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dna engine opticon 3 real time detection system software program  (Bio-Rad)


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    Bio-Rad dna engine opticon 3 real time detection system software program
    Dna Engine Opticon 3 Real Time Detection System Software Program, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 2788 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/dna+software+program/DNA+Engine/pmc10224410-299-6-17
    Average 99 stars, based on 2788 article reviews
    dna engine opticon 3 real time detection system software program - by Bioz Stars, 2026-11
    99/100 stars

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    Software:

    Article Title: A human CAGinSTEM platform for decoding HTT repeats' somatic instability links CAG interruption to HD pathology in neurons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pCAG-Flpe:GFP Addgene 13788 pCAG-Cre:GFP Addgene 13776 pUC57_HDR_RMCE_(CAG) 19 -CAACAG/21Q_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 43 -CAACAG/45Q_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 79 -CAACAG/81Q_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 105 -CAACAG/107Q_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_CAG 107 /107Q_LOI_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 105 (CAACAG) 2 / 107Q_DUP_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_([(CAG) 21 CAA] 4 (CAG) 17 CAACAG)/107Q_multi CAAs_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 78 (CAACAG) 2 CAACAG/81Q_DUP_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 45 /43Q_LOI_PuroR Genscript custom DNA sinthesis Software and algorithms nf-core rnaseq v3.14.0-gb89fac3 Nextflow pipeline Di Tommaso et al. 63 Patel et al. 64 https://doi.org/10.5281/zenodo.13986791 DESeq2 package v1.12.3 and Dependencies Love et al. 65 t http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html. .. R 4.3.1 N/A https://cran.r-project.org/bin/windows/ base/old/4.3.1/ GenomicAlignments v1.36.0 Pagè s et al. 66 https://doi.org/10.18129/B9.bioc.Biostrings Guppy v5.0.7 ONT proprietary software N/A Straglr v1.2.0 Chiu et al. 25 https://github.com/bcgsc/straglr BLASTN v2.12 Zhang et al. 67 N/A FIJI - ImageJ N/A https://fiji.sc/ CFX Manager Software N/A Bio-Rad GraphPad Prism N/A https://www.graphpad.com/ NIS-elements Analysis softwere Nikon N/A 20 Cell Reports 44, 116685, December 23, 2025 TTAAAACAGCCT) used for the integration of pUC57_HDR_107Q_PuroR donor plasmid were synthetized by IDT. .. Alt-R CRISPRCas9 tracrRNA (IDT 1072534) and the two designed Alt-R CRISPR-Cas9 crRNAs were assembled individually in duplex buffer (IDT #11050112) for 5 min at 95 ◦ C followed by slow cool down to RT.

    Article Title: Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions
    Article Snippet: .. Nuclease-free Water (IDT, cat. no. 11–05-01–04) Phusion Hot Start Flex 2X Master Mix (NEB, cat. no. M0536L) Custom DNA oligonucleotides (IDT, cat. no. n/a) 1X TE (10 mM Tris-Cl, 0.1 mM EDTA, pH 8.0; IDT, cat. no. 11–05-02–04) E. coli NEBα/pHB1 (MJM3287; Addgene Plasmid #204668, Table 1 ) QIAprep Spin Miniprep Kit (QIAgen, cat. no. 27106) Gel Loading Dye, Purple (6X; NEB, cat. no. B7024S) High-resolution Agarose, for Molecular Biology (Sigma-Aldrich, cat. no. A4718–25G) 50X TAE (see recipe) Ethidium Bromide (EtBr), 10 mg/ml (20,000X, see recipe; Sigma-Aldrich, cat. no. E7637) 1 kb DNA Ladder (NEB, cat. no. N3232) QIAquick Gel Extraction Kit (QIAgen, cat. no. 28706) Isopropanol (needed during gel extraction; Sigma-Aldrich, cat. no. 190764) Sodium acetate (NaOAc), 3 M, pH 5.0 (see recipe; Sigma-Aldrich, cat. no. 32319) Acetic Acid, Glacial (J. T. Baker, cat. no. 952202) 1.7 ml MaxyClear Snaplock microcentrifuge tube(s) (Corning Axygen, cat. No. MCT-175-C) 10-, 200-, and 1000-μl pipettes and filter tips Microcentrifuge (Eppendorf, cat. no. 5424) Scientific Industries Vortex-Genie 2 (Fisher, cat. no. 50–728-002) Fisherbrand 0.2 ml PCR Tube Strips (Fisher, cat. no. 14–230-215) Fisherbrand Standard Mini-Centrifuge (Fisher, cat. no. S67601B) C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module (Bio-Rad, cat. no. 1851196) Thermo Scientific Owl EasyCast B1A Mini Gel Electrophoresis Systems (Fisher, cat no. 09–528-110) PowerPac Basic Power Supply (Bio-Rad, cat. no. 1645050) Imaging system with UV lamp to visualize Ethidium Bromide-bound DNA (e.g., GelDoc Go Gel Imaging System with Image Lab Touch Software [Bio-Rad, cat. no. 12009077], or AlphaImager HP Imaging System [Cell Biosciences, cat. no. 92–13823-00]) Razor blades (Fisher, cat. no. 12640) NanoDrop Microvolume Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000) Set up a Master Mix of multiple 50 μl volume PCRs using pHB1 as template, and oligonucleotides HB42 and HB154 ( Table 3 ) as primers, to generate large quantities of the erm-bar DNA ( Fig. 2A ) as follows: Because we will be working with a Master Mix (MM) format, volumes will be given for 9 reactions (8 reactions and 1 additional). ..


