Recombinant:Article Title: Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.
Article Snippet: .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Recombinant DNA pHEE2E-TRI Jin & Marquardt (2020) Addgene Plasmid #71288 pKI1.1R Jin & Marquardt (2020) Addgene Plasmid #85808 pMOD_A0402 Cerm ak et al (2017) Addgene Plasmid #91009 pMOD_B2303 Cerm ak et al (2017) Addgene Plasmid #91068 pMOD_C3001 Cerm ak et al (2017) Addgene Plasmid #91094 pTRANS_230 Cerm ak et al (2017) Addgene Plasmid #91118 Chemicals, enzymes and other reagents Acidic phenol-chloroform-isoamyl alcohol 125:24:1 pH 4.5 ThermoFisher AM9720 AGAROSE BioShop AGA001.1 Agencourt AMPure XP Beckman Coulter A63881 Agencourt AMPure XP magnetic beads Beckman Coulter A63881 All oligonucleotides (except stated otherwise) Sigma-Aldrich N/A Beetle luciferin potassium salt Promega E1605 Beta-mercaptoethanol Sigma-Aldrich M6250-100ML Betaine 5M Sigma-Aldrich B0300-1VL Chloroform POCH 234431116 CloneJET PCR Cloning Kit ThermoFisher K1232 COmplete protease inhibitors Roche 5056489001 DAPI Sigma-Aldrich D9564-10MG Dextran T40 Sigma-Aldrich 31389-500G dNTP Mix 10 mM ThermoFisher R0192 DTT ThermoFisher DTT001.10 E. coli DNA Ligase New England Biolabs M0205L E. coli DNA polymerase New England Biolabs M0209L EDTA Sterile Solution 0.5 M pH 8.0 BioShop EDT111.500 Empigen Sigma-Aldrich 30326-50ML Ethanol 96 % POCH 396420113 Ficoll 400 BioShop FIC400.100 Formaldehyde Sigma-Aldrich F8775-4x25ML Formamide POCH 432200116 Glufosinate ammonium Sigma-Aldrich 45520-100MG Glycerol Chempur 114433204 HEPES ACROS FSBP31010 Hygromycin BioShop HYG002 Isopropanol POCH 751500111 KCl POCH 739740114 KH2PO4 Sigma-Aldrich P5655-100G Mannitol BioShop MAN509.500 Methanol Chempur 603-001-00-X MgCl2 ThermoFisher F 530-S Miracloth Sigma-Aldrich 475855-1R Murashige and Skoog (MS) medium Sigma-Aldrich M0404-10L Murine RNase inhibitors New England Biolabs M0314L N,N-Dimethylformamide Sigma-Aldrich 227056-250ML 2023 The Authors The EMBO Journal 42: e112443 | 2023 13 of 21 D ow nloaded from https://w w w .em bopress.org on N ovem ber 18, 2025 from IP 182.10.130.22. .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Na2HPO4 7H2O Sigma-Aldrich 30413-500G NaCl POCH 794121116 NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer New England Biolabs B6117S NP-40 BioShop NON505.100 Oligo(dT) Sigma-Aldrich N/A PEG 6000 Sigma-Aldrich 8.07491.1000 PEG 8000 50% New England Biolabs M0242S Percoll Sigma-Aldrich P1644 Phenol equilibrated stabilized Applichem A1153,0100 Phusion High-Fidelity DNA Polymerase ThermoFisher F 530-S Phusion High-Fidelity HF Buffer ThermoFisher F 530-S Plant Agar Duchefa P1001.1000 PMSF Sigma-Aldrich 93482-50ML-F Q5 Hot Start High-Fidelity 2X Master Mix New England Biolabs M0049S Qubit dsDNA HS LifeTechnololies Q32854 Random hexamers ThermoFisher N8080127 RiboLock 40 U/ll ThermoFisher EO0381 RNase H New England Biolabs M0297-S SDS BDH Prolabo 444464T Sodium acetate POCH 805640115 Spectinomycin BioShop SPE201.5 Sucrose CHEMPUR 117720907 SuperScript II ThermoFisher 18064014 SuperScript III ThermoFisher 18064014 SYBR Green mix Roche 4887352001 T4 RNA ligase 2 Truncated 200 U/ll New England Biolabs M0242S TRIS 1 M pH 7.5 Bioshop TRS111 TRIS 1 M pH 8.0 Bioshop TRS222 TRIS 1 M pH 8.5 Bioshop TRS333 Triton X-100 BioShop TRX777.500 TSO oligo FUTURE Synthesis N/A TURBO DNase kit Ambion AM1907 Urea BioShop URE001.500 Software PartSeg Bokota et al (2021) N/A Olympus xCellence Software Olympus N/A Napari Sofroniew et al (2022) N/A ImageJ https://imagej.nih.gov/ij/download.html N/A
Plasmid Preparation:Article Title: Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.
