ultra ii end repair da tailing module  (New England Biolabs)


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    Name:
    NEBNext Ultra II End Repair/dA-Tailing Module
    Description:

    Catalog Number:
    E7546L
    Price:
    None
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    New England Biolabs ultra ii end repair da tailing module

    https://www.bioz.com/result/ultra ii end repair da tailing module/product/New England Biolabs
    Average 99 stars, based on 50 article reviews
    Price from $9.99 to $1999.99
    ultra ii end repair da tailing module - by Bioz Stars, 2019-09
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    Related Articles

    Centrifugation:

    Article Title: Nanopore sequencing and assembly of a human genome with ultra-long reads
    Article Snippet: 1.5–2.5 μg human genomic DNA was sheared in a Covaris g-TUBE centrifuged at 5,000–6,000 r.p.m. in an Eppendorf 5424 (or equivalent) centrifuge for 2 × 1 min, inverting the tube between centrifugation steps. .. End repair and dA-tailing (NEBNext Ultra II End-Repair/dA-tailing Module) was then performed by adding 7 μl Ultra II End-Prep buffer, 3 μl Ultra II End-Prep enzyme mix, and 5 μl NFW.

    Amplification:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. .. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA.

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: The panel was split into 2 primer pools and amplified with 5× Ion AmpliSeq HiFi Master Mix, followed by FuPa treatment (Ion AmpliSeq DNA Library Kit 2.0; Thermo Fisher Scientific). .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Article Title: Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
    Article Snippet: 1000 ng of equimolar pooled amplicon from each SAV isolate was the input to a library generated with the Ligation Sequencing Kit 1D SQK-LSK108 (Oxford Nanopore Technologies). .. Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma).

    Whole Genome Amplification:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: The Illustra V2 Genomiphi, Illustra single cell Genomiphi, and Qiagen REPLI-g single cell kits were used to test identical sonicate fluid samples. .. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA. .. This approach also resulted in the presence of contaminant bacterial DNA and yielded fewer reads from the known pathogens.

    Real-time Polymerase Chain Reaction:

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB). .. Ligation products were purified and size selected using 0.8× Agencourt AMPure XP beads.

    Incubation:

    Article Title: Culture-independent analysis of liver abscess using nanopore sequencing
    Article Snippet: End-repair and dA-tailing. .. The fragmented DNA in 50 μL nuclease-free water was incubated in a 7 μL Ultra II End-Prep buffer and a 3 μL Ultra II End-Prep enzyme mix from NEBNext Ultra™ II End Repair/dA-Tailing Module (New England Biolabs, E7546S) at a temperature of 20°C for 5 minutes and 65°C for 5 minutes, respectively. .. The DNA was then purified with AMPure XP beads (Beckman Coulter, A63881).

    Article Title: De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
    Article Snippet: To reduce DNA shearing during the following bead clean-up, the sample was split in two 77.5-μL aliquots that were each eluted in 50.5 μL nuclease free water. .. For NEBNext Ultra II End Repair/dA-Tailing treatment (New England Biolabs), 100 μL of FFPE repaired DNA, together with 14.0 μL NEBNext Ultra II End Prep Reaction Buffer and 6 μL NEBNext Ultra II End Prep Enzyme Mix, was incubated for 30 min at 20°C followed by 20 min at 65°C and 4°C until further processing. .. For purification, the sample was split again into two aliquots of 60.0 μL and subjected to a bead clean up.

    Article Title: In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities
    Article Snippet: Briefly, 46 μL of DNA extract was used for a DNA repair step using NEBNext FFPE Repair Mix (New England Biolabs, Ipswich, MA), followed by clean-up using AMPure XP beads incubated with mixing at room temperature for 5 min. .. Water was then added to beads, and the 45 μL eluate used for end repair and dA-tailing of DNA using NEBNext Ultra II End-repair/dA tailing kit (New England Biolabs).

    Article Title: Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform
    Article Snippet: ∼500 ng gDNA was fragmented with a Covaris microTUBE using the manufacturer’s default 500-bp setting. .. ∼0.5 pmole of fragmented gDNA (165 ng ∼500-bp DNA) was subjected to a 30 µL end-repair/dA-tailing reaction using the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, Cat. E7546L) as detailed above with addition of 3 mM dATP after 5min incubation at 20°, followed by 5 min incubation at 65°. .. A Select-a-Size DNA Clean & Concentrator (Zymo, Cat. D4080) was used to purify each end-repair/dA-tail reaction following the manufacturer’s protocol.

    Article Title: Rapid resistome mapping using nanopore sequencing
    Article Snippet: The NEBNext Ultra II End Repair/dA Tailing module (E7546S, NEB, USA) was used to prepare 1000 ng of the functionally selected DNA. .. The NEBNext Ultra II End Repair/dA Tailing module (E7546S, NEB, USA) was used to prepare 1000 ng of the functionally selected DNA.

