Recombinant:Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. Materials: RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Magnetic Beads:Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. Materials: RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Membrane:Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. Materials: RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Saline:Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. Materials: RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Polymerase Chain Reaction:Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Article Title: EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA
Article Snippet: .. Materials: RNase Zap TM (Thermo Fisher Scientific, cat. No. AM9780) Nuclease-free water Calcium chloride dihydrate, molecular biology grade ≥99% (Sigma Aldrich, cat. No. C3306) Tris hydrochloride ≥99.0% (Sigma Aldrich, cat. No. T5941) Sodium chloride (Millipre Sigma, cat. No. SX0420-1) Glycerol, molecular biology grade ≥99% (Sigma Aldrich, cat. No. G5516) Endonuclease V recombinant protein (New England Biolabs, cat. No. M0305S) Diluent C solution (New England Biolabs, cat. No. M0305S) RNasin® Plus RNase Inhibitor (Promega, cat. No. N2611) Anti-MBP Magnetic Beads (New England Biolabs, cat. No. E8037S) Costar® Spin-X® Centrifuge Tube Filters, 0.22 μm pore, cellulose acetate membrane (Corning, cat. No. 8161) Monarch® RNA Cleanup Kit, 10μg capacity (New England Biolabs, cat. No. T2030S) Phosphate-Buffered Saline (PBS), 10X, pH 7.4, RNase-free (Thermo Fisher Scientific, cat. No. AM9624) Sodium acetate anhydrous, molecular biology grade, ≥99% (Sigma Aldrich, cat. No. S2889) Acetic acid, glacial, ≥99% (Sigma Aldrich, cat. No. A6283) Glycogen, RNA grade, 20 mg/mL (Thermo Fisher Scientific, cat. No. R0551) Ethanol, anhydrous, 200 Proof (Decon Labs, cat. No. 2701) Agilent 6000 RNA Pico Assay Kit (Agilent, cat. No. 5067-1514) Nuclease-free filter pipet tips Nuclease-free 0.25 mL PCR tubes Nuclease-free 1.5 mL microcentrifuge tubes DynaMagTM−2 Magnetic Stand (Thermo Fisher Scientific 12321D) Rotary shaker incubator Thermal cycler −20 °C freezer −80 °C ultrafreezer Refrigerated microcentrifuge Agilent 2100 Bioanalyzer instrument EndoVIPER Pulldown list-behavior=enumerated prefix-word= mark-type=decimal max-label-size=0 Prepare an EndoV dilution in “diluent C” (NEB). ..
Lambda DNA Preparation:Article Title: Using proteases to control star activity of restriction enzymes
Article Snippet: .. In this example, restriction endonuclease EcoRI, Diluent C, proteinase K, 6× STOP solution, and lambda DNA (substrate) were purchased from New England Biolabs. ..
Article Title: Using proteases to control restriction enzyme activity
Article Snippet: .. In this example, restriction endonuclease EcoRI, Diluent C, proteinase K, 6× STOP solution, and lambda DNA (substrate) were purchased from New England Biolabs. ..
other:
Binding Assay:Article Title: Spatial Visualization of A-to-I Editing in Cells Using Endonuclease V Immunostaining Assay (EndoVIA)
Article Snippet: .. For EndoV binding studies, varying amounts of EndoV (New England BioLabs) diluted in Diluent C (New England BioLabs) were combined with 0.4 pmol of the respective glyoxalated RNA A or RNA I targets in a final volume of 20 μL and incubated at room temperature for 30 minutes. .. Samples were then loaded into standard glass capillaries and MST was performed using a Nanotemper Monolith NT.115 Instrument.
Incubation:Article Title: Spatial Visualization of A-to-I Editing in Cells Using Endonuclease V Immunostaining Assay (EndoVIA)
Article Snippet: .. For EndoV binding studies, varying amounts of EndoV (New England BioLabs) diluted in Diluent C (New England BioLabs) were combined with 0.4 pmol of the respective glyoxalated RNA A or RNA I targets in a final volume of 20 μL and incubated at room temperature for 30 minutes. .. Samples were then loaded into standard glass capillaries and MST was performed using a Nanotemper Monolith NT.115 Instrument.
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