Article Snippet: .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Recombinant DNA pHEE2E-TRI Jin & Marquardt (2020) Addgene Plasmid #71288 pKI1.1R Jin & Marquardt (2020) Addgene Plasmid #85808 pMOD_A0402 Cerm ak et al (2017) Addgene Plasmid #91009 pMOD_B2303 Cerm ak et al (2017) Addgene Plasmid #91068 pMOD_C3001 Cerm ak et al (2017) Addgene Plasmid #91094 pTRANS_230 Cerm ak et al (2017) Addgene Plasmid #91118 Chemicals, enzymes and other reagents Acidic phenol-chloroform-isoamyl alcohol 125:24:1 pH 4.5 ThermoFisher AM9720 AGAROSE BioShop AGA001.1 Agencourt AMPure XP Beckman Coulter A63881 Agencourt AMPure XP magnetic beads Beckman Coulter A63881 All oligonucleotides (except stated otherwise) Sigma-Aldrich N/A Beetle luciferin potassium salt Promega E1605 Beta-mercaptoethanol Sigma-Aldrich M6250-100ML Betaine 5M Sigma-Aldrich B0300-1VL Chloroform POCH 234431116 CloneJET PCR Cloning Kit ThermoFisher K1232 COmplete protease inhibitors Roche 5056489001 DAPI Sigma-Aldrich D9564-10MG Dextran T40 Sigma-Aldrich 31389-500G dNTP Mix 10 mM ThermoFisher R0192 DTT ThermoFisher DTT001.10 E. coli DNA Ligase New England Biolabs M0205L E. coli DNA polymerase New England Biolabs M0209L EDTA Sterile Solution 0.5 M pH 8.0 BioShop EDT111.500 Empigen Sigma-Aldrich 30326-50ML Ethanol 96 % POCH 396420113 Ficoll 400 BioShop FIC400.100 Formaldehyde Sigma-Aldrich F8775-4x25ML Formamide POCH 432200116 Glufosinate ammonium Sigma-Aldrich 45520-100MG Glycerol Chempur 114433204 HEPES ACROS FSBP31010 Hygromycin BioShop HYG002 Isopropanol POCH 751500111 KCl POCH 739740114 KH2PO4 Sigma-Aldrich P5655-100G Mannitol BioShop MAN509.500 Methanol Chempur 603-001-00-X MgCl2 ThermoFisher F 530-S Miracloth Sigma-Aldrich 475855-1R Murashige and Skoog (MS) medium Sigma-Aldrich M0404-10L Murine RNase inhibitors New England Biolabs M0314L N,N-Dimethylformamide Sigma-Aldrich 227056-250ML 2023 The Authors The EMBO Journal 42: e112443 | 2023 13 of 21 D ow nloaded from https://w w w .em bopress.org on N ovem ber 18, 2025 from IP 182.10.130.22. .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Na2HPO4 7H2O Sigma-Aldrich 30413-500G NaCl POCH 794121116 NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer New England Biolabs B6117S NP-40 BioShop NON505.100 Oligo(dT) Sigma-Aldrich N/A PEG 6000 Sigma-Aldrich 8.07491.1000 PEG 8000 50% New England Biolabs M0242S Percoll Sigma-Aldrich P1644 Phenol equilibrated stabilized Applichem A1153,0100 Phusion High-Fidelity DNA Polymerase ThermoFisher F 530-S Phusion High-Fidelity HF Buffer ThermoFisher F 530-S Plant Agar Duchefa P1001.1000 PMSF Sigma-Aldrich 93482-50ML-F Q5 Hot Start High-Fidelity 2X Master Mix New England Biolabs M0049S Qubit dsDNA HS LifeTechnololies Q32854 Random hexamers ThermoFisher N8080127 RiboLock 40 U/ll ThermoFisher EO0381 RNase H New England Biolabs M0297-S SDS BDH Prolabo 444464T