    Article Title: Rapid re-identification of human samples using portable DNA sequencing
    Article Snippet: The DNA sample was end-repaired and dA-tailed using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs [NEB] E7546S; 5 min 20°C, and 5 min 65°C). .. The sample was then purified using AMPure magnetic beads and the DNA was eluted off the beads using 31 μl nuclease-free water.

    Article Title: A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
    Article Snippet: Preparation of a one-dimensional genomic DNA library was performed using the SQK-LSK108 system (Oxford Nanopore Technologies, Oxford, UK) according to the manufacturer's instructions. .. We performed dA-tailing and end-repair using the NEBNext Ultra II End-repair/dA-tail module with two step incubation periods, of 20 min each. .. A purification step using 0.7× Agencourt AMPure XP beads (Beckman Coulter) was then performed according to the manufacturer's instructions.

    Article Title: Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum
    Article Snippet: Four lab strains re-sequencing; 54 additional samples from North Sulawesi, Indonesia; 11 samples from Mahidol University, Bangkok, Thailand; 5 samples from NIHE, Hanoi, Vietnam; and 7 mixtures of 3D7 and Dd2 strains were prepared using the 1D2 Sequencing of Genomic DNA Kit (SQK-LSK308, ONT). .. Briefly, the protocol for SQK-LSK308 is as follow: a total 1 µg of input DNA (a mixture of PCR amplicons from nine genes) was end-repaired and A-tailed using 1x Ultra II End-prep enzyme (New England Biolabs) incubated in 20 °C for 5 minutes and 65 °C for 5 minutes. .. Following the reaction, we purified end-prepped PCR amplicons with 1x AMPure XP (Beckman Coulter) and eluted the DNA in 25 µl nuclease-free water.

    Article Title: Nanopore sequencing and assembly of a human genome with ultra-long reads
    Article Snippet: The mixture was incubated for 15 min at 20 °C, cleaned up using a 0.4× volume of AMPure XP beads (62 μl), incubated at room temperature with gentle mixing for 5 min, washed twice with 200 μl fresh 70% ethanol, pellet allowed to dry for 2 min, and DNA eluted in 46 μl NFW or EB (10 mM Tris pH 8.0). .. End repair and dA-tailing (NEBNext Ultra II End-Repair/dA-tailing Module) was then performed by adding 7 μl Ultra II End-Prep buffer, 3 μl Ultra II End-Prep enzyme mix, and 5 μl NFW.

    Formalin-fixed Paraffin-Embedded:

    Article Title: De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
    Article Snippet: To reduce DNA shearing during the following bead clean-up, the sample was split in two 77.5-μL aliquots that were each eluted in 50.5 μL nuclease free water. .. For NEBNext Ultra II End Repair/dA-Tailing treatment (New England Biolabs), 100 μL of FFPE repaired DNA, together with 14.0 μL NEBNext Ultra II End Prep Reaction Buffer and 6 μL NEBNext Ultra II End Prep Enzyme Mix, was incubated for 30 min at 20°C followed by 20 min at 65°C and 4°C until further processing. .. For purification, the sample was split again into two aliquots of 60.0 μL and subjected to a bead clean up.

    Article Title: Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast
    Article Snippet: The four samples were combined to a give an equimolar mix (assuming a molecular weight for each assembly based on the mean promoter length) with a total DNA content of 2.6 μg in 45 μl dH2 O. DNA underwent end repair using NEBNext FFPE DNA Repair Mix (M6630, New England Biolabs) according to the manufacturer's instructions. .. The repaired DNA was recovered using Agincourt AMPure XP beads (A63880, Beckman Coulter), washed twice in 200 μl 70% ethanol and eluted in 46 μl dH2 O. DNA was then dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (E7546, New England Biolabs) according to the manufacturer's instructions and recovered using Agincourt AMPure XP beads as before, eluting in 30 μl dH2 O.

    Article Title: In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities
    Article Snippet: Briefly, 46 μL of DNA extract was used for a DNA repair step using NEBNext FFPE Repair Mix (New England Biolabs, Ipswich, MA), followed by clean-up using AMPure XP beads incubated with mixing at room temperature for 5 min. .. Water was then added to beads, and the 45 μL eluate used for end repair and dA-tailing of DNA using NEBNext Ultra II End-repair/dA tailing kit (New England Biolabs).

    Article Title: Nanopore sequencing and assembly of a human genome with ultra-long reads
    Article Snippet: 8.5 μl nuclease-free water (NFW), 6.5 μl FFPE Repair Buffer and 2 μl FFPE DNA Repair Mix were added to the 46 μl sheared DNA. .. End repair and dA-tailing (NEBNext Ultra II End-Repair/dA-tailing Module) was then performed by adding 7 μl Ultra II End-Prep buffer, 3 μl Ultra II End-Prep enzyme mix, and 5 μl NFW.

    Activity Assay:

    Article Title: A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
    Article Snippet: We performed dA-tailing and end-repair using the NEBNext Ultra II End-repair/dA-tail module with two step incubation periods, of 20 min each. .. The library was then ready for MinION sequencing.

