nebnext da tailing module  (New England Biolabs)


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  • 99
    Name:
    NEBNext dA Tailing Module
    Description:
    NEBNext dA Tailing Module 100 rxns
    Catalog Number:
    E6053L
    Price:
    408
    Size:
    100 rxns
    Category:
    DNA Template Preparation for PCR
    Score:
    85
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    Structured Review

    New England Biolabs nebnext da tailing module
    NEBNext dA Tailing Module
    NEBNext dA Tailing Module 100 rxns
    https://www.bioz.com/result/nebnext da tailing module/product/New England Biolabs
    Average 99 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    nebnext da tailing module - by Bioz Stars, 2019-10
    99/100 stars

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    Related Articles

    Amplification:

    Article Title: Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    Article Snippet: Whole genome amplified (Repli-g Kit, Qiagen) Sal1 reference genomic DNA was sheared to an average size of 200 bp using an S-series Covaris Adaptive Focused Acoustic machine (Covaris). .. Samples underwent end-repair and dA-tailing (New England Biolabs) followed by ligation of Illumina TruSeq v. 3-style Y-adaptors carrying the T7 promoter sequence (Table S1).

    Article Title: Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases
    Article Snippet: The bound fragments (the 5´- and 3´-fragments of the amplified ds cDNAs carrying a terminal biotin) were thoroughly washed and their ends repaired using the NEBNext End Repair system (New England Biolabs). .. The polished fragments were then A-tailed using the NEB Next dA-tailing module (New England Biolabs).

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA. .. Purification of the fragments when necessary was performed with QIAquick PCR Purification Kit (Qiagen).

    Article Title: Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods
    Article Snippet: Paragraph title: Illumina amplicon sequencing of 16S rRNA gene (IA rrn ) ... End repaired amplicons were purified with a Qiaquick PCR purification kit (Qiagen, GmbH) and a single adenine was added to the 3′ ends using the NEBNext dA-Tailing Module (New England Biolabs Inc.).

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions. .. After purification, adaptors were ligated (Adaptor-Oligo 1: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' , Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3') by using 1x NEBnext Quick Ligation Buffer (NEB), 10x excess of DNA Adaptors, 5 µl Quick T4 DNA Ligase (NEB) at 50 µl total volume.

    Article Title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
    Article Snippet: Amplified cDNA from Round B was purified using AMPure XP beads (Beckman Coulter, Brea, CA), and 1 μg DNA was used as input into Oxford Nanopore Genomic DNA MAP-003 Kits (Chik1, Ebola1) or MAP-004 Kits (HepC1, Ebola2) for generation of MinION Oxford Nanopore-compatible libraries [ , ]. .. Briefly, the steps include: (1) addition of control lambda phage DNA, (2) end-repair with the NEBNext End Repair Module, (3) 1× AMPure purification, (4) dA-tailing with the NEBNext dA-tailing Module, (5) ligation to protein-linked adapters HP/AMP (Oxford Nanopore Technologies, Oxford, UK) using the NEBNext QuickLigation Module for 10 min at room temperature, (6) purification of ligated libraries using magnetic His-Tag Dynabeads (Life Technologies), and (7) elution in 25 μL buffer (Oxford Nanopore Technologies).

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: Paragraph title: Amplicon library preparation and Oxford Nanopore sequencing ... Briefly, a total of 850 ng (spike-in) and 1 μg (mixed heads) in 80 μL was end repaired using NEBNext End Repair Module (New England Biolabs, Cat No: E6050) and followed by dA tailing using NEBNext dA Tailing Module (New England Biolabs, Cat No: E6053).

    Article Title: A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster
    Article Snippet: The sheared DNA was then end-repaired and ligated using the NEBNext Ultra 2 end-repair and dA-tailing kit (New England Biolabs, Ipswich MA) according to the manufacturer’s instructions. .. The sheared DNA was then end-repaired and ligated using the NEBNext Ultra 2 end-repair and dA-tailing kit (New England Biolabs, Ipswich MA) according to the manufacturer’s instructions.

    Synthesized:

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: The second-strand cDNA was synthesized with 100 mM dATP, dCTP, dGTP and dUTP in the presence of RNase H, E. coli DNA polymerase I and DNA ligase (Invitrogen). .. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module.

    Construct:

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: Libraries were constructed using 1ug of genomic DNA in 100ul volume and sheared into fragments of approximately 300 base pairs in a Covaris plate with E210 system (Covaris, Inc. Woburn, MA). .. A-tailing was performed in a total reaction volume of 60ul containing end-repaired DNA, 6ul 10− uffer, 3ul Klenow Fragment (NEBNext dA-Tailing Module; Cat. No. E6053L) and H2 O followed by incubation at 37°C for 30 minutes.

    Article Title: Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Article Snippet: DNA was fragmented to 250 bp using the Covaris Sonicator and purified by Zymo DNA Clean & Concentrator Column Kit (Genesee Cat # 11-303 or 11-306) according to manufacturer’s instructions. .. Barcoded next-generation sequencing libraries were constructed using the NEBNext end repair (NEB, E6050L), dA-tailing module (NEB, E6053L) and quick ligation module (NEB, E6056L). .. Libraries were PCR amplified with NEBNext HiFi 2x PCRmix (NEB, M0541L).

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions. .. After purification, adaptors were ligated (Adaptor-Oligo 1: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' , Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3') by using 1x NEBnext Quick Ligation Buffer (NEB), 10x excess of DNA Adaptors, 5 µl Quick T4 DNA Ligase (NEB) at 50 µl total volume.

    Article Title: Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
    Article Snippet: Two sequencing libraries were constructed using the MAP-SQK006 reagents kit. .. The DNA was A-tailed using the NEBNext dA Tailing Module (E6053, NEB) by mixing 25 μl eluted DNA with 2 μl Klenow Fragment (3′-5′ exo− ) and 3 μl 10× NEBNext dA-Tailing Reaction Buffer.

    Concentration Assay:

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: DNA concentration was determined by pico green assays while DNA integrity was determined through Agilent Bioanalyzer traces and agarose gels. .. A-tailing was performed in a total reaction volume of 60ul containing end-repaired DNA, 6ul 10− uffer, 3ul Klenow Fragment (NEBNext dA-Tailing Module; Cat. No. E6053L) and H2 O followed by incubation at 37°C for 30 minutes.

    Article Title: Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
    Article Snippet: 1 μl of each library was used to measure the concentration of the eluate on a Qubit2.0 Fluorometer indicating 750 ng and 630 ng DNA post elution. .. The DNA was A-tailed using the NEBNext dA Tailing Module (E6053, NEB) by mixing 25 μl eluted DNA with 2 μl Klenow Fragment (3′-5′ exo− ) and 3 μl 10× NEBNext dA-Tailing Reaction Buffer.

    Article Title: Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
    Article Snippet: The DNA concentration was measured with a Qubit fluorometer and an aliquot was diluted up to 80 µL. .. DNA A-tailing was performed with the NEBNext dA-Tailing module (NEB).

    Real-time Polymerase Chain Reaction:

    Article Title: De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
    Article Snippet: Fragments were end-repaired using the NEBNext EndRepair Module (New England Biolabs, Ipswich, MA, USA) and A-tailed with the NEBNext dA-Tailing Module. .. Ligation products were purified with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA, USA).