Sodium acetate POCH 805640115 Spectinomycin BioShop SPE201.5 Sucrose CHEMPUR 117720907 SuperScript II ThermoFisher 18064014 SuperScript III ThermoFisher 18064014 SYBR Green mix Roche 4887352001 T4 RNA ligase 2 Truncated 200 U/ll New England Biolabs M0242S TRIS 1 M pH 7.5 Bioshop TRS111 TRIS 1 M pH 8.0 Bioshop TRS222 TRIS 1 M pH 8.5 Bioshop TRS333 Triton X-100 BioShop TRX777.500 TSO oligo FUTURE Synthesis N/A TURBO DNase kit Ambion AM1907 Urea BioShop URE001.500 Software PartSeg Bokota et al (2021) N/A Olympus xCellence Software Olympus N/A Napari Sofroniew et al (2022) N/A ImageJ https://imagej.nih.gov/ij/download.html N/A
Magnetic Beads:Article Title: Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.
Article Snippet: .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Recombinant DNA pHEE2E-TRI Jin & Marquardt (2020) Addgene Plasmid #71288 pKI1.1R Jin & Marquardt (2020) Addgene Plasmid #85808 pMOD_A0402 Cerm ak et al (2017) Addgene Plasmid #91009 pMOD_B2303 Cerm ak et al (2017) Addgene Plasmid #91068 pMOD_C3001 Cerm ak et al (2017) Addgene Plasmid #91094 pTRANS_230 Cerm ak et al (2017) Addgene Plasmid #91118 Chemicals, enzymes and other reagents Acidic phenol-chloroform-isoamyl alcohol 125:24:1 pH 4.5 ThermoFisher AM9720 AGAROSE BioShop AGA001.1 Agencourt AMPure XP Beckman Coulter A63881 Agencourt AMPure XP magnetic beads Beckman Coulter A63881 All oligonucleotides (except stated otherwise) Sigma-Aldrich N/A Beetle luciferin potassium salt Promega E1605 Beta-mercaptoethanol Sigma-Aldrich M6250-100ML Betaine 5M Sigma-Aldrich B0300-1VL Chloroform POCH 234431116 CloneJET PCR Cloning Kit ThermoFisher K1232 COmplete protease inhibitors Roche 5056489001 DAPI Sigma-Aldrich D9564-10MG Dextran T40 Sigma-Aldrich 31389-500G dNTP Mix 10 mM ThermoFisher R0192 DTT ThermoFisher DTT001.10 E. coli DNA Ligase New England Biolabs M0205L E. coli DNA polymerase New England Biolabs M0209L EDTA Sterile Solution 0.5 M pH 8.0 BioShop EDT111.500 Empigen Sigma-Aldrich 30326-50ML Ethanol 96 % POCH 396420113 Ficoll 400 BioShop FIC400.100 Formaldehyde Sigma-Aldrich F8775-4x25ML Formamide POCH 432200116 Glufosinate ammonium Sigma-Aldrich 45520-100MG Glycerol Chempur 114433204 HEPES ACROS FSBP31010 Hygromycin BioShop HYG002 Isopropanol POCH 751500111 KCl POCH 739740114 KH2PO4 Sigma-Aldrich P5655-100G Mannitol BioShop MAN509.500 Methanol Chempur 603-001-00-X MgCl2 ThermoFisher F 530-S Miracloth Sigma-Aldrich 475855-1R Murashige and Skoog (MS) medium Sigma-Aldrich M0404-10L Murine RNase inhibitors New England Biolabs M0314L N,N-Dimethylformamide Sigma-Aldrich 227056-250ML 2023 The Authors The EMBO Journal 42: e112443 | 2023 13 of 21 D ow nloaded from https://w w w .em bopress.org on N ovem ber 18, 2025 from IP 182.10.130.22. .