    Mass Spectrometry:

    Article Title: Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for “personalized monitoring” of residual disease in chronic myeloid leukemia patients
    Article Snippet: Paragraph title: Library preparation and MS ... According to the 2D Native barcoding genomic DNA (SQK-LSK 208) protocol, the amplicons were end-prepared using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs Inc.) and barcoded with the ligation of nanopore-specific Native Barcodes (NB01-NB10) using Blunt/TA Ligase Master Mix (New England Biolabs Inc.).

    Flow Cytometry:

    Article Title: De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
    Article Snippet: For NEBNext Ultra II End Repair/dA-Tailing treatment (New England Biolabs), 100 μL of FFPE repaired DNA, together with 14.0 μL NEBNext Ultra II End Prep Reaction Buffer and 6 μL NEBNext Ultra II End Prep Enzyme Mix, was incubated for 30 min at 20°C followed by 20 min at 65°C and 4°C until further processing. .. For NEBNext Ultra II End Repair/dA-Tailing treatment (New England Biolabs), 100 μL of FFPE repaired DNA, together with 14.0 μL NEBNext Ultra II End Prep Reaction Buffer and 6 μL NEBNext Ultra II End Prep Enzyme Mix, was incubated for 30 min at 20°C followed by 20 min at 65°C and 4°C until further processing.

    Article Title: Complete Genome Sequence Reveals Evolutionary Dynamics of an Emerging and Variant Pathovar of Xanthomonas euvesicatoria
    Article Snippet: DNA end repair was performed using NEBNext Ultra II End repair/dA-Tailing Module (NEB, Ipswich) and again Ampure XP beads (Beckman Coulter) were used to perform the cleanup. .. Fifty microliters of the pooled DNA sample was used for adapter ligation using T4 DNA ligase.

    Article Title: In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities
    Article Snippet: Water was then added to beads, and the 45 μL eluate used for end repair and dA-tailing of DNA using NEBNext Ultra II End-repair/dA tailing kit (New England Biolabs). .. The adapted and tethered DNA library was subsequently bound to purified MyOne C1 Streptavidin beads and suspended in resuspension buffer provided with the library prep kit.

    Article Title: A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
    Article Snippet: We performed dA-tailing and end-repair using the NEBNext Ultra II End-repair/dA-tail module with two step incubation periods, of 20 min each. .. The library was then ready for MinION sequencing.

    Article Title: Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
    Article Snippet: Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma). .. Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma).

    Ligation:

    Article Title: Culture-independent analysis of liver abscess using nanopore sequencing
    Article Snippet: The fragmented DNA in 50 μL nuclease-free water was incubated in a 7 μL Ultra II End-Prep buffer and a 3 μL Ultra II End-Prep enzyme mix from NEBNext Ultra™ II End Repair/dA-Tailing Module (New England Biolabs, E7546S) at a temperature of 20°C for 5 minutes and 65°C for 5 minutes, respectively. .. The fragmented DNA in 50 μL nuclease-free water was incubated in a 7 μL Ultra II End-Prep buffer and a 3 μL Ultra II End-Prep enzyme mix from NEBNext Ultra™ II End Repair/dA-Tailing Module (New England Biolabs, E7546S) at a temperature of 20°C for 5 minutes and 65°C for 5 minutes, respectively.

    Article Title: Complete Genome Sequence Reveals Evolutionary Dynamics of an Emerging and Variant Pathovar of Xanthomonas euvesicatoria
    Article Snippet: DNA end repair was performed using NEBNext Ultra II End repair/dA-Tailing Module (NEB, Ipswich) and again Ampure XP beads (Beckman Coulter) were used to perform the cleanup. .. The ONT library was prepared using ONT 1D ligation sequencing KIT (SQK-LSK108) with native barcoding kit (EXP-NBD103).

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: The 2 primer pools for each sample were then pooled and purified with 1.8× Agencourt AMPure XP magnetic beads (Beckman Coulter). .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB). .. Ligation products were purified and size selected using 0.8× Agencourt AMPure XP beads.

    Article Title: In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities
    Article Snippet: Water was then added to beads, and the 45 μL eluate used for end repair and dA-tailing of DNA using NEBNext Ultra II End-repair/dA tailing kit (New England Biolabs). .. Water was then added to beads, and the 45 μL eluate used for end repair and dA-tailing of DNA using NEBNext Ultra II End-repair/dA tailing kit (New England Biolabs).

    Article Title: Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform
    Article Snippet: ∼0.5 pmole of fragmented gDNA (165 ng ∼500-bp DNA) was subjected to a 30 µL end-repair/dA-tailing reaction using the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, Cat. E7546L) as detailed above with addition of 3 mM dATP after 5min incubation at 20°, followed by 5 min incubation at 65°. .. ∼0.5 pmole of fragmented gDNA (165 ng ∼500-bp DNA) was subjected to a 30 µL end-repair/dA-tailing reaction using the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, Cat. E7546L) as detailed above with addition of 3 mM dATP after 5min incubation at 20°, followed by 5 min incubation at 65°.