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module. .. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) as described followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems).

    Article Title: Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Article Snippet: Barcoded next-generation sequencing libraries were constructed using the NEBNext end repair (NEB, E6050L), dA-tailing module (NEB, E6053L) and quick ligation module (NEB, E6056L). .. Libraries were PCR amplified with NEBNext HiFi 2x PCRmix (NEB, M0541L).

    Article Title: RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics
    Article Snippet: A “with-bead” protocol was used for dA-tailing, end repair and adapter ligation (NEB) using “PCR-free” barcoded sequencing adaptors (Bioo Scientific, similar to the method of Korarewa et al . .. A “with-bead” protocol was used for dA-tailing, end repair and adapter ligation (NEB) using “PCR-free” barcoded sequencing adaptors (Bioo Scientific, similar to the method of Korarewa et al .

    cDNA Library Assay:

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions. .. After purification, adaptors were ligated (Adaptor-Oligo 1: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' , Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3') by using 1x NEBnext Quick Ligation Buffer (NEB), 10x excess of DNA Adaptors, 5 µl Quick T4 DNA Ligase (NEB) at 50 µl total volume.

    Incubation:

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: The fragmented DNA was end-repaired in 90ul total reaction volume containing sheared DNA, 9ul 10− buffer, 5ul END Repair Enzyme Mix and H2O (NEBNext End-Repair Module; Cat. No. E6050L) and then incubated at 20°C for 30 minutes. .. A-tailing was performed in a total reaction volume of 60ul containing end-repaired DNA, 6ul 10− uffer, 3ul Klenow Fragment (NEBNext dA-Tailing Module; Cat. No. E6053L) and H2 O followed by incubation at 37°C for 30 minutes. .. Illumina multiplex adapter ligation (NEBNext Quick Ligation Module Cat. No. E6056L) was performed in a total reaction volume of 90ul containing 18ul 5− buffer, 5ul ligase, 0.5ul 100uM adaptor and H2O at room temperature for 30 minutes.

    Article Title: On site DNA barcoding by nanopore sequencing
    Article Snippet: Only in the case of protocol 1, the purified amplicons were then processed using the NEBNext dA-tailing module (New England Biolabs), these steps were skipped in protocol 2 and 3. .. Amplicons from the three protocols were used to prepare sequencing libraries using the ONT DNA Sequencing kits (SQK-MAP004, SQK-MAP005, and SQK-MAP006).

    Article Title: Candidate genes responsible for early key events of phenobarbital-promoted mouse hepatocellular tumorigenesis based on differentiation of regulating genes between wild type mice and humanized chimeric mice †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7tx00163k
    Article Snippet: Sonicated DNA was then end-repaired by incubation for 30 min at 20 °C using the NEBNext End Repair Module (NEB). .. The reaction mixture was purified using the Agencourt AMPure XP (Beckman Coulter), and subjected to 3′-dA tailing by incubation for 30 min at 37 °C using the NEBNext dA-Tailing Module (NEB). .. After purification as described above, linker ligation was performed by incubation in a reaction containing 2.5 μM linkers for 1 h at 20 °C using the NEBNext Ultra Ligation Module (NEB).

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: DNA was precipitated with 2 volumes of ethanol, 1/3 volumes of 7.5 M ammonium acetate and 20 µg glycogen with an overnight incubation at −20°C. .. Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions.

    Article Title: Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
    Article Snippet: After incubation the reaction was cleaned up using a 0.45× AMPure XP ratio (45 μl AMPure XP beads) and eluted in 26 μl water. .. The DNA was A-tailed using the NEBNext dA Tailing Module (E6053, NEB) by mixing 25 μl eluted DNA with 2 μl Klenow Fragment (3′-5′ exo− ) and 3 μl 10× NEBNext dA-Tailing Reaction Buffer.

    Article Title: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    Article Snippet: Following incubation, the treated DNA was purified using AMPure XP beads (Agencourt). .. Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs).

    Modification:

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: A-tailing was performed in a total reaction volume of 60ul containing end-repaired DNA, 6ul 10− uffer, 3ul Klenow Fragment (NEBNext dA-Tailing Module; Cat. No. E6053L) and H2 O followed by incubation at 37°C for 30 minutes. .. Illumina multiplex adapter ligation (NEBNext Quick Ligation Module Cat. No. E6056L) was performed in a total reaction volume of 90ul containing 18ul 5− buffer, 5ul ligase, 0.5ul 100uM adaptor and H2O at room temperature for 30 minutes.

    Article Title: RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics
    Article Snippet: A modified RNA-seq protocol (“DAFT-seq”, Chappell et al ., in preparation) was used to account for the extreme AT-content of the P . falciparum transcriptome. .. A “with-bead” protocol was used for dA-tailing, end repair and adapter ligation (NEB) using “PCR-free” barcoded sequencing adaptors (Bioo Scientific, similar to the method of Korarewa et al .

    Article Title: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    Article Snippet: Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs). .. Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs).

    Flow Cytometry:

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: Preparation of genomic DNA from kanR colonies was followed by ligation of standard adapters, P5A and P7A, containing Illumina flow-cell binding sites. .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA.

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: Briefly, a total of 850 ng (spike-in) and 1 μg (mixed heads) in 80 μL was end repaired using NEBNext End Repair Module (New England Biolabs, Cat No: E6050) and followed by dA tailing using NEBNext dA Tailing Module (New England Biolabs, Cat No: E6053). .. This reaction mixture was then purified using Agencourt AMPure XP (Beckman Coulter Inc., cat. no. A63880) beads and washed and eluted in nanopore supplied reagents in 25 μL ultrapure water.

    Ligation:

    Article Title: Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    Article Snippet: Whole genome amplified (Repli-g Kit, Qiagen) Sal1 reference genomic DNA was sheared to an average size of 200 bp using an S-series Covaris Adaptive Focused Acoustic machine (Covaris). .. Samples underwent end-repair and dA-tailing (New England Biolabs) followed by ligation of Illumina TruSeq v. 3-style Y-adaptors carrying the T7 promoter sequence (Table S1). .. The T7 ligated library was run on a 2% agarose gel and a band corresponding to 200 bp was cut and purified in 20 ul of TE buffer with MinElute spin columns (Qiagen).

    Article Title: Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases
    Article Snippet: 25 μl of the amplification product (i.e. half of the reaction) was immobilized on 20 μl streptavidin-coated beads (Dynabeads MyOne Streptavidin C1; Life / Invitrogen) and processed to a final sequencing library according to the previously published protocol [ ] with the difference that the SalI digestion and ADP2 ligation were performed separately with immobilization and three washes with 50 μl EBT in-between. .. The polished fragments were then A-tailed using the NEB Next dA-tailing module (New England Biolabs).

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: A-tailing was performed in a total reaction volume of 60ul containing end-repaired DNA, 6ul 10− uffer, 3ul Klenow Fragment (NEBNext dA-Tailing Module; Cat. No. E6053L) and H2 O followed by incubation at 37°C for 30 minutes. .. Illumina multiplex adapter ligation (NEBNext Quick Ligation Module Cat. No. E6056L) was performed in a total reaction volume of 90ul containing 18ul 5− buffer, 5ul ligase, 0.5ul 100uM adaptor and H2O at room temperature for 30 minutes.