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Na2HPO4 7H2O Sigma-Aldrich 30413-500G NaCl POCH 794121116 NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer New England Biolabs B6117S NP-40 BioShop NON505.100 Oligo(dT) Sigma-Aldrich N/A PEG 6000 Sigma-Aldrich 8.07491.1000 PEG 8000 50% New England Biolabs M0242S Percoll Sigma-Aldrich P1644 Phenol equilibrated stabilized Applichem A1153,0100 Phusion High-Fidelity DNA Polymerase ThermoFisher F 530-S Phusion High-Fidelity HF Buffer ThermoFisher F 530-S Plant Agar Duchefa P1001.1000 PMSF Sigma-Aldrich 93482-50ML-F Q5 Hot Start High-Fidelity 2X Master Mix New England Biolabs M0049S Qubit dsDNA HS LifeTechnololies Q32854 Random hexamers ThermoFisher N8080127 RiboLock 40 U/ll ThermoFisher EO0381 RNase H New England Biolabs M0297-S SDS BDH Prolabo 444464T Sodium acetate POCH 805640115 Spectinomycin BioShop SPE201.5 Sucrose CHEMPUR 117720907 SuperScript II ThermoFisher 18064014 SuperScript III ThermoFisher 18064014 SYBR Green mix Roche 4887352001 T4 RNA ligase 2 Truncated 200 U/ll New England Biolabs M0242S TRIS 1 M pH 7.5 Bioshop TRS111 TRIS 1 M pH 8.0 Bioshop TRS222 TRIS 1 M pH 8.5 Bioshop TRS333 Triton X-100 BioShop TRX777.500 TSO oligo FUTURE Synthesis N/A TURBO DNase kit Ambion AM1907 Urea BioShop URE001.500 Software PartSeg Bokota et al (2021) N/A Olympus xCellence Software Olympus N/A Napari Sofroniew et al (2022) N/A ImageJ https://imagej.nih.gov/ij/download.html N/A
Polymerase Chain Reaction:Article Title: Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.
Article Snippet: .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Recombinant DNA pHEE2E-TRI Jin & Marquardt (2020) Addgene Plasmid #71288 pKI1.1R Jin & Marquardt (2020) Addgene Plasmid #85808 pMOD_A0402 Cerm ak et al (2017) Addgene Plasmid #91009 pMOD_B2303 Cerm ak et al (2017) Addgene Plasmid #91068 pMOD_C3001 Cerm ak et al (2017) Addgene Plasmid #91094 pTRANS_230 Cerm ak et al (2017) Addgene Plasmid #91118 Chemicals, enzymes and other reagents Acidic phenol-chloroform-isoamyl alcohol 125:24:1 pH 4.5 ThermoFisher AM9720 AGAROSE BioShop AGA001.1 Agencourt AMPure XP Beckman Coulter A63881 Agencourt AMPure XP magnetic beads Beckman Coulter A63881 All oligonucleotides (except stated otherwise) Sigma-Aldrich N/A Beetle luciferin potassium salt Promega E1605 Beta-mercaptoethanol Sigma-Aldrich M6250-100ML Betaine 5M Sigma-Aldrich B0300-1VL Chloroform POCH 234431116 CloneJET PCR Cloning Kit ThermoFisher K1232 COmplete protease inhibitors Roche 5056489001 DAPI Sigma-Aldrich D9564-10MG Dextran T40 Sigma-Aldrich 31389-500G dNTP Mix 10 mM ThermoFisher R0192 DTT ThermoFisher DTT001.10 E. coli DNA Ligase New England Biolabs M0205L E. coli DNA polymerase New England Biolabs M0209L EDTA Sterile Solution 0.5 M pH 8.0 BioShop EDT111.500 Empigen Sigma-Aldrich 30326-50ML Ethanol 96 % POCH 396420113 Ficoll 400 BioShop FIC400.100 Formaldehyde Sigma-Aldrich F8775-4x25ML Formamide POCH 432200116 Glufosinate