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nebnext ultra ii end prep reaction buffer  (New England Biolabs)


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    Structured Review

    New England Biolabs nebnext ultra ii end prep reaction buffer
    Nebnext Ultra Ii End Prep Reaction Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 98/100, based on 929 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/nebnext+ultra+ii+end+prep+reaction+buffer/NEBNext+Ultra+II+Non/pm41590694-86-10-10
    Average 98 stars, based on 929 article reviews
    nebnext ultra ii end prep reaction buffer - by Bioz Stars, 2026-10
    98/100 stars

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    Incubation:

    Article Title: RECAP-seq: restriction enzyme-based CpG-methylated fragment amplification for early cancer detection
    Article Snippet: Reactions were incubated at 60 °C for 1 h. Size selection of digested fragments was performed using a 1X volume of AMPure XP beads (Beckman Coulter) at room temperature for 1 h, and the supernatant was further purified with an Oligo Clean & Concentrator (Zymo Research), eluting in 25 μL of nuclease-free water. .. Fragment ends were repaired and A-tailed by adding 3.5 μL of NEBNext Ultra II End Prep Reaction Buffer and 1.5 μL of NEBNext Ultra II End Prep Enzyme Mix (New England Biolabs), followed by incubation at 20 °C for 30 min and 65 °C for 30 min. Adapter ligation was carried out by adding 15 μL of NEBNext Ultra II Ligation Master Mix, 0.5 μL of NEBNext Ligation Enhancer, and 1.25 μL of Nextera adapter (0.6 μM), then incubating at 20 °C for 15 min. For clinical samples, an additional incubation at 45 °C for 30 min and 50 °C for 30 min was performed to maximize ligation efficiency . ..

    Article Title: RECAP-seq: restriction enzyme-based CpG-methylated fragment amplification for early cancer detection.
    Article Snippet: Reactions were incubated at 60 °C for 1 h. Size selection of digested fragments was performed using a 1X volume of AMPure XP beads (Beckman Coulter) at room temperature for 1 h, and the supernatant was further purified with an Oligo Clean & Concentrator (Zymo Research), eluting in 25 μL of nuclease-free water. .. Fragment ends were repaired and A-tailed by adding 3.5 μL of NEBNext Ultra II End Prep Reaction Buffer and 1.5 μL of NEBNext Ultra II End Prep Enzyme Mix (New England Biolabs), followed by incubation at 20 °C for 30 min and 65 °C for 30 min. Adapter ligation was carried out by adding 15 μL of NEBNext Ultra II Ligation Master Mix, 0.5 μL of NEBNext Ligation Enhancer, and 1.25 μL of Nextera adapter (0.6 μM), then incubating at 20 °C for 15 min. For clinical samples, an additional incubation at 45 °C for 30 min and 50 °C for 30 min was performed to maximize ligation efficiency63. ..

    Adapter Ligation:

    Article Title: RECAP-seq: restriction enzyme-based CpG-methylated fragment amplification for early cancer detection
    Article Snippet: Reactions were incubated at 60 °C for 1 h. Size selection of digested fragments was performed using a 1X volume of AMPure XP beads (Beckman Coulter) at room temperature for 1 h, and the supernatant was further purified with an Oligo Clean & Concentrator (Zymo Research), eluting in 25 μL of nuclease-free water. .. Fragment ends were repaired and A-tailed by adding 3.5 μL of NEBNext Ultra II End Prep Reaction Buffer and 1.5 μL of NEBNext Ultra II End Prep Enzyme Mix (New England Biolabs), followed by incubation at 20 °C for 30 min and 65 °C for 30 min. Adapter ligation was carried out by adding 15 μL of NEBNext Ultra II Ligation Master Mix, 0.5 μL of NEBNext Ligation Enhancer, and 1.25 μL of Nextera adapter (0.6 μM), then incubating at 20 °C for 15 min. For clinical samples, an additional incubation at 45 °C for 30 min and 50 °C for 30 min was performed to maximize ligation efficiency . ..

    Article Title: RECAP-seq: restriction enzyme-based CpG-methylated fragment amplification for early cancer detection.
    Article Snippet: Reactions were incubated at 60 °C for 1 h. Size selection of digested fragments was performed using a 1X volume of AMPure XP beads (Beckman Coulter) at room temperature for 1 h, and the supernatant was further purified with an Oligo Clean & Concentrator (Zymo Research), eluting in 25 μL of nuclease-free water. .. Fragment ends were repaired and A-tailed by adding 3.5 μL of NEBNext Ultra II End Prep Reaction Buffer and 1.5 μL of NEBNext Ultra II End Prep Enzyme Mix (New England Biolabs), followed by incubation at 20 °C for 30 min and 65 °C for 30 min. Adapter ligation was carried out by adding 15 μL of NEBNext Ultra II Ligation Master Mix, 0.5 μL of NEBNext Ligation Enhancer, and 1.25 μL of Nextera adapter (0.6 μM), then incubating at 20 °C for 15 min. For clinical samples, an additional incubation at 45 °C for 30 min and 50 °C for 30 min was performed to maximize ligation efficiency63. ..

    Ligation:

    Article Title: RECAP-seq: restriction enzyme-based CpG-methylated fragment amplification for early cancer detection
    Article Snippet: Reactions were incubated at 60 °C for 1 h. Size selection of digested fragments was performed using a 1X volume of AMPure XP beads (Beckman Coulter) at room temperature for 1 h, and the supernatant was further purified with an Oligo Clean & Concentrator (Zymo Research), eluting in 25 μL of nuclease-free water. .. Fragment ends were repaired and A-tailed by adding 3.5 μL of NEBNext Ultra II End Prep Reaction Buffer and 1.5 μL of NEBNext Ultra II End Prep Enzyme Mix (New England Biolabs), followed by incubation at 20 °C for 30 min and 65 °C for 30 min. Adapter ligation was carried out by adding 15 μL of NEBNext Ultra II Ligation Master Mix, 0.5 μL of NEBNext Ligation Enhancer, and 1.25 μL of Nextera adapter (0.6 μM), then incubating at 20 °C for 15 min. For clinical samples, an additional incubation at 45 °C for 30 min and 50 °C for 30 min was performed to maximize ligation efficiency . ..