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: End repair of fragmented DNA was performed using a NEBNext End Repair Module. .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA. .. The Phusion High-Fidelity PCR Master Mix was used for PCR enrichment of adapter-ligated DNA.

    Article Title: De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
    Article Snippet: Fragments were end-repaired using the NEBNext EndRepair Module (New England Biolabs, Ipswich, MA, USA) and A-tailed with the NEBNext dA-Tailing Module. .. Illumina adapters were added using the NEBNext Quick Ligation Module.

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: The second-strand cDNA was synthesized with 100 mM dATP, dCTP, dGTP and dUTP in the presence of RNase H, E. coli DNA polymerase I and DNA ligase (Invitrogen). .. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module. .. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) as described followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems).

    Article Title: On site DNA barcoding by nanopore sequencing
    Article Snippet: Only in the case of protocol 1, the purified amplicons were then processed using the NEBNext dA-tailing module (New England Biolabs), these steps were skipped in protocol 2 and 3. .. The adapter mix HPA consists of a linear double strand sequence and a hairpin sequence that links the positive and negative strand of each fragment to allow the sequencing of both strands (2D reads).

    Article Title: Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Article Snippet: DNA was fragmented to 250 bp using the Covaris Sonicator and purified by Zymo DNA Clean & Concentrator Column Kit (Genesee Cat # 11-303 or 11-306) according to manufacturer’s instructions. .. Barcoded next-generation sequencing libraries were constructed using the NEBNext end repair (NEB, E6050L), dA-tailing module (NEB, E6053L) and quick ligation module (NEB, E6056L). .. Libraries were PCR amplified with NEBNext HiFi 2x PCRmix (NEB, M0541L).

    Article Title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
    Article Snippet: Amplified cDNA from Round B was purified using AMPure XP beads (Beckman Coulter, Brea, CA), and 1 μg DNA was used as input into Oxford Nanopore Genomic DNA MAP-003 Kits (Chik1, Ebola1) or MAP-004 Kits (HepC1, Ebola2) for generation of MinION Oxford Nanopore-compatible libraries [ , ]. .. Briefly, the steps include: (1) addition of control lambda phage DNA, (2) end-repair with the NEBNext End Repair Module, (3) 1× AMPure purification, (4) dA-tailing with the NEBNext dA-tailing Module, (5) ligation to protein-linked adapters HP/AMP (Oxford Nanopore Technologies, Oxford, UK) using the NEBNext QuickLigation Module for 10 min at room temperature, (6) purification of ligated libraries using magnetic His-Tag Dynabeads (Life Technologies), and (7) elution in 25 μL buffer (Oxford Nanopore Technologies). .. Lambda phage DNA was not added during preparation of the Ebola2 sample library.

    Article Title: Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
    Article Snippet: The DNA was A-tailed using the NEBNext dA Tailing Module (E6053, NEB) by mixing 25 μl eluted DNA with 2 μl Klenow Fragment (3′-5′ exo− ) and 3 μl 10× NEBNext dA-Tailing Reaction Buffer. .. The reaction was incubated for 10 min at 37 °C in a G-Storm GS1 thermal cycler without heated lid.

    Article Title: RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics
    Article Snippet: The resulting cDNA was fragmented using a Covaris AFA sonicator. .. A “with-bead” protocol was used for dA-tailing, end repair and adapter ligation (NEB) using “PCR-free” barcoded sequencing adaptors (Bioo Scientific, similar to the method of Korarewa et al . .. After 2 rounds of SPRI clean-up the libraries were eluted in EB buffer and USER enzyme mix (NEB) was used to digest the second strand cDNA, generating directional libraries.

    Article Title: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    Article Snippet: Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs). .. Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs).

    Generated:

    Article Title: Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods
    Article Snippet: 16S rRNA gene amplicons were generated using DNA Free Sensitive Taq polymerase (Bioron, GMbH) and primers Ar915aF and Ar1386R by Kittelmann et al ., (2013) . .. End repaired amplicons were purified with a Qiaquick PCR purification kit (Qiagen, GmbH) and a single adenine was added to the 3′ ends using the NEBNext dA-Tailing Module (New England Biolabs Inc.).

    Activation Assay:

    Article Title: Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases
    Article Snippet: The polished fragments were then A-tailed using the NEB Next dA-tailing module (New England Biolabs). .. The dual-adaptor carrying products (STRT handle on one end and the ligated adaptor on the other) were then PCR amplified using 2 units of Phusion polymerase (Thermo Fisher Scientific / Finnzymes; Vantaa, Finland) in a 100 μl reaction (divided into two 50 μl reactions) containing 1 μM of forward primer (carrying the STRT handle fused to one of the Illumina adaptors; for sequence see ), 1 μM of reverse primer (encompassing the ligated adaptor sequence fused to the other Illumina adaptor; for sequence see ), 200 μM dNTPs in 1x Phusion HF buffer (Thermo Fisher Scientific / Finnzymes).

    Polymerase Chain Reaction:

    Article Title: Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    Article Snippet: Samples underwent end-repair and dA-tailing (New England Biolabs) followed by ligation of Illumina TruSeq v. 3-style Y-adaptors carrying the T7 promoter sequence (Table S1). .. The T7 ligated library was run on a 2% agarose gel and a band corresponding to 200 bp was cut and purified in 20 ul of TE buffer with MinElute spin columns (Qiagen).

    Article Title: Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases
    Article Snippet: The polished fragments were then A-tailed using the NEB Next dA-tailing module (New England Biolabs). .. The polished fragments were then A-tailed using the NEB Next dA-tailing module (New England Biolabs).

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: A-tailing was performed in a total reaction volume of 60ul containing end-repaired DNA, 6ul 10− uffer, 3ul Klenow Fragment (NEBNext dA-Tailing Module; Cat. No. E6053L) and H2 O followed by incubation at 37°C for 30 minutes. .. A-tailing was performed in a total reaction volume of 60ul containing end-repaired DNA, 6ul 10− uffer, 3ul Klenow Fragment (NEBNext dA-Tailing Module; Cat. No. E6053L) and H2 O followed by incubation at 37°C for 30 minutes.

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA. .. The Phusion High-Fidelity PCR Master Mix was used for PCR enrichment of adapter-ligated DNA.

    Article Title: De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
    Article Snippet: Paragraph title: Illumina PCR-free library preparation and sequencing ... Fragments were end-repaired using the NEBNext EndRepair Module (New England Biolabs, Ipswich, MA, USA) and A-tailed with the NEBNext dA-Tailing Module.

    Article Title: On site DNA barcoding by nanopore sequencing
    Article Snippet: DNA libraries were prepared from 1.5μg of the purified PCR products. .. Only in the case of protocol 1, the purified amplicons were then processed using the NEBNext dA-tailing module (New England Biolabs), these steps were skipped in protocol 2 and 3.