ammonium Sigma-Aldrich 45520-100MG Glycerol Chempur 114433204 HEPES ACROS FSBP31010 Hygromycin BioShop HYG002 Isopropanol POCH 751500111 KCl POCH 739740114 KH2PO4 Sigma-Aldrich P5655-100G Mannitol BioShop MAN509.500 Methanol Chempur 603-001-00-X MgCl2 ThermoFisher F 530-S Miracloth Sigma-Aldrich 475855-1R Murashige and Skoog (MS) medium Sigma-Aldrich M0404-10L Murine RNase inhibitors New England Biolabs M0314L N,N-Dimethylformamide Sigma-Aldrich 227056-250ML 2023 The Authors The EMBO Journal 42: e112443 | 2023 13 of 21 D ow nloaded from https://w w w .em bopress.org on N ovem ber 18, 2025 from IP 182.10.130.22. .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Na2HPO4 7H2O Sigma-Aldrich 30413-500G NaCl POCH 794121116 NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer New England Biolabs B6117S NP-40 BioShop NON505.100 Oligo(dT) Sigma-Aldrich N/A PEG 6000 Sigma-Aldrich 8.07491.1000 PEG 8000 50% New England Biolabs M0242S Percoll Sigma-Aldrich P1644 Phenol equilibrated stabilized Applichem A1153,0100 Phusion High-Fidelity DNA Polymerase ThermoFisher F 530-S Phusion High-Fidelity HF Buffer ThermoFisher F 530-S Plant Agar Duchefa P1001.1000 PMSF Sigma-Aldrich 93482-50ML-F Q5 Hot Start High-Fidelity 2X Master Mix New England Biolabs M0049S Qubit dsDNA HS LifeTechnololies Q32854 Random hexamers ThermoFisher N8080127 RiboLock 40 U/ll ThermoFisher EO0381 RNase H New England Biolabs M0297-S SDS BDH Prolabo 444464T Sodium acetate POCH 805640115 Spectinomycin BioShop SPE201.5 Sucrose CHEMPUR 117720907 SuperScript II ThermoFisher 18064014 SuperScript III ThermoFisher 18064014 SYBR Green mix Roche 4887352001 T4 RNA ligase 2 Truncated 200 U/ll New England Biolabs M0242S TRIS 1 M pH 7.5 Bioshop TRS111 TRIS 1 M pH 8.0 Bioshop TRS222 TRIS 1 M pH 8.5 Bioshop TRS333 Triton X-100 BioShop TRX777.500 TSO oligo FUTURE Synthesis N/A TURBO DNase kit Ambion AM1907 Urea BioShop URE001.500 Software PartSeg Bokota et al (2021) N/A Olympus xCellence Software Olympus N/A Napari Sofroniew et al (2022) N/A ImageJ https://imagej.nih.gov/ij/download.html N/A
Cloning:Article Title: Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.
Article Snippet: .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Recombinant DNA pHEE2E-TRI Jin & Marquardt (2020) Addgene Plasmid #71288 pKI1.1R Jin & Marquardt (2020) Addgene Plasmid #85808 pMOD_A0402 Cerm ak et al (2017) Addgene Plasmid #91009 pMOD_B2303 Cerm ak et al (2017) Addgene Plasmid #91068 pMOD_C3001 Cerm ak et al (2017) Addgene Plasmid #91094 pTRANS_230 Cerm ak et al (2017) Addgene Plasmid #91118 Chemicals, enzymes and other reagents Acidic phenol-chloroform-isoamyl alcohol 125:24:1 pH 4.5 ThermoFisher AM9720 AGAROSE BioShop AGA001.1 Agencourt AMPure XP Beckman Coulter A63881 Agencourt AMPure XP magnetic beads Beckman Coulter A63881 All oligonucleotides (except stated otherwise) Sigma-Aldrich