    Plasmid Preparation:

    Article Title: A human CAGinSTEM platform for decoding HTT repeats' somatic instability links CAG interruption to HD pathology in neurons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pCAG-Flpe:GFP Addgene 13788 pCAG-Cre:GFP Addgene 13776 pUC57_HDR_RMCE_(CAG) 19 -CAACAG/21Q_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 43 -CAACAG/45Q_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 79 -CAACAG/81Q_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 105 -CAACAG/107Q_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_CAG 107 /107Q_LOI_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 105 (CAACAG) 2 / 107Q_DUP_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_([(CAG) 21 CAA] 4 (CAG) 17 CAACAG)/107Q_multi CAAs_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 78 (CAACAG) 2 CAACAG/81Q_DUP_PuroR Genscript custom DNA sinthesis pUC57_HDR_RMCE_(CAG) 45 /43Q_LOI_PuroR Genscript custom DNA sinthesis Software and algorithms nf-core rnaseq v3.14.0-gb89fac3 Nextflow pipeline Di Tommaso et al. 63 Patel et al. 64 https://doi.org/10.5281/zenodo.13986791 DESeq2 package v1.12.3 and Dependencies Love et al. 65 t http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html. .. R 4.3.1 N/A https://cran.r-project.org/bin/windows/ base/old/4.3.1/ GenomicAlignments v1.36.0 Pagè s et al. 66 https://doi.org/10.18129/B9.bioc.Biostrings Guppy v5.0.7 ONT proprietary software N/A Straglr v1.2.0 Chiu et al. 25 https://github.com/bcgsc/straglr BLASTN v2.12 Zhang et al. 67 N/A FIJI - ImageJ N/A https://fiji.sc/ CFX Manager Software N/A Bio-Rad GraphPad Prism N/A https://www.graphpad.com/ NIS-elements Analysis softwere Nikon N/A 20 Cell Reports 44, 116685, December 23, 2025 TTAAAACAGCCT) used for the integration of pUC57_HDR_107Q_PuroR donor plasmid were synthetized by IDT. .. Alt-R CRISPRCas9 tracrRNA (IDT 1072534) and the two designed Alt-R CRISPR-Cas9 crRNAs were assembled individually in duplex buffer (IDT #11050112) for 5 min at 95 ◦ C followed by slow cool down to RT.