    Article Title: Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress
    Article Snippet: The RAD libraries for marker development were constructed as previously described [ , ]. .. Briefly, this procedure followed nine main steps: digesting gDNA with restriction enzyme Eco RI (New England BioLabs, or NEB, Ipswich, MA, USA); adding P1 adapters (Illumina, San Diego, CA, USA) to each digested fragment by T4 DNA ligase (NEB); pooling and shearing these fragments; purifying sheared DNA fragments using QIAquick PCR Purification kit; selecting 200- to 400-bp DNA fragments by agarose gel electrophoresis; repairing and flattening fragment ends using a Quick Blunting kit (NEB); adding the overhang (A 3′-dA) to these fragments by a dA-tailing module (NEB); adding P2 adapters (Illumina) to these fragments; and enriching tagged DNA by PCR-amplification. .. Sequencing was performed on an Illumina Hiseq2500 platform at Novogene Co. (Beijing, China), applying PE250 strategy according to the Illumina protocol.

    Article Title: Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods
    Article Snippet: 500 ng of each purified amplicon was then end repaired using the NEBNext End Repair Module (New England Biolabs Inc.). .. End repaired amplicons were purified with a Qiaquick PCR purification kit (Qiagen, GmbH) and a single adenine was added to the 3′ ends using the NEBNext dA-Tailing Module (New England Biolabs Inc.). .. Partial Truseq standard paired end Illumina adapters with 6 bp barcodes (Integrated DNA Technologies) were ligated to the adenylated amplicons using the Quick Ligation Kit (New England Biolabs Inc.) and resulting adapter-ligated amplicons were purified with a Qiaquick PCR purification kit (Qiagen, GmbH).

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions. .. After purification, adaptors were ligated (Adaptor-Oligo 1: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' , Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3') by using 1x NEBnext Quick Ligation Buffer (NEB), 10x excess of DNA Adaptors, 5 µl Quick T4 DNA Ligase (NEB) at 50 µl total volume.

    Article Title: A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster
    Article Snippet: The sheared DNA was then end-repaired and ligated using the NEBNext Ultra 2 end-repair and dA-tailing kit (New England Biolabs, Ipswich MA) according to the manufacturer’s instructions. .. Duplex Sequencing adapters, described previously , were ligated to the DNA library using the NEBNext Ultra 2 ligation kit (New England Biolabs, Ipswich MA) according to the manufacturer’s instructions.

    Article Title: RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics
    Article Snippet: The resulting cDNA was fragmented using a Covaris AFA sonicator. .. A “with-bead” protocol was used for dA-tailing, end repair and adapter ligation (NEB) using “PCR-free” barcoded sequencing adaptors (Bioo Scientific, similar to the method of Korarewa et al . .. After 2 rounds of SPRI clean-up the libraries were eluted in EB buffer and USER enzyme mix (NEB) was used to digest the second strand cDNA, generating directional libraries.

    Article Title: De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
    Article Snippet: Paragraph title: Illumina PCR-Free library preparation and sequencing ... Fragments were end-repaired using the NEBNext End Repair Module (New England Biolabs, Ipswich, MA, USA) and 3΄-adenylated with the NEBNext dA-Tailing Module (New England Biolabs).

    Sonication:

    Article Title: De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
    Article Snippet: DNA (1 ug) was sonicated to a 400 to 600 bp size range using a Covaris LE220 acoustic shearing device (Covaris, Woburn, MA, USA). .. Fragments were end-repaired using the NEBNext EndRepair Module (New England Biolabs, Ipswich, MA, USA) and A-tailed with the NEBNext dA-Tailing Module.

    Article Title: Candidate genes responsible for early key events of phenobarbital-promoted mouse hepatocellular tumorigenesis based on differentiation of regulating genes between wild type mice and humanized chimeric mice †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7tx00163k
    Article Snippet: Sonicated DNA was then end-repaired by incubation for 30 min at 20 °C using the NEBNext End Repair Module (NEB). .. The reaction mixture was purified using the Agencourt AMPure XP (Beckman Coulter), and subjected to 3′-dA tailing by incubation for 30 min at 37 °C using the NEBNext dA-Tailing Module (NEB).

    Article Title: A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster
    Article Snippet: The DNA was sonicated using a Covaris AFA S2 ultrasonicator (Covaris Inc., Woburn MA) with the following settings: Duty cycle: 10%; Intensity: 5; Cycles/burst: 100; Time: 15 s × 3. .. The sheared DNA was then end-repaired and ligated using the NEBNext Ultra 2 end-repair and dA-tailing kit (New England Biolabs, Ipswich MA) according to the manufacturer’s instructions.

    Article Title: De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
    Article Snippet: DNA (4.5 to 6 μg) was sonicated to a 100- to 1500-bp size range using a Covaris E210 sonicator (Covaris, Woburn, MA, USA). .. Fragments were end-repaired using the NEBNext End Repair Module (New England Biolabs, Ipswich, MA, USA) and 3΄-adenylated with the NEBNext dA-Tailing Module (New England Biolabs).

    Article Title: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    Article Snippet: Briefly, genomic DNA (2 μg) was sonicated using a Covaris instrument to an average molecular weight of 150 bp. .. Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs).

    Binding Assay:

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: Preparation of genomic DNA from kanR colonies was followed by ligation of standard adapters, P5A and P7A, containing Illumina flow-cell binding sites. .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA.

    Methylated DNA Immunoprecipitation:

    Article Title: Candidate genes responsible for early key events of phenobarbital-promoted mouse hepatocellular tumorigenesis based on differentiation of regulating genes between wild type mice and humanized chimeric mice †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7tx00163k
    Article Snippet: Paragraph title: MeDIP and HmeDIP (5mC and 5hmC immunoprecipitation) ... The reaction mixture was purified using the Agencourt AMPure XP (Beckman Coulter), and subjected to 3′-dA tailing by incubation for 30 min at 37 °C using the NEBNext dA-Tailing Module (NEB).

    DNA Extraction:

    Article Title: Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress
    Article Snippet: Paragraph title: DNA extraction, RAD libraries construction and sequencing ... Briefly, this procedure followed nine main steps: digesting gDNA with restriction enzyme Eco RI (New England BioLabs, or NEB, Ipswich, MA, USA); adding P1 adapters (Illumina, San Diego, CA, USA) to each digested fragment by T4 DNA ligase (NEB); pooling and shearing these fragments; purifying sheared DNA fragments using QIAquick PCR Purification kit; selecting 200- to 400-bp DNA fragments by agarose gel electrophoresis; repairing and flattening fragment ends using a Quick Blunting kit (NEB); adding the overhang (A 3′-dA) to these fragments by a dA-tailing module (NEB); adding P2 adapters (Illumina) to these fragments; and enriching tagged DNA by PCR-amplification.

    RNA Sequencing Assay:

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: Paragraph title: RNA-seq analysis ... Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module.

    Article Title: RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics
    Article Snippet: Paragraph title: RNA-seq ... A “with-bead” protocol was used for dA-tailing, end repair and adapter ligation (NEB) using “PCR-free” barcoded sequencing adaptors (Bioo Scientific, similar to the method of Korarewa et al .

    ChIP-sequencing:

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: A ChIP-Seq library was prepared by the Deep Sequencing Facility of the Biotechnology Center/SFB655 of Dresden University of Technology. .. Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions.