N/A Beetle luciferin potassium salt Promega E1605 Beta-mercaptoethanol Sigma-Aldrich M6250-100ML Betaine 5M Sigma-Aldrich B0300-1VL Chloroform POCH 234431116 CloneJET PCR Cloning Kit ThermoFisher K1232 COmplete protease inhibitors Roche 5056489001 DAPI Sigma-Aldrich D9564-10MG Dextran T40 Sigma-Aldrich 31389-500G dNTP Mix 10 mM ThermoFisher R0192 DTT ThermoFisher DTT001.10 E. coli DNA Ligase New England Biolabs M0205L E. coli DNA polymerase New England Biolabs M0209L EDTA Sterile Solution 0.5 M pH 8.0 BioShop EDT111.500 Empigen Sigma-Aldrich 30326-50ML Ethanol 96 % POCH 396420113 Ficoll 400 BioShop FIC400.100 Formaldehyde Sigma-Aldrich F8775-4x25ML Formamide POCH 432200116 Glufosinate ammonium Sigma-Aldrich 45520-100MG Glycerol Chempur 114433204 HEPES ACROS FSBP31010 Hygromycin BioShop HYG002 Isopropanol POCH 751500111 KCl POCH 739740114 KH2PO4 Sigma-Aldrich P5655-100G Mannitol BioShop MAN509.500 Methanol Chempur 603-001-00-X MgCl2 ThermoFisher F 530-S Miracloth Sigma-Aldrich 475855-1R Murashige and Skoog (MS) medium Sigma-Aldrich M0404-10L Murine RNase inhibitors New England Biolabs M0314L N,N-Dimethylformamide Sigma-Aldrich 227056-250ML 2023 The Authors The EMBO Journal 42: e112443 | 2023 13 of 21 D ow nloaded from https://w w w .em bopress.org on N ovem ber 18, 2025 from IP 182.10.130.22. .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Na2HPO4 7H2O Sigma-Aldrich 30413-500G NaCl POCH 794121116 NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer New England Biolabs B6117S NP-40 BioShop NON505.100 Oligo(dT) Sigma-Aldrich N/A PEG 6000 Sigma-Aldrich 8.07491.1000 PEG 8000 50% New England Biolabs M0242S Percoll Sigma-Aldrich P1644 Phenol equilibrated stabilized Applichem A1153,0100 Phusion High-Fidelity DNA Polymerase ThermoFisher F 530-S Phusion High-Fidelity HF Buffer ThermoFisher F 530-S Plant Agar Duchefa P1001.1000 PMSF Sigma-Aldrich 93482-50ML-F Q5 Hot Start High-Fidelity 2X Master Mix New England Biolabs M0049S Qubit dsDNA HS LifeTechnololies Q32854 Random hexamers ThermoFisher N8080127 RiboLock 40 U/ll ThermoFisher EO0381 RNase H New England Biolabs M0297-S SDS BDH Prolabo 444464T Sodium acetate POCH 805640115 Spectinomycin BioShop SPE201.5 Sucrose CHEMPUR 117720907 SuperScript II ThermoFisher 18064014 SuperScript III ThermoFisher 18064014 SYBR Green mix Roche 4887352001 T4 RNA ligase 2 Truncated 200 U/ll New England Biolabs M0242S TRIS 1 M pH 7.5 Bioshop TRS111 TRIS 1 M pH 8.0 Bioshop TRS222 TRIS 1 M pH 8.5 Bioshop TRS333 Triton X-100 BioShop TRX777.500 TSO oligo FUTURE Synthesis N/A TURBO DNase kit Ambion AM1907 Urea BioShop URE001.500 Software PartSeg Bokota et al (2021) N/A Olympus xCellence Software Olympus N/A Napari Sofroniew et al (2022) N/A ImageJ https://imagej.nih.gov/ij/download.html N/A
Sterility:Article Title: Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt.