    Article Title: Forensic SNP Genotyping using Nanopore MinION Sequencing
    Article Snippet: The quality of the ligation products was assessed using the Agilent High-Sensitivity DNA kit (Bioanalyser, Agilent Technologies, California, USA). .. End-repair was performed on 1.034 μg of the concatenated amplicons using the Ultra II End-Repair/dA-Tailing module (NEB, Ipswich, USA) according to the manufacturer’s instructions.

    Article Title: A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
    Article Snippet: We performed dA-tailing and end-repair using the NEBNext Ultra II End-repair/dA-tail module with two step incubation periods, of 20 min each. .. A purification step using 0.7× Agencourt AMPure XP beads (Beckman Coulter) was then performed according to the manufacturer's instructions.

    Article Title: Nanopore sequencing and assembly of a human genome with ultra-long reads
    Article Snippet: Paragraph title: Library preparation (SQK-LSK108 1D ligation genomic DNA) ... End repair and dA-tailing (NEBNext Ultra II End-Repair/dA-tailing Module) was then performed by adding 7 μl Ultra II End-Prep buffer, 3 μl Ultra II End-Prep enzyme mix, and 5 μl NFW.

    Article Title: Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia
    Article Snippet: For each sample, 300 ng of PCR purified products from each long-PCR were pooled, in a final volume of 25 uL in nuclease-free water and used for library preparation. .. According to the 2D Native barcoding genomic DNA (SQK-LSK 208) protocol, the amplicons were end-prepared using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs Inc.) and barcoded with the ligation of nanopore-specific Native Barcodes (NB01-NB12) using Blunt/TA Ligase Master Mix (New England Biolabs Inc.). .. Equimolar amounts of each barcoded amplicon were then pulled and 540 ng of the final pool were diluted to 58 μl in nuclease-free water and prepared for sequencing with the ligation of Native Barcoding adapters and the tether using NEBNext Quick Ligation Module (New England Biolabs Inc.).

    Article Title: Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
    Article Snippet: 1000 ng of equimolar pooled amplicon from each SAV isolate was the input to a library generated with the Ligation Sequencing Kit 1D SQK-LSK108 (Oxford Nanopore Technologies). .. Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma).

    Genomic Sequencing:

    Article Title: Rapid resistome mapping using nanopore sequencing
    Article Snippet: Sequencing library preparation was carried out with Nanopore Genomic Sequencing Kit SQK-MAP006 (Oxford Nanopore, UK) and a PCR-free ‘native barcoding’ kit according to the manufacturer's protocol. .. The NEBNext Ultra II End Repair/dA Tailing module (E7546S, NEB, USA) was used to prepare 1000 ng of the functionally selected DNA.

    Article Title: The use of Oxford Nanopore native barcoding for complete genome assembly
    Article Snippet: Sequencing library preparation was carried out with Nanopore Genomic Sequencing Kit SQK-MAP006 (ONT, UK) and a PCR-free ‘native barcoding’ kit provided by ONT. .. The NEBNext Ultra II End Repair/dA Tailing kit (E7546S, NEB) was used to prepare 1000 ng of sheared genomic DNA (1000 ng DNA in 50 μl nuclease free water, 7 μl of Ultra II End-Prep Buffer, 3 μl Ultra II End-Prep Enzyme Mix in a total volume of 60 μl).

    Infection:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. .. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA.

    Generated:

    Article Title: Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
    Article Snippet: 1000 ng of equimolar pooled amplicon from each SAV isolate was the input to a library generated with the Ligation Sequencing Kit 1D SQK-LSK108 (Oxford Nanopore Technologies). .. Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma).

    Polymerase Chain Reaction:

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: DNA (10 ng) was amplified for 18 cycles of PCR with the Ion AmpliSeq custom DNA panel (Thermo Fisher Scientific), enriching the 195 target amplicons. .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Article Title: Rapid resistome mapping using nanopore sequencing
    Article Snippet: Sequencing library preparation was carried out with Nanopore Genomic Sequencing Kit SQK-MAP006 (Oxford Nanopore, UK) and a PCR-free ‘native barcoding’ kit according to the manufacturer's protocol. .. The NEBNext Ultra II End Repair/dA Tailing module (E7546S, NEB, USA) was used to prepare 1000 ng of the functionally selected DNA.

    Article Title: The use of Oxford Nanopore native barcoding for complete genome assembly
    Article Snippet: Sequencing library preparation was carried out with Nanopore Genomic Sequencing Kit SQK-MAP006 (ONT, UK) and a PCR-free ‘native barcoding’ kit provided by ONT. .. The NEBNext Ultra II End Repair/dA Tailing kit (E7546S, NEB) was used to prepare 1000 ng of sheared genomic DNA (1000 ng DNA in 50 μl nuclease free water, 7 μl of Ultra II End-Prep Buffer, 3 μl Ultra II End-Prep Enzyme Mix in a total volume of 60 μl).