    Magnetic Beads:

    Article Title: Candidate genes responsible for early key events of phenobarbital-promoted mouse hepatocellular tumorigenesis based on differentiation of regulating genes between wild type mice and humanized chimeric mice †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7tx00163k
    Article Snippet: The reaction mixture was purified using the Agencourt AMPure XP (Beckman Coulter), and subjected to 3′-dA tailing by incubation for 30 min at 37 °C using the NEBNext dA-Tailing Module (NEB). .. Denatured DNA (600 ng for MeDIP and 500 ng for HmeDIP) was then immunoprecipitated with each antibody.

    Article Title: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    Article Snippet: Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs). .. Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs).

    Isolation:

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The sheared DNA was visualized on a 0.7% (w/v) agarose gel stained with ethidium bromide and fragments in the range of 200 bp–800 bp were isolated from the gel with a QIAquick Gel Extraction Kit (Qiagen). .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA.

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: In brief, RNA was isolated with an RNeasy Plus Mini Kit (Qiagen), and mRNA was obtained by poly(A) selection with a Dynabeads mRNA purification kit (Invitrogen), followed by fragmentation by heating at 94 °C for 3 min (in fragmentation buffer). .. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module.

    Article Title: Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress
    Article Snippet: Genomic DNA in young leaves sampled from 362 individuals and their parents (gDNA) was isolated using a DNAsecure Plant Kit (Tiangen Biotech Co., Beijing, China). .. Briefly, this procedure followed nine main steps: digesting gDNA with restriction enzyme Eco RI (New England BioLabs, or NEB, Ipswich, MA, USA); adding P1 adapters (Illumina, San Diego, CA, USA) to each digested fragment by T4 DNA ligase (NEB); pooling and shearing these fragments; purifying sheared DNA fragments using QIAquick PCR Purification kit; selecting 200- to 400-bp DNA fragments by agarose gel electrophoresis; repairing and flattening fragment ends using a Quick Blunting kit (NEB); adding the overhang (A 3′-dA) to these fragments by a dA-tailing module (NEB); adding P2 adapters (Illumina) to these fragments; and enriching tagged DNA by PCR-amplification.

    Article Title: Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Article Snippet: Exome libraries were constructed from DNA isolated by LCM from in situ and invasive regions, in addition to matched normal tissues. .. Barcoded next-generation sequencing libraries were constructed using the NEBNext end repair (NEB, E6050L), dA-tailing module (NEB, E6053L) and quick ligation module (NEB, E6056L).

    Size-exclusion Chromatography:

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The total DNA (2 µg in 100 µl final volume of TE buffer) was fragmented using a Bioruptor Standard (Diagenode) with the following parameters: 30 min of 30 sec on/off cycles at 4°C. .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA.

    Labeling:

    Article Title: Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    Article Snippet: Samples underwent end-repair and dA-tailing (New England Biolabs) followed by ligation of Illumina TruSeq v. 3-style Y-adaptors carrying the T7 promoter sequence (Table S1). .. Five ul of purified library was then enriched with 14 cycles of PCR using Phusion MasterMix HF (New England Biolabs) (Table S1).

    Purification:

    Article Title: Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    Article Snippet: Samples underwent end-repair and dA-tailing (New England Biolabs) followed by ligation of Illumina TruSeq v. 3-style Y-adaptors carrying the T7 promoter sequence (Table S1). .. The T7 ligated library was run on a 2% agarose gel and a band corresponding to 200 bp was cut and purified in 20 ul of TE buffer with MinElute spin columns (Qiagen).

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA. .. The Phusion High-Fidelity PCR Master Mix was used for PCR enrichment of adapter-ligated DNA.

    Article Title: De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
    Article Snippet: Fragments were end-repaired using the NEBNext EndRepair Module (New England Biolabs, Ipswich, MA, USA) and A-tailed with the NEBNext dA-Tailing Module. .. Illumina adapters were added using the NEBNext Quick Ligation Module.

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: In brief, RNA was isolated with an RNeasy Plus Mini Kit (Qiagen), and mRNA was obtained by poly(A) selection with a Dynabeads mRNA purification kit (Invitrogen), followed by fragmentation by heating at 94 °C for 3 min (in fragmentation buffer). .. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module.

    Article Title: On site DNA barcoding by nanopore sequencing
    Article Snippet: Double strand DNA molecules were end-repaired using the NEBNext End Repair Module (New England Biolabs, Ipswich, USA), followed by purification with Agencourt AMPure XP at 1.8:1 beads to DNA ratio. .. Only in the case of protocol 1, the purified amplicons were then processed using the NEBNext dA-tailing module (New England Biolabs), these steps were skipped in protocol 2 and 3. .. Amplicons from the three protocols were used to prepare sequencing libraries using the ONT DNA Sequencing kits (SQK-MAP004, SQK-MAP005, and SQK-MAP006).

    Article Title: Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress
    Article Snippet: The RAD libraries for marker development were constructed as previously described [ , ]. .. Briefly, this procedure followed nine main steps: digesting gDNA with restriction enzyme Eco RI (New England BioLabs, or NEB, Ipswich, MA, USA); adding P1 adapters (Illumina, San Diego, CA, USA) to each digested fragment by T4 DNA ligase (NEB); pooling and shearing these fragments; purifying sheared DNA fragments using QIAquick PCR Purification kit; selecting 200- to 400-bp DNA fragments by agarose gel electrophoresis; repairing and flattening fragment ends using a Quick Blunting kit (NEB); adding the overhang (A 3′-dA) to these fragments by a dA-tailing module (NEB); adding P2 adapters (Illumina) to these fragments; and enriching tagged DNA by PCR-amplification. .. Sequencing was performed on an Illumina Hiseq2500 platform at Novogene Co. (Beijing, China), applying PE250 strategy according to the Illumina protocol.

    Article Title: Candidate genes responsible for early key events of phenobarbital-promoted mouse hepatocellular tumorigenesis based on differentiation of regulating genes between wild type mice and humanized chimeric mice †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7tx00163k
    Article Snippet: Sonicated DNA was then end-repaired by incubation for 30 min at 20 °C using the NEBNext End Repair Module (NEB). .. The reaction mixture was purified using the Agencourt AMPure XP (Beckman Coulter), and subjected to 3′-dA tailing by incubation for 30 min at 37 °C using the NEBNext dA-Tailing Module (NEB). .. After purification as described above, linker ligation was performed by incubation in a reaction containing 2.5 μM linkers for 1 h at 20 °C using the NEBNext Ultra Ligation Module (NEB).

    Article Title: Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Article Snippet: DNA was fragmented to 250 bp using the Covaris Sonicator and purified by Zymo DNA Clean & Concentrator Column Kit (Genesee Cat # 11-303 or 11-306) according to manufacturer’s instructions. .. Barcoded next-generation sequencing libraries were constructed using the NEBNext end repair (NEB, E6050L), dA-tailing module (NEB, E6053L) and quick ligation module (NEB, E6056L).