    Article Title: Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions
    Article Snippet: .. Nuclease-free Water (IDT, cat. no. 11–05-01–04) Phusion Hot Start Flex 2X Master Mix (NEB, cat. no. M0536L) Custom DNA oligonucleotides (IDT, cat. no. n/a) 1X TE (10 mM Tris-Cl, 0.1 mM EDTA, pH 8.0; IDT, cat. no. 11–05-02–04) E. coli NEBα/pHB1 (MJM3287; Addgene Plasmid #204668, Table 1 ) QIAprep Spin Miniprep Kit (QIAgen, cat. no. 27106) Gel Loading Dye, Purple (6X; NEB, cat. no. B7024S) High-resolution Agarose, for Molecular Biology (Sigma-Aldrich, cat. no. A4718–25G) 50X TAE (see recipe) Ethidium Bromide (EtBr), 10 mg/ml (20,000X, see recipe; Sigma-Aldrich, cat. no. E7637) 1 kb DNA Ladder (NEB, cat. no. N3232) QIAquick Gel Extraction Kit (QIAgen, cat. no. 28706) Isopropanol (needed during gel extraction; Sigma-Aldrich, cat. no. 190764) Sodium acetate (NaOAc), 3 M, pH 5.0 (see recipe; Sigma-Aldrich, cat. no. 32319) Acetic Acid, Glacial (J. T. Baker, cat. no. 952202) 1.7 ml MaxyClear Snaplock microcentrifuge tube(s) (Corning Axygen, cat. No. MCT-175-C) 10-, 200-, and 1000-μl pipettes and filter tips Microcentrifuge (Eppendorf, cat. no. 5424) Scientific Industries Vortex-Genie 2 (Fisher, cat. no. 50–728-002) Fisherbrand 0.2 ml PCR Tube Strips (Fisher, cat. no. 14–230-215) Fisherbrand Standard Mini-Centrifuge (Fisher, cat. no. S67601B) C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module (Bio-Rad, cat. no. 1851196) Thermo Scientific Owl EasyCast B1A Mini Gel Electrophoresis Systems (Fisher, cat no. 09–528-110) PowerPac Basic Power Supply (Bio-Rad, cat. no. 1645050) Imaging system with UV lamp to visualize Ethidium Bromide-bound DNA (e.g., GelDoc Go Gel Imaging System with Image Lab Touch Software [Bio-Rad, cat. no. 12009077], or AlphaImager HP Imaging System [Cell Biosciences, cat. no. 92–13823-00]) Razor blades (Fisher, cat. no. 12640) NanoDrop Microvolume Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000) Set up a Master Mix of multiple 50 μl volume PCRs using pHB1 as template, and oligonucleotides HB42 and HB154 ( Table 3 ) as primers, to generate large quantities of the erm-bar DNA ( Fig. 2A ) as follows: Because we will be working with a Master Mix (MM) format, volumes will be given for 9 reactions (8 reactions and 1 additional). ..

    Gel Extraction:

    Article Title: Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions
    Article Snippet: .. Nuclease-free Water (IDT, cat. no. 11–05-01–04) Phusion Hot Start Flex 2X Master Mix (NEB, cat. no. M0536L) Custom DNA oligonucleotides (IDT, cat. no. n/a) 1X TE (10 mM Tris-Cl, 0.1 mM EDTA, pH 8.0; IDT, cat. no. 11–05-02–04) E. coli NEBα/pHB1 (MJM3287; Addgene Plasmid #204668, Table 1 ) QIAprep Spin Miniprep Kit (QIAgen, cat. no. 27106) Gel Loading Dye, Purple (6X; NEB, cat. no. B7024S) High-resolution Agarose, for Molecular Biology (Sigma-Aldrich, cat. no. A4718–25G) 50X TAE (see recipe) Ethidium Bromide (EtBr), 10 mg/ml (20,000X, see recipe; Sigma-Aldrich, cat. no. E7637) 1 kb DNA Ladder (NEB, cat. no. N3232) QIAquick Gel Extraction Kit (QIAgen, cat. no. 28706) Isopropanol (needed during gel extraction; Sigma-Aldrich, cat. no. 190764) Sodium acetate (NaOAc), 3 M, pH 5.0 (see recipe; Sigma-Aldrich, cat. no. 32319) Acetic Acid, Glacial (J. T. Baker, cat. no. 952202) 1.7 ml MaxyClear Snaplock microcentrifuge tube(s) (Corning Axygen, cat. No. MCT-175-C) 10-, 200-, and 1000-μl pipettes and filter tips Microcentrifuge (Eppendorf, cat. no. 5424) Scientific Industries Vortex-Genie 2 (Fisher, cat. no. 50–728-002) Fisherbrand 0.2 ml PCR Tube Strips (Fisher, cat. no. 14–230-215) Fisherbrand Standard Mini-Centrifuge (Fisher, cat. no. S67601B) C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module (Bio-Rad, cat. no. 1851196) Thermo Scientific Owl EasyCast B1A Mini Gel Electrophoresis Systems (Fisher, cat no. 09–528-110) PowerPac Basic Power Supply (Bio-Rad, cat. no. 1645050) Imaging system with UV lamp to visualize Ethidium Bromide-bound DNA (e.g., GelDoc Go Gel Imaging System with Image Lab Touch Software [Bio-Rad, cat. no. 12009077], or AlphaImager HP Imaging System [Cell Biosciences, cat. no. 92–13823-00]) Razor blades (Fisher, cat. no. 12640) NanoDrop Microvolume Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000) Set up a Master Mix of multiple 50 μl volume PCRs using pHB1 as template, and oligonucleotides HB42 and HB154 ( Table 3 ) as primers, to generate large quantities of the erm-bar DNA ( Fig. 2A ) as follows: Because we will be working with a Master Mix (MM) format, volumes will be given for 9 reactions (8 reactions and 1 additional). ..