    Article Title: Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum
    Article Snippet: Four lab strains re-sequencing; 54 additional samples from North Sulawesi, Indonesia; 11 samples from Mahidol University, Bangkok, Thailand; 5 samples from NIHE, Hanoi, Vietnam; and 7 mixtures of 3D7 and Dd2 strains were prepared using the 1D2 Sequencing of Genomic DNA Kit (SQK-LSK308, ONT). .. Briefly, the protocol for SQK-LSK308 is as follow: a total 1 µg of input DNA (a mixture of PCR amplicons from nine genes) was end-repaired and A-tailed using 1x Ultra II End-prep enzyme (New England Biolabs) incubated in 20 °C for 5 minutes and 65 °C for 5 minutes. .. Following the reaction, we purified end-prepped PCR amplicons with 1x AMPure XP (Beckman Coulter) and eluted the DNA in 25 µl nuclease-free water.

    Article Title: Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia
    Article Snippet: For each sample, 300 ng of PCR purified products from each long-PCR were pooled, in a final volume of 25 uL in nuclease-free water and used for library preparation. .. According to the 2D Native barcoding genomic DNA (SQK-LSK 208) protocol, the amplicons were end-prepared using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs Inc.) and barcoded with the ligation of nanopore-specific Native Barcodes (NB01-NB12) using Blunt/TA Ligase Master Mix (New England Biolabs Inc.).

    Sonication:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: Three WGA kits were tested for their utility in a metagenomics approach to identify the pathogens in sonicate fluid comprised of biofilms and other materials dislodged from the surfaces of explanted prosthetic joints using sonication. .. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA.

    Binding Assay:

    Article Title: De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
    Article Snippet: For NEBNext Ultra II End Repair/dA-Tailing treatment (New England Biolabs), 100 μL of FFPE repaired DNA, together with 14.0 μL NEBNext Ultra II End Prep Reaction Buffer and 6 μL NEBNext Ultra II End Prep Enzyme Mix, was incubated for 30 min at 20°C followed by 20 min at 65°C and 4°C until further processing. .. For NEBNext Ultra II End Repair/dA-Tailing treatment (New England Biolabs), 100 μL of FFPE repaired DNA, together with 14.0 μL NEBNext Ultra II End Prep Reaction Buffer and 6 μL NEBNext Ultra II End Prep Enzyme Mix, was incubated for 30 min at 20°C followed by 20 min at 65°C and 4°C until further processing.

    Article Title: Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform
    Article Snippet: ∼0.5 pmole of fragmented gDNA (165 ng ∼500-bp DNA) was subjected to a 30 µL end-repair/dA-tailing reaction using the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, Cat. E7546L) as detailed above with addition of 3 mM dATP after 5min incubation at 20°, followed by 5 min incubation at 65°. .. ∼0.5 pmole of fragmented gDNA (165 ng ∼500-bp DNA) was subjected to a 30 µL end-repair/dA-tailing reaction using the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, Cat. E7546L) as detailed above with addition of 3 mM dATP after 5min incubation at 20°, followed by 5 min incubation at 65°.

    Article Title: A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
    Article Snippet: We performed dA-tailing and end-repair using the NEBNext Ultra II End-repair/dA-tail module with two step incubation periods, of 20 min each. .. A purification step using 0.7× Agencourt AMPure XP beads (Beckman Coulter) was then performed according to the manufacturer's instructions.

    Article Title: Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum
    Article Snippet: Briefly, the protocol for SQK-LSK308 is as follow: a total 1 µg of input DNA (a mixture of PCR amplicons from nine genes) was end-repaired and A-tailed using 1x Ultra II End-prep enzyme (New England Biolabs) incubated in 20 °C for 5 minutes and 65 °C for 5 minutes. .. After purification of adapted PCR-amplicons with 1x AMPure XP (DNA was eluted in 46 µl of nuclease-free water), we ligated 400 ng of Barcode Adapter Mix (ONT) to the adapted PCR-amplicons with 1x Blunt/TA Ligase (New England Biolabs) for 10 minutes in room temperature.

    Article Title: Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
    Article Snippet: Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma). .. Sequencing adapters (AMX1D) (ONT) were ligated to the DNA using Blunt/TA Ligation Master Mix (New England Biolabs) by incubation at room temperature for 10 min.

    Molecular Weight:

    Article Title: Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast
    Article Snippet: The four samples were combined to a give an equimolar mix (assuming a molecular weight for each assembly based on the mean promoter length) with a total DNA content of 2.6 μg in 45 μl dH2 O. DNA underwent end repair using NEBNext FFPE DNA Repair Mix (M6630, New England Biolabs) according to the manufacturer's instructions. .. The repaired DNA was recovered using Agincourt AMPure XP beads (A63880, Beckman Coulter), washed twice in 200 μl 70% ethanol and eluted in 46 μl dH2 O. DNA was then dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (E7546, New England Biolabs) according to the manufacturer's instructions and recovered using Agincourt AMPure XP beads as before, eluting in 30 μl dH2 O.