    Article Title: RECAP-seq: restriction enzyme-based CpG-methylated fragment amplification for early cancer detection.
    Article Snippet: Reactions were incubated at 60 °C for 1 h. Size selection of digested fragments was performed using a 1X volume of AMPure XP beads (Beckman Coulter) at room temperature for 1 h, and the supernatant was further purified with an Oligo Clean & Concentrator (Zymo Research), eluting in 25 μL of nuclease-free water. .. Fragment ends were repaired and A-tailed by adding 3.5 μL of NEBNext Ultra II End Prep Reaction Buffer and 1.5 μL of NEBNext Ultra II End Prep Enzyme Mix (New England Biolabs), followed by incubation at 20 °C for 30 min and 65 °C for 30 min. Adapter ligation was carried out by adding 15 μL of NEBNext Ultra II Ligation Master Mix, 0.5 μL of NEBNext Ligation Enhancer, and 1.25 μL of Nextera adapter (0.6 μM), then incubating at 20 °C for 15 min. For clinical samples, an additional incubation at 45 °C for 30 min and 50 °C for 30 min was performed to maximize ligation efficiency63. ..

    Formalin-fixed Paraffin-Embedded:

    Article Title: Structural variation in 1,019 diverse humans based on long-read sequencing.
    Article Snippet: A DNA amount of 3 μg as input material was transferred into a 0.2-ml thin-walled PCR tube and the total volume was adjusted to 48 μl with nuclease-free water (Thermo Fisher, AM9937). .. DNA fragments were repaired and end-prepped as follows: 3.5 μl of NEBNext FFPE DNA Repair Buffer, 2 μl of NEBNext FFPE DNA Repair Mix, 3.5 μl of NEBNext Ultra II End Prep Reaction Buffer and 3 μl NEBNext Ultra II End Prep Enzyme Mix were added to each tube. ..

    Article Title: Multi-pathogen wastewater surveillance in Malawi: An assessment of culture-based, RT-PCR, and long-read metagenomics methods with multiple ongoing outbreaks.
    Article Snippet: .. End-repair was performed using NEBNext Ultra II End prep reaction buffer, Ultra II End prep Enzyme mix (NEB, E7546), NEBNext FFPE DNA Repair Mix (NEB, cat #M6630), and NEB NEXT FFPE DNA repair buffer. ..

    Control:

    Article Title: Nanoplastic exposure affects the intestinal microbiota of adult Drosophila flies.
    Article Snippet: .. The reaction mix included 49 μL of the pooled DNA library, 1 μL of a DNA control sample, 7 μL of NEBNext Ultra II End Prep Reaction Buffer (New England Biolabs), and 3 μL of NEBNext Ultra II End Prep Enzyme Mix (New England Biolabs). .. After the EndPrep reaction, the DNA was purified using the AMPure XP bead system (Beckman Coulter, Inc.), with a bead-to-sample volume ratio of 1:1.

    Transferring:

    Article Title: An optimized protocol to detect high‐throughput DNA methylation from custom targeted sequences on 96 samples simultaneously
    Article Snippet: .. End repair/dA‐tailing ▢ Set the heated lid of the thermocycler to 75 °C ▢ Transfer 50 μL of the sheared DNA (or sheared DNA Controls) in a well plate recommended for the thermocycler ▢ On ice, add the following components to sheared DNA: ▢ NEBNext Ultra II End prep Reaction Buffer: 7 μL ▢ NEBNext Ultra II End prep Enzyme Mix: 3 μL Total volume: 60 μL ▢ Gently pipette the entire volume up and down at least 10 times to mix thoroughly ▢ Perform a quick spin to collect all liquid from the sides of the well plate The presence of a small amount of bubbles will not interfere with performance ▢ Place the plate in a thermocycler and run the following program: 2.2. .. Methylated adaptor ligation ▢ On ice, add the following components to repaired DNA: ▢ NEBNext ® EM‐seqTM Adaptor: 2.5 μL Total volume: 62.5 μL ▢ Gently pipette the entire volume up and down at least 10 times to mix thoroughly ▢ Perform a quick spin to collect all liquid from the sides of the well plate ▢ On ice, add the following components to repaired DNA: ▢ NEBNext ® Ligation Enhancer: 1 μL ▢ NEBNext ® UltraTM II Ligation Master Mix: 30 μL Total volume: 93.5 μL The Ligation Master Mix is viscous.

    Purification:

    Article Title: Artificial Neural Network Elucidates the Role of Transport Proteins in Rhodopseudomonas palustris CGA009 During Lignin Breakdown Product Catabolism.
    Article Snippet: .. Subsequently, endprep reaction was performed by adding 7 μL of NEBNext Ultra II End Prep Reaction Buffer and 3 μL of NEBNext Ultra II End Prep Enzyme Mix into 50 μL purified cDNA. .. Endprep reaction was incubated at 20 ◦C 30 min and 65 ◦C 20 min. Adaptor ligation reaction was then performed by adding 1 μL of NEBNext Ligation Enhancer, 30 μL of NEBNext Ultra II Ligation Master Mix, and 2.5 μL of NEBNext Adaptor, diluted to 0.5 μM in Adaptor Dilution Buffer.



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