    Polymerase Chain Reaction:

    Article Title: Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions
    Article Snippet: .. Nuclease-free Water (IDT, cat. no. 11–05-01–04) Phusion Hot Start Flex 2X Master Mix (NEB, cat. no. M0536L) Custom DNA oligonucleotides (IDT, cat. no. n/a) 1X TE (10 mM Tris-Cl, 0.1 mM EDTA, pH 8.0; IDT, cat. no. 11–05-02–04) E. coli NEBα/pHB1 (MJM3287; Addgene Plasmid #204668, Table 1 ) QIAprep Spin Miniprep Kit (QIAgen, cat. no. 27106) Gel Loading Dye, Purple (6X; NEB, cat. no. B7024S) High-resolution Agarose, for Molecular Biology (Sigma-Aldrich, cat. no. A4718–25G) 50X TAE (see recipe) Ethidium Bromide (EtBr), 10 mg/ml (20,000X, see recipe; Sigma-Aldrich, cat. no. E7637) 1 kb DNA Ladder (NEB, cat. no. N3232) QIAquick Gel Extraction Kit (QIAgen, cat. no. 28706) Isopropanol (needed during gel extraction; Sigma-Aldrich, cat. no. 190764) Sodium acetate (NaOAc), 3 M, pH 5.0 (see recipe; Sigma-Aldrich, cat. no. 32319) Acetic Acid, Glacial (J. T. Baker, cat. no. 952202) 1.7 ml MaxyClear Snaplock microcentrifuge tube(s) (Corning Axygen, cat. No. MCT-175-C) 10-, 200-, and 1000-μl pipettes and filter tips Microcentrifuge (Eppendorf, cat. no. 5424) Scientific Industries Vortex-Genie 2 (Fisher, cat. no. 50–728-002) Fisherbrand 0.2 ml PCR Tube Strips (Fisher, cat. no. 14–230-215) Fisherbrand Standard Mini-Centrifuge (Fisher, cat. no. S67601B) C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module (Bio-Rad, cat. no. 1851196) Thermo Scientific Owl EasyCast B1A Mini Gel Electrophoresis Systems (Fisher, cat no. 09–528-110) PowerPac Basic Power Supply (Bio-Rad, cat. no. 1645050) Imaging system with UV lamp to visualize Ethidium Bromide-bound DNA (e.g., GelDoc Go Gel Imaging System with Image Lab Touch Software [Bio-Rad, cat. no. 12009077], or AlphaImager HP Imaging System [Cell Biosciences, cat. no. 92–13823-00]) Razor blades (Fisher, cat. no. 12640) NanoDrop Microvolume Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000) Set up a Master Mix of multiple 50 μl volume PCRs using pHB1 as template, and oligonucleotides HB42 and HB154 ( Table 3 ) as primers, to generate large quantities of the erm-bar DNA ( Fig. 2A ) as follows: Because we will be working with a Master Mix (MM) format, volumes will be given for 9 reactions (8 reactions and 1 additional). ..

    Gel Electrophoresis:

    Article Title: Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions
    Article Snippet: .. Nuclease-free Water (IDT, cat. no. 11–05-01–04) Phusion Hot Start Flex 2X Master Mix (NEB, cat. no. M0536L) Custom DNA oligonucleotides (IDT, cat. no. n/a) 1X TE (10 mM Tris-Cl, 0.1 mM EDTA, pH 8.0; IDT, cat. no. 11–05-02–04) E. coli NEBα/pHB1 (MJM3287; Addgene Plasmid #204668, Table 1 ) QIAprep Spin Miniprep Kit (QIAgen, cat. no. 27106) Gel Loading Dye, Purple (6X; NEB, cat. no. B7024S) High-resolution Agarose, for Molecular Biology (Sigma-Aldrich, cat. no. A4718–25G) 50X TAE (see recipe) Ethidium Bromide (EtBr), 10 mg/ml (20,000X, see recipe; Sigma-Aldrich, cat. no. E7637) 1 kb DNA Ladder (NEB, cat. no. N3232) QIAquick Gel Extraction Kit (QIAgen, cat. no. 28706) Isopropanol (needed during gel extraction; Sigma-Aldrich, cat. no. 190764) Sodium acetate (NaOAc), 3 M, pH 5.0 (see recipe; Sigma-Aldrich, cat. no. 32319) Acetic Acid, Glacial (J. T. Baker, cat. no. 952202) 1.7 ml MaxyClear Snaplock microcentrifuge tube(s) (Corning Axygen, cat. No. MCT-175-C) 10-, 200-, and 1000-μl pipettes and filter tips Microcentrifuge (Eppendorf, cat. no. 5424) Scientific Industries Vortex-Genie 2 (Fisher, cat. no. 50–728-002) Fisherbrand 0.2 ml PCR Tube Strips (Fisher, cat. no. 14–230-215) Fisherbrand Standard Mini-Centrifuge (Fisher, cat. no. S67601B) C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module (Bio-Rad, cat. no. 1851196) Thermo Scientific Owl EasyCast B1A Mini Gel Electrophoresis Systems (Fisher, cat no. 09–528-110) PowerPac Basic Power Supply (Bio-Rad, cat. no. 1645050) Imaging system with UV lamp to visualize Ethidium Bromide-bound DNA (e.g., GelDoc Go Gel Imaging System with Image Lab Touch Software [Bio-Rad, cat. no. 12009077], or AlphaImager HP Imaging System [Cell Biosciences, cat. no. 92–13823-00]) Razor blades (Fisher, cat. no. 12640) NanoDrop Microvolume Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000) Set up a Master Mix of multiple 50 μl volume PCRs using pHB1 as template, and oligonucleotides HB42 and HB154 ( Table 3 ) as primers, to generate large quantities of the erm-bar DNA ( Fig. 2A ) as follows: Because we will be working with a Master Mix (MM) format, volumes will be given for 9 reactions (8 reactions and 1 additional). ..

