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user enzyme mix  (New England Biolabs)


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    Structured Review

    New England Biolabs user enzyme mix
    User Enzyme Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 3744 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/user/USER+Enzyme/pm42914465-186-14-17
    Average 99 stars, based on 3744 article reviews
    user enzyme mix - by Bioz Stars, 2026-11
    99/100 stars

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    Related Articles

    Sequencing:

    Article Title: Ancient East Asian dog lineage is revealed by genome of ancient Korean dogs
    Article Snippet: We used Illumina iSeq 100 reads to assess DNA damage patterns. .. For genome sequencing, we treated the DNA with the USER (Uracil-Specific Excision Reagent) Enzyme (New England Biolabs) to remove uracil and reconstructed the DNA libraries. .. Paired-end sequencing (2 × 150 bp) was performed on the Illumina NovaSeq 6000 platform ( ).

    Amplification:

    Article Title: A sequence motif for DNA double-strand break and telomere healing during programmed DNA elimination
    Article Snippet: .. Hairpins were digested with USER (NEB, Cat# M5505), and the DNA was amplified with Illumina TruSeq primers and barcodes. .. The libraries were sequenced with an Illumina NovaSeq 6000.

    Article Title: Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing
    Article Snippet: .. I suggest that the authors validate the results by adding a USER (NEB) enzyme step (a mixture of UDG and endonuclease VIII) immediately prior to amplification. ..

    Article Title: Asymmetrical end structures of leading and lagging telomeres in Saccharomyces cerevisiae dictate the nature of the end replication problem.
    Article Snippet: DNA used for sequencing was followed by end-repair with T4 DNA polymerase, Klenow fragment and T4 polynucleotide kinase (NEB) and second A-tailing with Klenow fragment exo− (NEB), allowing the ligation of distal hairpin adaptors with p7 Illumina primers (Phosphate-5′ GATCGGAAGAGCACACGTCUUUUU UUUAGACGTGTGCTCTTCCGATC*T). .. Finally, after USER (NEB) enzyme digestion, libraries were PCR amplified (Roche) and recovered. .. Sequencing was performed on the Illumina DNBSEQ-T7 (150 bp paired-end reads).

    Expressing:

    Article Title: CAS9 proteins including ligand-dependent inteins
    Article Snippet: A plasmid encoding the human codon-optimized Streptococcus pyogenes Cas9 nuclease with an NLS and 3×FLAG tag (Addgene plasmid 43861)5 was used as the wild-type Cas9 expression plasmid. .. Intein 37R3-2 was subcloned at the described positions into the wild-type Cas9 expression plasmid using USER (NEB M5505) cloning. sgRNA expression plasmids used in this study have been described previously11. .. Plasmid constructs generated in this work will be deposited with Addgene.

    Plasmid Preparation:

    Article Title: CAS9 proteins including ligand-dependent inteins
    Article Snippet: A plasmid encoding the human codon-optimized Streptococcus pyogenes Cas9 nuclease with an NLS and 3×FLAG tag (Addgene plasmid 43861)5 was used as the wild-type Cas9 expression plasmid. .. Intein 37R3-2 was subcloned at the described positions into the wild-type Cas9 expression plasmid using USER (NEB M5505) cloning. sgRNA expression plasmids used in this study have been described previously11. .. Plasmid constructs generated in this work will be deposited with Addgene.

    Cloning:

    Article Title: CAS9 proteins including ligand-dependent inteins
    Article Snippet: A plasmid encoding the human codon-optimized Streptococcus pyogenes Cas9 nuclease with an NLS and 3×FLAG tag (Addgene plasmid 43861)5 was used as the wild-type Cas9 expression plasmid. .. Intein 37R3-2 was subcloned at the described positions into the wild-type Cas9 expression plasmid using USER (NEB M5505) cloning. sgRNA expression plasmids used in this study have been described previously11. .. Plasmid constructs generated in this work will be deposited with Addgene.

    Derivative Assay:

    Article Title: Museum genomics links MC1R alleles to adaptive winter coat color polymorphism in the long-tailed weasel
    Article Snippet: .. Double-indexed genomic libraries were prepared using a custom protocol derived from , including the USER (Uracil-Specific Excision Reagent) enzyme (New England BioLabs) in the blunt-end repair step ( ). ..

    Binding Assay:

    Article Title: NAP-seq for full-length noncapped RNA sequencing.
    Article Snippet: The majority of the mammalian genome is transcribed into RNAs, most of which are noncapped RNAs (napRNAs) that not only regulate diverse biological processes through their functions as noncoding RNAs but also serve as processing products to delineate specific RNA biogenesis pathways.. However, due to their heterogeneous lengths, diverse terminal modifications and complex secondary structures, identifying these napRNAs poses substantial challenges.. Recently, we developed a napRNA sequencing technique (NAP-seq) to identify full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution.

    Reverse Transcription:

    Article Title: NAP-seq for full-length noncapped RNA sequencing.
    Article Snippet: The majority of the mammalian genome is transcribed into RNAs, most of which are noncapped RNAs (napRNAs) that not only regulate diverse biological processes through their functions as noncoding RNAs but also serve as processing products to delineate specific RNA biogenesis pathways.. However, due to their heterogeneous lengths, diverse terminal modifications and complex secondary structures, identifying these napRNAs poses substantial challenges.. Recently, we developed a napRNA sequencing technique (NAP-seq) to identify full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution.

    Ligation:

    Article Title: NAP-seq for full-length noncapped RNA sequencing.
    Article Snippet: The majority of the mammalian genome is transcribed into RNAs, most of which are noncapped RNAs (napRNAs) that not only regulate diverse biological processes through their functions as noncoding RNAs but also serve as processing products to delineate specific RNA biogenesis pathways.. However, due to their heterogeneous lengths, diverse terminal modifications and complex secondary structures, identifying these napRNAs poses substantial challenges.. Recently, we developed a napRNA sequencing technique (NAP-seq) to identify full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution.

    Polymerase Chain Reaction:

    Article Title: Asymmetrical end structures of leading and lagging telomeres in Saccharomyces cerevisiae dictate the nature of the end replication problem.
    Article Snippet: DNA used for sequencing was followed by end-repair with T4 DNA polymerase, Klenow fragment and T4 polynucleotide kinase (NEB) and second A-tailing with Klenow fragment exo− (NEB), allowing the ligation of distal hairpin adaptors with p7 Illumina primers (Phosphate-5′ GATCGGAAGAGCACACGTCUUUUU UUUAGACGTGTGCTCTTCCGATC*T). .. Finally, after USER (NEB) enzyme digestion, libraries were PCR amplified (Roche) and recovered. .. Sequencing was performed on the Illumina DNBSEQ-T7 (150 bp paired-end reads).

    Purification:

    Article Title: Sequencing DNA methylation and hydroxymethylation at co-occurring chromatin features
    Article Snippet: .. 15.5 μL tagmented DNA were first gap-filled with 8U of Phi29 DNA polymerase (NEB Cat No M0269) in Phi29 reaction buffer (1X Phi29 buffer, 200 μM dNTPs, 100 μg/ml albumin) by incubating at 30 °C for 30 min, followed by denaturation at 65 °C for 10 min. DNA was then purified with 0.9X SPRI beads and subjected to USER (NEB Cat No 5505) digestion (in 1X rCutSmart buffer, NEB B6004S) to cleave the original ME1U hairpin strand. ..



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