Article Snippet: .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Recombinant DNA pHEE2E-TRI Jin & Marquardt (2020) Addgene Plasmid #71288 pKI1.1R Jin & Marquardt (2020) Addgene Plasmid #85808 pMOD_A0402 Cerm ak et al (2017) Addgene Plasmid #91009 pMOD_B2303 Cerm ak et al (2017) Addgene Plasmid #91068 pMOD_C3001 Cerm ak et al (2017) Addgene Plasmid #91094 pTRANS_230 Cerm ak et al (2017) Addgene Plasmid #91118 Chemicals, enzymes and other reagents Acidic phenol-chloroform-isoamyl alcohol 125:24:1 pH 4.5 ThermoFisher AM9720 AGAROSE BioShop AGA001.1 Agencourt AMPure XP Beckman Coulter A63881 Agencourt AMPure XP magnetic beads Beckman Coulter A63881 All oligonucleotides (except stated otherwise) Sigma-Aldrich N/A Beetle luciferin potassium salt Promega E1605 Beta-mercaptoethanol Sigma-Aldrich M6250-100ML Betaine 5M Sigma-Aldrich B0300-1VL Chloroform POCH 234431116 CloneJET PCR Cloning Kit ThermoFisher K1232 COmplete protease inhibitors Roche 5056489001 DAPI Sigma-Aldrich D9564-10MG Dextran T40 Sigma-Aldrich 31389-500G dNTP Mix 10 mM ThermoFisher R0192 DTT ThermoFisher DTT001.10 E. coli DNA Ligase New England Biolabs M0205L E. coli DNA polymerase New England Biolabs M0209L EDTA Sterile Solution 0.5 M pH 8.0 BioShop EDT111.500 Empigen Sigma-Aldrich 30326-50ML Ethanol 96 % POCH 396420113 Ficoll 400 BioShop FIC400.100 Formaldehyde Sigma-Aldrich F8775-4x25ML Formamide POCH 432200116 Glufosinate ammonium Sigma-Aldrich 45520-100MG Glycerol Chempur 114433204 HEPES ACROS FSBP31010 Hygromycin BioShop HYG002 Isopropanol POCH 751500111 KCl POCH 739740114 KH2PO4 Sigma-Aldrich P5655-100G Mannitol BioShop MAN509.500 Methanol Chempur 603-001-00-X MgCl2 ThermoFisher F 530-S Miracloth Sigma-Aldrich 475855-1R Murashige and Skoog (MS) medium Sigma-Aldrich M0404-10L Murine RNase inhibitors New England Biolabs M0314L N,N-Dimethylformamide Sigma-Aldrich 227056-250ML 2023 The Authors The EMBO Journal 42: e112443 | 2023 13 of 21 D ow nloaded from https://w w w .em bopress.org on N ovem ber 18, 2025 from IP 182.10.130.22. .. Reagents and Tools table (continued) Reagent/Resource Reference or Source Identifier or Catalog Number Na2HPO4 7H2O Sigma-Aldrich 30413-500G NaCl POCH 794121116 NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer New England Biolabs B6117S NP-40 BioShop NON505.100 Oligo(dT) Sigma-Aldrich N/A PEG 6000 Sigma-Aldrich 8.07491.1000 PEG 8000 50% New England Biolabs M0242S Percoll Sigma-Aldrich P1644 Phenol equilibrated stabilized Applichem A1153,0100 Phusion High-Fidelity DNA Polymerase ThermoFisher F 530-S Phusion High-Fidelity HF Buffer ThermoFisher F 530-S Plant Agar Duchefa P1001.1000 PMSF Sigma-Aldrich 93482-50ML-F Q5 Hot Start High-Fidelity 2X Master Mix New England Biolabs M0049S Qubit dsDNA HS LifeTechnololies Q32854 Random hexamers ThermoFisher N8080127 RiboLock 40 U/ll ThermoFisher EO0381 RNase H New England Biolabs M0297-S SDS BDH Prolabo 444464T Sodium acetate POCH 805640115 Spectinomycin BioShop SPE201.5 Sucrose CHEMPUR 117720907 SuperScript II ThermoFisher 18064014 SuperScript III ThermoFisher 18064014 SYBR Green mix Roche 4887352001 T4 RNA ligase 2 Truncated 200 U/ll New England Biolabs M0242S TRIS 1 M pH 7.5 Bioshop TRS111 TRIS 1 M pH 8.0 Bioshop TRS222 TRIS 1 M pH 8.5 Bioshop TRS333 Triton X-100 BioShop TRX777.500 TSO oligo FUTURE Synthesis N/A TURBO DNase kit Ambion AM1907 Urea BioShop URE001.500 Software PartSeg Bokota et al (2021) N/A Olympus xCellence Software Olympus N/A Napari Sofroniew et al (2022) N/A ImageJ https://imagej.nih.gov/ij/download.html N/A
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