    Imaging:

    Article Title: Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions
    Article Snippet: .. Nuclease-free Water (IDT, cat. no. 11–05-01–04) Phusion Hot Start Flex 2X Master Mix (NEB, cat. no. M0536L) Custom DNA oligonucleotides (IDT, cat. no. n/a) 1X TE (10 mM Tris-Cl, 0.1 mM EDTA, pH 8.0; IDT, cat. no. 11–05-02–04) E. coli NEBα/pHB1 (MJM3287; Addgene Plasmid #204668, Table 1 ) QIAprep Spin Miniprep Kit (QIAgen, cat. no. 27106) Gel Loading Dye, Purple (6X; NEB, cat. no. B7024S) High-resolution Agarose, for Molecular Biology (Sigma-Aldrich, cat. no. A4718–25G) 50X TAE (see recipe) Ethidium Bromide (EtBr), 10 mg/ml (20,000X, see recipe; Sigma-Aldrich, cat. no. E7637) 1 kb DNA Ladder (NEB, cat. no. N3232) QIAquick Gel Extraction Kit (QIAgen, cat. no. 28706) Isopropanol (needed during gel extraction; Sigma-Aldrich, cat. no. 190764) Sodium acetate (NaOAc), 3 M, pH 5.0 (see recipe; Sigma-Aldrich, cat. no. 32319) Acetic Acid, Glacial (J. T. Baker, cat. no. 952202) 1.7 ml MaxyClear Snaplock microcentrifuge tube(s) (Corning Axygen, cat. No. MCT-175-C) 10-, 200-, and 1000-μl pipettes and filter tips Microcentrifuge (Eppendorf, cat. no. 5424) Scientific Industries Vortex-Genie 2 (Fisher, cat. no. 50–728-002) Fisherbrand 0.2 ml PCR Tube Strips (Fisher, cat. no. 14–230-215) Fisherbrand Standard Mini-Centrifuge (Fisher, cat. no. S67601B) C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module (Bio-Rad, cat. no. 1851196) Thermo Scientific Owl EasyCast B1A Mini Gel Electrophoresis Systems (Fisher, cat no. 09–528-110) PowerPac Basic Power Supply (Bio-Rad, cat. no. 1645050) Imaging system with UV lamp to visualize Ethidium Bromide-bound DNA (e.g., GelDoc Go Gel Imaging System with Image Lab Touch Software [Bio-Rad, cat. no. 12009077], or AlphaImager HP Imaging System [Cell Biosciences, cat. no. 92–13823-00]) Razor blades (Fisher, cat. no. 12640) NanoDrop Microvolume Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000) Set up a Master Mix of multiple 50 μl volume PCRs using pHB1 as template, and oligonucleotides HB42 and HB154 ( Table 3 ) as primers, to generate large quantities of the erm-bar DNA ( Fig. 2A ) as follows: Because we will be working with a Master Mix (MM) format, volumes will be given for 9 reactions (8 reactions and 1 additional). ..