    DNA Extraction:

    Article Title: Complete Genome Sequence Reveals Evolutionary Dynamics of an Emerging and Variant Pathovar of Xanthomonas euvesicatoria
    Article Snippet: Paragraph title: Bacterial Genomic DNA Isolation and ONT MinION Sequencing ... DNA end repair was performed using NEBNext Ultra II End repair/dA-Tailing Module (NEB, Ipswich) and again Ampure XP beads (Beckman Coulter) were used to perform the cleanup.

    Sensitive Assay:

    Article Title: Rapid resistome mapping using nanopore sequencing
    Article Snippet: DNA QC was performed using Qubit dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific, USA) and 2200 TapeStation (Agilent, USA). .. The NEBNext Ultra II End Repair/dA Tailing module (E7546S, NEB, USA) was used to prepare 1000 ng of the functionally selected DNA.

    Magnetic Beads:

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: The 2 primer pools for each sample were then pooled and purified with 1.8× Agencourt AMPure XP magnetic beads (Beckman Coulter). .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Article Title: Rapid re-identification of human samples using portable DNA sequencing
    Article Snippet: The DNA sample was end-repaired and dA-tailed using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs [NEB] E7546S; 5 min 20°C, and 5 min 65°C). .. After an AMPure purification, the DNA fragments were subject to ligation using Blunt/TA Ligase Master Mix (NEB M0367S) for 5 min at 20°C and then 5 min at 65°C.

    Isolation:

    Article Title: Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast
    Article Snippet: Restriction digest products ranging from 5,616 to 6,117 bp were isolated by agarose gel electrophoresis and purified using a QIAquick gel extraction kit (Qiagen). .. The repaired DNA was recovered using Agincourt AMPure XP beads (A63880, Beckman Coulter), washed twice in 200 μl 70% ethanol and eluted in 46 μl dH2 O. DNA was then dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (E7546, New England Biolabs) according to the manufacturer's instructions and recovered using Agincourt AMPure XP beads as before, eluting in 30 μl dH2 O.

    Article Title: Recovery of the first full-length genome sequence of a parapoxvirus directly from a clinical sample
    Article Snippet: Briefly, 1 µg of the genomic DNA isolated from skin lesions was fragmented to an average size of 8–15 kb using g-TUBEs (Covaris). .. DNA fragments were end-repaired and adenylated using NEBNext Ultra II End-Repair/dA-tailing Module (NEB) followed by cleanup with Ampure XP beads (Beckmann Coulter).

    Purification:

    Article Title: Complete Genome Sequence Reveals Evolutionary Dynamics of an Emerging and Variant Pathovar of Xanthomonas euvesicatoria
    Article Snippet: Purification of the genomic DNA was again performed with AMPure beads to ensure the concentration remains > 1 µg (in 45 µl). .. DNA end repair was performed using NEBNext Ultra II End repair/dA-Tailing Module (NEB, Ipswich) and again Ampure XP beads (Beckman Coulter) were used to perform the cleanup.

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: The 2 primer pools for each sample were then pooled and purified with 1.8× Agencourt AMPure XP magnetic beads (Beckman Coulter). .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Article Title: Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast
    Article Snippet: Restriction digest products ranging from 2,062 to 2,229, 2,549 to 2,716 and 1,885 to 2,052 bp for the pcbC , pclA and penDE assemblies, respectively, were purified. .. The repaired DNA was recovered using Agincourt AMPure XP beads (A63880, Beckman Coulter), washed twice in 200 μl 70% ethanol and eluted in 46 μl dH2 O. DNA was then dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (E7546, New England Biolabs) according to the manufacturer's instructions and recovered using Agincourt AMPure XP beads as before, eluting in 30 μl dH2 O.

    Article Title: In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities
    Article Snippet: Water was then added to beads, and the 45 μL eluate used for end repair and dA-tailing of DNA using NEBNext Ultra II End-repair/dA tailing kit (New England Biolabs). .. The 10 μL of eluate was used for adapter ligation using the NEB Blunt/TA Ligase Master Mix (New England Bioloabs) with the Low Input Hairpin Tether from the low input expansion pack (EXP-LWI001).

    Article Title: Forensic SNP Genotyping using Nanopore MinION Sequencing
    Article Snippet: End-repair was performed on 1.034 μg of the concatenated amplicons using the Ultra II End-Repair/dA-Tailing module (NEB, Ipswich, USA) according to the manufacturer’s instructions. .. End-repair was performed on 1.034 μg of the concatenated amplicons using the Ultra II End-Repair/dA-Tailing module (NEB, Ipswich, USA) according to the manufacturer’s instructions.

    Article Title: Rapid re-identification of human samples using portable DNA sequencing
    Article Snippet: The DNA sample was end-repaired and dA-tailed using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs [NEB] E7546S; 5 min 20°C, and 5 min 65°C). .. After an AMPure purification, the DNA fragments were subject to ligation using Blunt/TA Ligase Master Mix (NEB M0367S) for 5 min at 20°C and then 5 min at 65°C.