    Article Title: Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods
    Article Snippet: 500 ng of each purified amplicon was then end repaired using the NEBNext End Repair Module (New England Biolabs Inc.). .. End repaired amplicons were purified with a Qiaquick PCR purification kit (Qiagen, GmbH) and a single adenine was added to the 3′ ends using the NEBNext dA-Tailing Module (New England Biolabs Inc.). .. Partial Truseq standard paired end Illumina adapters with 6 bp barcodes (Integrated DNA Technologies) were ligated to the adenylated amplicons using the Quick Ligation Kit (New England Biolabs Inc.) and resulting adapter-ligated amplicons were purified with a Qiaquick PCR purification kit (Qiagen, GmbH).

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: A ChIP-Seq library was prepared by the Deep Sequencing Facility of the Biotechnology Center/SFB655 of Dresden University of Technology. .. Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions. .. After purification, adaptors were ligated (Adaptor-Oligo 1: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' , Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3') by using 1x NEBnext Quick Ligation Buffer (NEB), 10x excess of DNA Adaptors, 5 µl Quick T4 DNA Ligase (NEB) at 50 µl total volume.

    Article Title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
    Article Snippet: Amplified cDNA from Round B was purified using AMPure XP beads (Beckman Coulter, Brea, CA), and 1 μg DNA was used as input into Oxford Nanopore Genomic DNA MAP-003 Kits (Chik1, Ebola1) or MAP-004 Kits (HepC1, Ebola2) for generation of MinION Oxford Nanopore-compatible libraries [ , ]. .. Briefly, the steps include: (1) addition of control lambda phage DNA, (2) end-repair with the NEBNext End Repair Module, (3) 1× AMPure purification, (4) dA-tailing with the NEBNext dA-tailing Module, (5) ligation to protein-linked adapters HP/AMP (Oxford Nanopore Technologies, Oxford, UK) using the NEBNext QuickLigation Module for 10 min at room temperature, (6) purification of ligated libraries using magnetic His-Tag Dynabeads (Life Technologies), and (7) elution in 25 μL buffer (Oxford Nanopore Technologies). .. Lambda phage DNA was not added during preparation of the Ebola2 sample library.

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: Briefly, a total of 850 ng (spike-in) and 1 μg (mixed heads) in 80 μL was end repaired using NEBNext End Repair Module (New England Biolabs, Cat No: E6050) and followed by dA tailing using NEBNext dA Tailing Module (New England Biolabs, Cat No: E6053). .. The dA tailed amplicons were then adapter ligated in a total of 100 μL reaction volume and incubated at room temperature for 10 min.

    Article Title: A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster
    Article Snippet: Total DNA was purified from individual fly heads using a QIAamp DNA micro kit (Qiagen Inc., Germantown MD). .. The sheared DNA was then end-repaired and ligated using the NEBNext Ultra 2 end-repair and dA-tailing kit (New England Biolabs, Ipswich MA) according to the manufacturer’s instructions.

    Article Title: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    Article Snippet: Following incubation, the treated DNA was purified using AMPure XP beads (Agencourt). .. Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs).

    Article Title: Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
    Article Snippet: The DNA was purified with AMPure beads and eluted in 25.2 µL of deionized water. .. DNA A-tailing was performed with the NEBNext dA-Tailing module (NEB).

    Sequencing:

    Article Title: Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    Article Snippet: Whole genome amplified (Repli-g Kit, Qiagen) Sal1 reference genomic DNA was sheared to an average size of 200 bp using an S-series Covaris Adaptive Focused Acoustic machine (Covaris). .. Samples underwent end-repair and dA-tailing (New England Biolabs) followed by ligation of Illumina TruSeq v. 3-style Y-adaptors carrying the T7 promoter sequence (Table S1). .. The T7 ligated library was run on a 2% agarose gel and a band corresponding to 200 bp was cut and purified in 20 ul of TE buffer with MinElute spin columns (Qiagen).

    Article Title: Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases
    Article Snippet: Paragraph title: Sequence analysis at the template-switching junction ... The polished fragments were then A-tailed using the NEB Next dA-tailing module (New England Biolabs).

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: Paragraph title: Description of whole genome sequencing and calling ... A-tailing was performed in a total reaction volume of 60ul containing end-repaired DNA, 6ul 10− uffer, 3ul Klenow Fragment (NEBNext dA-Tailing Module; Cat. No. E6053L) and H2 O followed by incubation at 37°C for 30 minutes.

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA. .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA.

    Article Title: De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms
    Article Snippet: Paragraph title: Illumina PCR-free library preparation and sequencing ... Fragments were end-repaired using the NEBNext EndRepair Module (New England Biolabs, Ipswich, MA, USA) and A-tailed with the NEBNext dA-Tailing Module.

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: The second-strand cDNA was synthesized with 100 mM dATP, dCTP, dGTP and dUTP in the presence of RNase H, E. coli DNA polymerase I and DNA ligase (Invitrogen). .. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module. .. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) as described followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems).

    Article Title: On site DNA barcoding by nanopore sequencing
    Article Snippet: Paragraph title: Library preparation and MinION sequencing ... Only in the case of protocol 1, the purified amplicons were then processed using the NEBNext dA-tailing module (New England Biolabs), these steps were skipped in protocol 2 and 3.

    Article Title: Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress
    Article Snippet: Paragraph title: DNA extraction, RAD libraries construction and sequencing ... Briefly, this procedure followed nine main steps: digesting gDNA with restriction enzyme Eco RI (New England BioLabs, or NEB, Ipswich, MA, USA); adding P1 adapters (Illumina, San Diego, CA, USA) to each digested fragment by T4 DNA ligase (NEB); pooling and shearing these fragments; purifying sheared DNA fragments using QIAquick PCR Purification kit; selecting 200- to 400-bp DNA fragments by agarose gel electrophoresis; repairing and flattening fragment ends using a Quick Blunting kit (NEB); adding the overhang (A 3′-dA) to these fragments by a dA-tailing module (NEB); adding P2 adapters (Illumina) to these fragments; and enriching tagged DNA by PCR-amplification.

    Article Title: Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Article Snippet: Paragraph title: Exome Library Construction and Sequencing ... Barcoded next-generation sequencing libraries were constructed using the NEBNext end repair (NEB, E6050L), dA-tailing module (NEB, E6053L) and quick ligation module (NEB, E6056L).

    Article Title: Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods
    Article Snippet: Paragraph title: Illumina amplicon sequencing of 16S rRNA gene (IA rrn ) ... End repaired amplicons were purified with a Qiaquick PCR purification kit (Qiagen, GmbH) and a single adenine was added to the 3′ ends using the NEBNext dA-Tailing Module (New England Biolabs Inc.).

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) and deep sequencing ... Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions.

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: The library preparation for amplicon sequencing was done using SQK-MAP003 following manufacturer’s protocol (ONT). .. Briefly, a total of 850 ng (spike-in) and 1 μg (mixed heads) in 80 μL was end repaired using NEBNext End Repair Module (New England Biolabs, Cat No: E6050) and followed by dA tailing using NEBNext dA Tailing Module (New England Biolabs, Cat No: E6053).

    Article Title: A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster
    Article Snippet: Paragraph title: Duplex sequencing ... The sheared DNA was then end-repaired and ligated using the NEBNext Ultra 2 end-repair and dA-tailing kit (New England Biolabs, Ipswich MA) according to the manufacturer’s instructions.