    Spectrophotometry:

    Article Title: Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions
    Article Snippet: .. Nuclease-free Water (IDT, cat. no. 11–05-01–04) Phusion Hot Start Flex 2X Master Mix (NEB, cat. no. M0536L) Custom DNA oligonucleotides (IDT, cat. no. n/a) 1X TE (10 mM Tris-Cl, 0.1 mM EDTA, pH 8.0; IDT, cat. no. 11–05-02–04) E. coli NEBα/pHB1 (MJM3287; Addgene Plasmid #204668, Table 1 ) QIAprep Spin Miniprep Kit (QIAgen, cat. no. 27106) Gel Loading Dye, Purple (6X; NEB, cat. no. B7024S) High-resolution Agarose, for Molecular Biology (Sigma-Aldrich, cat. no. A4718–25G) 50X TAE (see recipe) Ethidium Bromide (EtBr), 10 mg/ml (20,000X, see recipe; Sigma-Aldrich, cat. no. E7637) 1 kb DNA Ladder (NEB, cat. no. N3232) QIAquick Gel Extraction Kit (QIAgen, cat. no. 28706) Isopropanol (needed during gel extraction; Sigma-Aldrich, cat. no. 190764) Sodium acetate (NaOAc), 3 M, pH 5.0 (see recipe; Sigma-Aldrich, cat. no. 32319) Acetic Acid, Glacial (J. T. Baker, cat. no. 952202) 1.7 ml MaxyClear Snaplock microcentrifuge tube(s) (Corning Axygen, cat. No. MCT-175-C) 10-, 200-, and 1000-μl pipettes and filter tips Microcentrifuge (Eppendorf, cat. no. 5424) Scientific Industries Vortex-Genie 2 (Fisher, cat. no. 50–728-002) Fisherbrand 0.2 ml PCR Tube Strips (Fisher, cat. no. 14–230-215) Fisherbrand Standard Mini-Centrifuge (Fisher, cat. no. S67601B) C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module (Bio-Rad, cat. no. 1851196) Thermo Scientific Owl EasyCast B1A Mini Gel Electrophoresis Systems (Fisher, cat no. 09–528-110) PowerPac Basic Power Supply (Bio-Rad, cat. no. 1645050) Imaging system with UV lamp to visualize Ethidium Bromide-bound DNA (e.g., GelDoc Go Gel Imaging System with Image Lab Touch Software [Bio-Rad, cat. no. 12009077], or AlphaImager HP Imaging System [Cell Biosciences, cat. no. 92–13823-00]) Razor blades (Fisher, cat. no. 12640) NanoDrop Microvolume Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000) Set up a Master Mix of multiple 50 μl volume PCRs using pHB1 as template, and oligonucleotides HB42 and HB154 ( Table 3 ) as primers, to generate large quantities of the erm-bar DNA ( Fig. 2A ) as follows: Because we will be working with a Master Mix (MM) format, volumes will be given for 9 reactions (8 reactions and 1 additional). ..

    Amplification:

    Article Title: UV Light Inhibited HRV1b Replication but Reduced Adherens Epithelial Junction and Antiviral Responses via SOCS1 in Human Respiratory Epithelial Cells
    Article Snippet: The qPCR plates were loaded into a C1000TM thermal cycler (BIO-RAD Laboratories, Hercules, CA, USA). .. The DNA was amplified using the BioRad CFX Maestro software version number 2.3, and the protocol was followed (105 °C, 30 min at 94 °C, 30 min at 50 °C, 2 min at 72 °C). .. The results of all the primers and the viral load (RV) were then analyzed by plotting the housekeeping genes (HPRT and RPL30) against each of the primers using GraphPad.

    Article Title: UV Light Inhibited HRV1b Replication but Reduced Adherens Epithelial Junction and Antiviral Responses via SOCS1 in Human Respiratory Epithelial Cells.
    Article Snippet: The qPCR plates were loaded into a C1000TM thermal cycler (BIO-RAD Laboratories, Hercules, CA, USA). .. The DNA was amplified using the BioRad CFX Maestro software version number 2.3, and the protocol was followed (105 ◦C, 30 min at 94 ◦C, 30 min at 50 ◦C, 2 min at 72 ◦C). .. The results of all the primers and the viral load (RV) were then analyzed by plotting the housekeeping genes (HPRT and RPL30) against each of the primers using GraphPad. https://doi.org/10.3390/v18030303

    Maestro Software:

    Article Title: UV Light Inhibited HRV1b Replication but Reduced Adherens Epithelial Junction and Antiviral Responses via SOCS1 in Human Respiratory Epithelial Cells
    Article Snippet: The qPCR plates were loaded into a C1000TM thermal cycler (BIO-RAD Laboratories, Hercules, CA, USA). .. The DNA was amplified using the BioRad CFX Maestro software version number 2.3, and the protocol was followed (105 °C, 30 min at 94 °C, 30 min at 50 °C, 2 min at 72 °C). .. The results of all the primers and the viral load (RV) were then analyzed by plotting the housekeeping genes (HPRT and RPL30) against each of the primers using GraphPad.

