MA https://chemaxon.com/products/instant-jchem Prism 8.4.2 GraphPad Software, San Diego, CA https://www.graphpad.com/scientific-software/prism/ MScreen (Jacob et al., 2012) https://mscreen.lsi.umich.edu/ ImageJ 2.0.0 (Schindelin et al., 2012) https://imagej.net/software/fiji/ ..
|
Bio-Rad is a verified supplier 
Bio-Rad manufactures this product 