    Article Title: Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
    Article Snippet: Paragraph title: MinION sequencing library construction ... The DNA was A-tailed using the NEBNext dA Tailing Module (E6053, NEB) by mixing 25 μl eluted DNA with 2 μl Klenow Fragment (3′-5′ exo− ) and 3 μl 10× NEBNext dA-Tailing Reaction Buffer.

    Article Title: RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics
    Article Snippet: The resulting cDNA was fragmented using a Covaris AFA sonicator. .. A “with-bead” protocol was used for dA-tailing, end repair and adapter ligation (NEB) using “PCR-free” barcoded sequencing adaptors (Bioo Scientific, similar to the method of Korarewa et al . .. After 2 rounds of SPRI clean-up the libraries were eluted in EB buffer and USER enzyme mix (NEB) was used to digest the second strand cDNA, generating directional libraries.

    Article Title: De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing
    Article Snippet: Paragraph title: Illumina PCR-Free library preparation and sequencing ... Fragments were end-repaired using the NEBNext End Repair Module (New England Biolabs, Ipswich, MA, USA) and 3΄-adenylated with the NEBNext dA-Tailing Module (New England Biolabs).

    Article Title: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    Article Snippet: Paragraph title: Nucleosome occupancy and DNA methylation sequencing (NOMe-seq) ... Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs).

    Gel Extraction:

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The sheared DNA was visualized on a 0.7% (w/v) agarose gel stained with ethidium bromide and fragments in the range of 200 bp–800 bp were isolated from the gel with a QIAquick Gel Extraction Kit (Qiagen). .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA.

    IA:

    Article Title: Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods
    Article Snippet: Paragraph title: Illumina amplicon sequencing of 16S rRNA gene (IA rrn ) ... End repaired amplicons were purified with a Qiaquick PCR purification kit (Qiagen, GmbH) and a single adenine was added to the 3′ ends using the NEBNext dA-Tailing Module (New England Biolabs Inc.).

    Article Title: A mitochondrial DNA hypomorph of cytochrome oxidase specifically impairs male fertility in Drosophila melanogaster
    Article Snippet: The sheared DNA was then end-repaired and ligated using the NEBNext Ultra 2 end-repair and dA-tailing kit (New England Biolabs, Ipswich MA) according to the manufacturer’s instructions. .. 1.5 ng of total DNA was then PCR amplified using KAPA HiFi DNA polymerase (Roche Inc., Basel Switzerland) according to the manufacturer’s recommendations.

    Mouse Assay:

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module. .. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module.

    Chromatin Immunoprecipitation:

    Article Title: Candidate genes responsible for early key events of phenobarbital-promoted mouse hepatocellular tumorigenesis based on differentiation of regulating genes between wild type mice and humanized chimeric mice †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7tx00163k
    Article Snippet: The reaction mixture was purified using the Agencourt AMPure XP (Beckman Coulter), and subjected to 3′-dA tailing by incubation for 30 min at 37 °C using the NEBNext dA-Tailing Module (NEB). .. Denatured DNA (600 ng for MeDIP and 500 ng for HmeDIP) was then immunoprecipitated with each antibody.

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) and deep sequencing ... Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions.

    Article Title: RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics
    Article Snippet: A Bioanalyzer Nano chip (Agilent) was used to QC and quantify total RNA. .. A “with-bead” protocol was used for dA-tailing, end repair and adapter ligation (NEB) using “PCR-free” barcoded sequencing adaptors (Bioo Scientific, similar to the method of Korarewa et al .

    In Vitro:

    Article Title: Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    Article Snippet: Samples underwent end-repair and dA-tailing (New England Biolabs) followed by ligation of Illumina TruSeq v. 3-style Y-adaptors carrying the T7 promoter sequence (Table S1). .. Samples underwent end-repair and dA-tailing (New England Biolabs) followed by ligation of Illumina TruSeq v. 3-style Y-adaptors carrying the T7 promoter sequence (Table S1).

    Electrophoresis:

    Article Title: Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases
    Article Snippet: The outcome of the latter reaction was run on a 1.2% agarose gel with SYBR Safe (Life / Invitrogen) in an E-Gel electrophoresis system (Life / Invitrogen). .. The polished fragments were then A-tailed using the NEB Next dA-tailing module (New England Biolabs).

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The quality and quantity of the resulting DNA was assessed using electrophoresis in a 0.7% (w/v) agarose gel stained with ethidium bromide and NanoDrop (Thermo Scientific), respectively. .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA.

    Article Title: Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress
    Article Snippet: The DNA quantity and quality were determined with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, NC, USA) and by electrophoresis in 1.0% agarose gels with a λDNA/HindIII marker. .. Briefly, this procedure followed nine main steps: digesting gDNA with restriction enzyme Eco RI (New England BioLabs, or NEB, Ipswich, MA, USA); adding P1 adapters (Illumina, San Diego, CA, USA) to each digested fragment by T4 DNA ligase (NEB); pooling and shearing these fragments; purifying sheared DNA fragments using QIAquick PCR Purification kit; selecting 200- to 400-bp DNA fragments by agarose gel electrophoresis; repairing and flattening fragment ends using a Quick Blunting kit (NEB); adding the overhang (A 3′-dA) to these fragments by a dA-tailing module (NEB); adding P2 adapters (Illumina) to these fragments; and enriching tagged DNA by PCR-amplification.

    Selection:

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: In brief, RNA was isolated with an RNeasy Plus Mini Kit (Qiagen), and mRNA was obtained by poly(A) selection with a Dynabeads mRNA purification kit (Invitrogen), followed by fragmentation by heating at 94 °C for 3 min (in fragmentation buffer). .. Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module.

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions. .. Large-scale amplification of library constructs was performed by using the PCR Enrich Adaptor Ligated cDNA Library module (NEB).

    Agarose Gel Electrophoresis:

    Article Title: Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases
    Article Snippet: The outcome of the latter reaction was run on a 1.2% agarose gel with SYBR Safe (Life / Invitrogen) in an E-Gel electrophoresis system (Life / Invitrogen). .. The polished fragments were then A-tailed using the NEB Next dA-tailing module (New England Biolabs).

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The sheared DNA was visualized on a 0.7% (w/v) agarose gel stained with ethidium bromide and fragments in the range of 200 bp–800 bp were isolated from the gel with a QIAquick Gel Extraction Kit (Qiagen). .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA.

    Article Title: Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress
    Article Snippet: The RAD libraries for marker development were constructed as previously described [ , ]. .. Briefly, this procedure followed nine main steps: digesting gDNA with restriction enzyme Eco RI (New England BioLabs, or NEB, Ipswich, MA, USA); adding P1 adapters (Illumina, San Diego, CA, USA) to each digested fragment by T4 DNA ligase (NEB); pooling and shearing these fragments; purifying sheared DNA fragments using QIAquick PCR Purification kit; selecting 200- to 400-bp DNA fragments by agarose gel electrophoresis; repairing and flattening fragment ends using a Quick Blunting kit (NEB); adding the overhang (A 3′-dA) to these fragments by a dA-tailing module (NEB); adding P2 adapters (Illumina) to these fragments; and enriching tagged DNA by PCR-amplification. .. Sequencing was performed on an Illumina Hiseq2500 platform at Novogene Co. (Beijing, China), applying PE250 strategy according to the Illumina protocol.