    Article Title: UV Light Inhibited HRV1b Replication but Reduced Adherens Epithelial Junction and Antiviral Responses via SOCS1 in Human Respiratory Epithelial Cells.
    Article Snippet: The qPCR plates were loaded into a C1000TM thermal cycler (BIO-RAD Laboratories, Hercules, CA, USA). .. The DNA was amplified using the BioRad CFX Maestro software version number 2.3, and the protocol was followed (105 ◦C, 30 min at 94 ◦C, 30 min at 50 ◦C, 2 min at 72 ◦C). .. The results of all the primers and the viral load (RV) were then analyzed by plotting the housekeeping genes (HPRT and RPL30) against each of the primers using GraphPad. https://doi.org/10.3390/v18030303

    DNA Amplification:


    Recombinant:


    other:

    Article Title: Mitochondrial transfer protects against cisplatin-induced hearing loss by fumarate-mediated activation of mitophagy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Phosphatase Inhibitor Cocktail 2 Sigma‒Aldrich Cat#P5726 Phosphatase Inhibitor Cocktail 3 Sigma‒Aldrich Cat#P0044 CM5 sensor chip Cytiva Cat#BR100530 Recombinant PPP1CB protein Sino Biological Cat#P14-20G Recombinant PPP1CB protein Sangon Cat#D621143 Critical commercial assays Reactive Oxygen Species Assay Kit Beyotime Cat#S0033S GreenNucTM Caspase-3 Assay Kit for Live Cells Beyotime Cat#C1168M BeyoClickTM EdU Cell Proliferation Kit with AF555 Beyotime Cat#C0075S Pierce BCA Protein Assay Kit Beyotime Cat#P0011 FastPure Cell/Tissue DNA Isolation Mini Kit Vazyme Cat#DC102-01 Mitophagy Detection Kit Dojindo Cat#MD01 EnzChek Phosphatase Assay Kit Thermo Fisher Scientific Cat#E12020 PierceTM Streptavidin Magnetic Beads Thermo Fisher Scientific Cat#88817 PureProteome Protein A/G Mix magnetic beads MeckMillpore Cat#LSKMAGAG02 Deposited data Bulk RNA-seq data files of SGNs This study GEO: GSE308431 Metabolomics data This study NMDR: PR003357 Experimental models: Cell lines Human: umbilical cord MSCs Jiangsu Renocell Biotech N/A Human: HEK293T cells ATCC Cat#CRL-3216; RRID: CVCL_0063 Rat: SGNs provided by Shandong Provincial ENT Hospital N/A Experimental models: Organisms/strains Mouse: C57BL/6J mice Vital River Laboratory Animal Technology Cat#219 Mouse: Ppp1cb-flox mice Gempharmatech Cat#T008169 Mouse: Pax2-Cre mice provided by Lin Gan, University of Rochester N/A Oligonucleotides Primers for qPCR, see Table S1 Sangon N/A Software and algorithms FlowJo, version 10.4 Tree Star www.flowjo.com GraphPad Prism, version 10.1.2 GraphPad Software www.graphpad.com Image Lab, version 6.0.1 Bio-Rad www.Bio-Radad.com ImageJ, version 1.53a National Institutes of Health ImageJ.net/ij/ R project R Core Team www.r-project.org Analyst 1.7.3 SCIEX www.sciex.com clusterProfiler v4.12.6 Bioconductor www.bioconductor.org Biacore Insight Evaluation 2.0 Cytiva www.cytiva.com MO.Affinity Analysis v.3.0.5 NanoTemper Technologies www.nanotempertech.com 20 Cell Reports 45, 118107, October 27, 2026 The 7-day period was considered one treatment cycle, and the mice were subjected to two consecutive cycles.