    Article Title: A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
    Article Snippet: DNA was purified using 0.4× Agencourt AMPure XP beads (Beckman Coulter) and fragment distribution size was assessed using an Agilent 4200TapeStation (Agilent). .. We performed dA-tailing and end-repair using the NEBNext Ultra II End-repair/dA-tail module with two step incubation periods, of 20 min each.

    Article Title: The use of Oxford Nanopore native barcoding for complete genome assembly
    Article Snippet: The NEBNext Ultra II End Repair/dA Tailing kit (E7546S, NEB) was used to prepare 1000 ng of sheared genomic DNA (1000 ng DNA in 50 μl nuclease free water, 7 μl of Ultra II End-Prep Buffer, 3 μl Ultra II End-Prep Enzyme Mix in a total volume of 60 μl). .. The NEBNext Ultra II End Repair/dA Tailing kit (E7546S, NEB) was used to prepare 1000 ng of sheared genomic DNA (1000 ng DNA in 50 μl nuclease free water, 7 μl of Ultra II End-Prep Buffer, 3 μl Ultra II End-Prep Enzyme Mix in a total volume of 60 μl).

    Article Title: Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum
    Article Snippet: Briefly, the protocol for SQK-LSK308 is as follow: a total 1 µg of input DNA (a mixture of PCR amplicons from nine genes) was end-repaired and A-tailed using 1x Ultra II End-prep enzyme (New England Biolabs) incubated in 20 °C for 5 minutes and 65 °C for 5 minutes. .. Briefly, the protocol for SQK-LSK308 is as follow: a total 1 µg of input DNA (a mixture of PCR amplicons from nine genes) was end-repaired and A-tailed using 1x Ultra II End-prep enzyme (New England Biolabs) incubated in 20 °C for 5 minutes and 65 °C for 5 minutes.

    Article Title: Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia
    Article Snippet: For each sample, 300 ng of PCR purified products from each long-PCR were pooled, in a final volume of 25 uL in nuclease-free water and used for library preparation. .. According to the 2D Native barcoding genomic DNA (SQK-LSK 208) protocol, the amplicons were end-prepared using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs Inc.) and barcoded with the ligation of nanopore-specific Native Barcodes (NB01-NB12) using Blunt/TA Ligase Master Mix (New England Biolabs Inc.).

    Article Title: Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
    Article Snippet: 1000 ng of equimolar pooled amplicon from each SAV isolate was the input to a library generated with the Ligation Sequencing Kit 1D SQK-LSK108 (Oxford Nanopore Technologies). .. Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma). .. Sequencing adapters (AMX1D) (ONT) were ligated to the DNA using Blunt/TA Ligation Master Mix (New England Biolabs) by incubation at room temperature for 10 min.

    Sequencing:

    Article Title: Complete Genome Sequence Reveals Evolutionary Dynamics of an Emerging and Variant Pathovar of Xanthomonas euvesicatoria
    Article Snippet: Paragraph title: Bacterial Genomic DNA Isolation and ONT MinION Sequencing ... DNA end repair was performed using NEBNext Ultra II End repair/dA-Tailing Module (NEB, Ipswich) and again Ampure XP beads (Beckman Coulter) were used to perform the cleanup.

    Article Title: In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities
    Article Snippet: Paragraph title: MinION sequencing and analysis ... Water was then added to beads, and the 45 μL eluate used for end repair and dA-tailing of DNA using NEBNext Ultra II End-repair/dA tailing kit (New England Biolabs).

    Article Title: Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform
    Article Snippet: Paragraph title: Rapid multiplex MinION Sequencing library preparation ... ∼0.5 pmole of fragmented gDNA (165 ng ∼500-bp DNA) was subjected to a 30 µL end-repair/dA-tailing reaction using the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, Cat. E7546L) as detailed above with addition of 3 mM dATP after 5min incubation at 20°, followed by 5 min incubation at 65°.

    Article Title: Recovery of the first full-length genome sequence of a parapoxvirus directly from a clinical sample
    Article Snippet: Paragraph title: Oxford Nanopore library preparation and MinION sequencing ... DNA fragments were end-repaired and adenylated using NEBNext Ultra II End-Repair/dA-tailing Module (NEB) followed by cleanup with Ampure XP beads (Beckmann Coulter).

    Article Title: Rapid resistome mapping using nanopore sequencing
    Article Snippet: Sequencing library preparation was carried out with Nanopore Genomic Sequencing Kit SQK-MAP006 (Oxford Nanopore, UK) and a PCR-free ‘native barcoding’ kit according to the manufacturer's protocol. .. The NEBNext Ultra II End Repair/dA Tailing module (E7546S, NEB, USA) was used to prepare 1000 ng of the functionally selected DNA.

    Article Title: A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
    Article Snippet: Paragraph title: MinION library preparation and sequencing ... We performed dA-tailing and end-repair using the NEBNext Ultra II End-repair/dA-tail module with two step incubation periods, of 20 min each.