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions. .. Large-scale amplification of library constructs was performed by using the PCR Enrich Adaptor Ligated cDNA Library module (NEB).

    In Situ:

    Article Title: Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Article Snippet: Exome libraries were constructed from DNA isolated by LCM from in situ and invasive regions, in addition to matched normal tissues. .. Barcoded next-generation sequencing libraries were constructed using the NEBNext end repair (NEB, E6050L), dA-tailing module (NEB, E6053L) and quick ligation module (NEB, E6056L).

    Next-Generation Sequencing:

    Article Title: Essential role of the transcription factor Bhlhe41 in regulating the development, self-renewal and BCR repertoire of B-1a cells
    Article Snippet: Sequencing libraries were prepared with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-tailing module or NEBNext Ultra Ligation Module and NEBNext End Repair/dA-tailing module. .. For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) as described followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems).

    Article Title: Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Article Snippet: DNA was fragmented to 250 bp using the Covaris Sonicator and purified by Zymo DNA Clean & Concentrator Column Kit (Genesee Cat # 11-303 or 11-306) according to manufacturer’s instructions. .. Barcoded next-generation sequencing libraries were constructed using the NEBNext end repair (NEB, E6050L), dA-tailing module (NEB, E6053L) and quick ligation module (NEB, E6056L). .. Libraries were PCR amplified with NEBNext HiFi 2x PCRmix (NEB, M0541L).

    Laser Capture Microdissection:

    Article Title: Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
    Article Snippet: Exome libraries were constructed from DNA isolated by LCM from in situ and invasive regions, in addition to matched normal tissues. .. Barcoded next-generation sequencing libraries were constructed using the NEBNext end repair (NEB, E6050L), dA-tailing module (NEB, E6053L) and quick ligation module (NEB, E6056L).

    Spectrophotometry:

    Article Title: Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress
    Article Snippet: The DNA quantity and quality were determined with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, NC, USA) and by electrophoresis in 1.0% agarose gels with a λDNA/HindIII marker. .. Briefly, this procedure followed nine main steps: digesting gDNA with restriction enzyme Eco RI (New England BioLabs, or NEB, Ipswich, MA, USA); adding P1 adapters (Illumina, San Diego, CA, USA) to each digested fragment by T4 DNA ligase (NEB); pooling and shearing these fragments; purifying sheared DNA fragments using QIAquick PCR Purification kit; selecting 200- to 400-bp DNA fragments by agarose gel electrophoresis; repairing and flattening fragment ends using a Quick Blunting kit (NEB); adding the overhang (A 3′-dA) to these fragments by a dA-tailing module (NEB); adding P2 adapters (Illumina) to these fragments; and enriching tagged DNA by PCR-amplification.

    DNA Methylation Assay:

    Article Title: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    Article Snippet: Paragraph title: Nucleosome occupancy and DNA methylation sequencing (NOMe-seq) ... Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs).

    Immunoprecipitation:

    Article Title: Candidate genes responsible for early key events of phenobarbital-promoted mouse hepatocellular tumorigenesis based on differentiation of regulating genes between wild type mice and humanized chimeric mice †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7tx00163k
    Article Snippet: Paragraph title: MeDIP and HmeDIP (5mC and 5hmC immunoprecipitation) ... The reaction mixture was purified using the Agencourt AMPure XP (Beckman Coulter), and subjected to 3′-dA tailing by incubation for 30 min at 37 °C using the NEBNext dA-Tailing Module (NEB).

    Article Title: Stage-Specific Binding Profiles of Cohesin in Resting and Activated B Lymphocytes Suggest a Role for Cohesin in Immunoglobulin Class Switching and Maturation
    Article Snippet: A ChIP-Seq library was prepared by the Deep Sequencing Facility of the Biotechnology Center/SFB655 of Dresden University of Technology. .. Immunoprecipitated fragments were end-repaired with NEBnext End Repair Module (NEB) and purified by using Agencourt Ampure XP - beads (Beckman Coulter) and A-tailed using the NEBnext dA-Tailing Module according to manufacturers' instructions. .. After purification, adaptors were ligated (Adaptor-Oligo 1: 5'ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' , Adaptor-Oligo 2: 5'-P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3') by using 1x NEBnext Quick Ligation Buffer (NEB), 10x excess of DNA Adaptors, 5 µl Quick T4 DNA Ligase (NEB) at 50 µl total volume.

    Molecular Weight:

    Article Title: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
    Article Snippet: Briefly, genomic DNA (2 μg) was sonicated using a Covaris instrument to an average molecular weight of 150 bp. .. Following end repair, A-tailing was performed using the dA-tailing module according to the manufacturer’s instructions (New England Biolabs).

    Marker:

    Article Title: Mapping QTLs for water-use efficiency reveals the potential candidate genes involved in regulating the trait in apple under drought stress
    Article Snippet: The RAD libraries for marker development were constructed as previously described [ , ]. .. Briefly, this procedure followed nine main steps: digesting gDNA with restriction enzyme Eco RI (New England BioLabs, or NEB, Ipswich, MA, USA); adding P1 adapters (Illumina, San Diego, CA, USA) to each digested fragment by T4 DNA ligase (NEB); pooling and shearing these fragments; purifying sheared DNA fragments using QIAquick PCR Purification kit; selecting 200- to 400-bp DNA fragments by agarose gel electrophoresis; repairing and flattening fragment ends using a Quick Blunting kit (NEB); adding the overhang (A 3′-dA) to these fragments by a dA-tailing module (NEB); adding P2 adapters (Illumina) to these fragments; and enriching tagged DNA by PCR-amplification.

    Staining:

    Article Title: Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
    Article Snippet: The sheared DNA was visualized on a 0.7% (w/v) agarose gel stained with ethidium bromide and fragments in the range of 200 bp–800 bp were isolated from the gel with a QIAquick Gel Extraction Kit (Qiagen). .. The NEBNext dA-Tailing Module and NEBNext Quick Ligation Module were utilized for dA-tailing of the end-repaired DNA and adapter ligation of dA-tailed DNA.

    Nanopore Sequencing:

    Article Title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
    Article Snippet: Paragraph title: Preparation of nanopore sequencing libraries ... Briefly, the steps include: (1) addition of control lambda phage DNA, (2) end-repair with the NEBNext End Repair Module, (3) 1× AMPure purification, (4) dA-tailing with the NEBNext dA-tailing Module, (5) ligation to protein-linked adapters HP/AMP (Oxford Nanopore Technologies, Oxford, UK) using the NEBNext QuickLigation Module for 10 min at room temperature, (6) purification of ligated libraries using magnetic His-Tag Dynabeads (Life Technologies), and (7) elution in 25 μL buffer (Oxford Nanopore Technologies).

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: Paragraph title: Amplicon library preparation and Oxford Nanopore sequencing ... Briefly, a total of 850 ng (spike-in) and 1 μg (mixed heads) in 80 μL was end repaired using NEBNext End Repair Module (New England Biolabs, Cat No: E6050) and followed by dA tailing using NEBNext dA Tailing Module (New England Biolabs, Cat No: E6053).

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    New England Biolabs nebnext da tailing module
    Nebnext Da Tailing Module, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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