    Article Title: Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions
    Article Snippet: Nuclease-free Water (IDT, cat. no. 11–05-01–04) OneTaq Quick-Load 2X Master Mix with Standard Buffer (NEB, cat. no. M0486L) Custom DNA oligonucleotides (IDT, cat. no. n/a) 1X TE (10 mM Tris-Cl, 0.1 mM EDTA, pH 8.0; IDT, cat. no. 11–05-02–04) High-resolution Agarose, for Molecular Biology (Sigma-Aldrich, cat. no. A4718–25G) 50X TAE (see recipe) Ethidium Bromide, 10 mg/ml (20,000X, see recipe; Sigma-Aldrich, cat. no. E7637) 100 bp DNA Ladder (NEB, cat. no. N3231) Agencourt Ampure XP beads, 60 ml (Beckman Coulter, cat. no. A63881) Ethanol 200 Proof (100%)(Fisher, cat. no. 04–355-451) Quant-iT dsDNA Broad-range (BR) Assay Kit, 2–1000 ng (Invitrogen, cat. no. Q33130 ) 1.7 ml MaxyClear Snaplock microcentrifuge tube(s) (Corning Axygen, cat. No. MCT-175-C) 10-, 20-, 200-, 1000-μl pipettes and filter tips Microcentrifuge (Eppendorf, cat. no. 5424) Fisherbrand 0.2 ml PCR 8-Tube Strips (Fisher, cat. no. 14–230-215) Fisherbrand Standard Mini-Centrifuge (Fisher, cat. no. S67601B) PIPETMAN L Multichannel Pipettor, Model P8×10L (Gilson, cat. no. FA10013) C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module (Bio-Rad, cat. no. 1851196) Thermo Scientific Owl D3–14 Wide Gel Electrophoresis System (Fisher, cat. no. 09–528-128) PowerPac Basic Power Supply (Bio-Rad, cat. no. 1645050) Imaging system with UV lamp to visualize EtBr-bound DNA (e.g., GelDoc Go Gel Imaging System with Image Lab Touch Software [Bio-Rad, cat. no. 12009077], or AlphaImager HP Imaging System [Cell Biosciences, cat. no. 92–13823-00]) DynaMag-96 Side 96-well and strip tube magnet (Life Technologies, cat. no. 12331D) 96-well skirted V-bottom PCR microplate (Corning, cat. no. PCR-96-FS-C) 15-, 50-ml Centrifuge Tubes with CentriStar Cap (Corning, cat. no. 05–538-59A, 05–526B) Synergy Neo2 Multi-Mode Microplate Reader (Biotek, cat. no. NEO2SMB) Nunc 96-Well Optical Bottom Plates, Black (VWR, cat. no. 37000–550) Sequencing of the bar scar regions from each sample requires PCR amplification of the templates using One-Step Indexed Oligonucleotides ( Fig. 6A ).

    Nucleic Acid Electrophoresis:

    Article Title: Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions
    Article Snippet: .. Nuclease-free Water (IDT, cat. no. 11–05-01–04) Phusion Hot Start Flex 2X Master Mix (NEB, cat. no. M0536L) Custom DNA oligonucleotides (IDT, cat. no. n/a) 1X TE (10 mM Tris-Cl, 0.1 mM EDTA, pH 8.0; IDT, cat. no. 11–05-02–04) E. coli NEBα/pHB1 (MJM3287; Addgene Plasmid #204668, Table 1 ) QIAprep Spin Miniprep Kit (QIAgen, cat. no. 27106) Gel Loading Dye, Purple (6X; NEB, cat. no. B7024S) High-resolution Agarose, for Molecular Biology (Sigma-Aldrich, cat. no. A4718–25G) 50X TAE (see recipe) Ethidium Bromide (EtBr), 10 mg/ml (20,000X, see recipe; Sigma-Aldrich, cat. no. E7637) 1 kb DNA Ladder (NEB, cat. no. N3232) QIAquick Gel Extraction Kit (QIAgen, cat. no. 28706) Isopropanol (needed during gel extraction; Sigma-Aldrich, cat. no. 190764) Sodium acetate (NaOAc), 3 M, pH 5.0 (see recipe; Sigma-Aldrich, cat. no. 32319) Acetic Acid, Glacial (J. T. Baker, cat. no. 952202) 1.7 ml MaxyClear Snaplock microcentrifuge tube(s) (Corning Axygen, cat. No. MCT-175-C) 10-, 200-, and 1000-μl pipettes and filter tips Microcentrifuge (Eppendorf, cat. no. 5424) Scientific Industries Vortex-Genie 2 (Fisher, cat. no. 50–728-002) Fisherbrand 0.2 ml PCR Tube Strips (Fisher, cat. no. 14–230-215) Fisherbrand Standard Mini-Centrifuge (Fisher, cat. no. S67601B) C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module (Bio-Rad, cat. no. 1851196) Thermo Scientific Owl EasyCast B1A Mini Gel Electrophoresis Systems (Fisher, cat no. 09–528-110) PowerPac Basic Power Supply (Bio-Rad, cat. no. 1645050) Imaging system with UV lamp to visualize Ethidium Bromide-bound DNA (e.g., GelDoc Go Gel Imaging System with Image Lab Touch Software [Bio-Rad, cat. no. 12009077], or AlphaImager HP Imaging System [Cell Biosciences, cat. no. 92–13823-00]) Razor blades (Fisher, cat. no. 12640) NanoDrop Microvolume Spectrophotometer (ThermoFisher Scientific, cat. no. ND-2000) Set up a Master Mix of multiple 50 μl volume PCRs using pHB1 as template, and oligonucleotides HB42 and HB154 ( Table 3 ) as primers, to generate large quantities of the erm-bar DNA ( Fig. 2A ) as follows: Because we will be working with a Master Mix (MM) format, volumes will be given for 9 reactions (8 reactions and 1 additional). ..



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