    Article Title: Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for “personalized monitoring” of residual disease in chronic myeloid leukemia patients
    Article Snippet: According to the 2D Native barcoding genomic DNA (SQK-LSK 208) protocol, the amplicons were end-prepared using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs Inc.) and barcoded with the ligation of nanopore-specific Native Barcodes (NB01-NB10) using Blunt/TA Ligase Master Mix (New England Biolabs Inc.). .. According to the 2D Native barcoding genomic DNA (SQK-LSK 208) protocol, the amplicons were end-prepared using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs Inc.) and barcoded with the ligation of nanopore-specific Native Barcodes (NB01-NB10) using Blunt/TA Ligase Master Mix (New England Biolabs Inc.).

    Article Title: The use of Oxford Nanopore native barcoding for complete genome assembly
    Article Snippet: Paragraph title: MinION(TM) library construction and sequencing ... The NEBNext Ultra II End Repair/dA Tailing kit (E7546S, NEB) was used to prepare 1000 ng of sheared genomic DNA (1000 ng DNA in 50 μl nuclease free water, 7 μl of Ultra II End-Prep Buffer, 3 μl Ultra II End-Prep Enzyme Mix in a total volume of 60 μl).

    Article Title: Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum
    Article Snippet: Four lab strains re-sequencing; 54 additional samples from North Sulawesi, Indonesia; 11 samples from Mahidol University, Bangkok, Thailand; 5 samples from NIHE, Hanoi, Vietnam; and 7 mixtures of 3D7 and Dd2 strains were prepared using the 1D2 Sequencing of Genomic DNA Kit (SQK-LSK308, ONT). .. Briefly, the protocol for SQK-LSK308 is as follow: a total 1 µg of input DNA (a mixture of PCR amplicons from nine genes) was end-repaired and A-tailed using 1x Ultra II End-prep enzyme (New England Biolabs) incubated in 20 °C for 5 minutes and 65 °C for 5 minutes.

    Article Title: Nanopore sequencing and assembly of a human genome with ultra-long reads
    Article Snippet: End repair and dA-tailing (NEBNext Ultra II End-Repair/dA-tailing Module) was then performed by adding 7 μl Ultra II End-Prep buffer, 3 μl Ultra II End-Prep enzyme mix, and 5 μl NFW. .. End repair and dA-tailing (NEBNext Ultra II End-Repair/dA-tailing Module) was then performed by adding 7 μl Ultra II End-Prep buffer, 3 μl Ultra II End-Prep enzyme mix, and 5 μl NFW.

    Article Title: Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia
    Article Snippet: Paragraph title: Library preparation and sequencing ... According to the 2D Native barcoding genomic DNA (SQK-LSK 208) protocol, the amplicons were end-prepared using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs Inc.) and barcoded with the ligation of nanopore-specific Native Barcodes (NB01-NB12) using Blunt/TA Ligase Master Mix (New England Biolabs Inc.).

    Article Title: Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
    Article Snippet: 1000 ng of equimolar pooled amplicon from each SAV isolate was the input to a library generated with the Ligation Sequencing Kit 1D SQK-LSK108 (Oxford Nanopore Technologies). .. Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma). .. Sequencing adapters (AMX1D) (ONT) were ligated to the DNA using Blunt/TA Ligation Master Mix (New England Biolabs) by incubation at room temperature for 10 min.

    Shotgun Sequencing:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. .. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA.

    Plasmid Preparation:

    Article Title: Culture-independent analysis of liver abscess using nanopore sequencing
    Article Snippet: DNA treated with Plasmid-Safe ATP-Dependent DNase (Epicentre, E3101K) was sheared in a Covaris g-Tube (Covaris, 520079) using a centrifuge (Eppendorf, 5424R) at a speed of 6,000 rpm for 1 minute. .. The fragmented DNA in 50 μL nuclease-free water was incubated in a 7 μL Ultra II End-Prep buffer and a 3 μL Ultra II End-Prep enzyme mix from NEBNext Ultra™ II End Repair/dA-Tailing Module (New England Biolabs, E7546S) at a temperature of 20°C for 5 minutes and 65°C for 5 minutes, respectively.

    Software:

    Article Title: Complete Genome Sequence Reveals Evolutionary Dynamics of an Emerging and Variant Pathovar of Xanthomonas euvesicatoria
    Article Snippet: DNA end repair was performed using NEBNext Ultra II End repair/dA-Tailing Module (NEB, Ipswich) and again Ampure XP beads (Beckman Coulter) were used to perform the cleanup. .. Fifty microliters of the pooled DNA sample was used for adapter ligation using T4 DNA ligase.

    Article Title: A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
    Article Snippet: We performed dA-tailing and end-repair using the NEBNext Ultra II End-repair/dA-tail module with two step incubation periods, of 20 min each. .. The library was then ready for MinION sequencing.

    Article Title: Nanopore sequencing for rapid diagnostics of salmonid RNA viruses
    Article Snippet: Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma). .. Before ligating sequencing adaptors, DNA was end-repaired using the NEBNext Ultra II End Repair/dA Tailing kit (New England Biolabs), purified using AMPure XP beads (Beckman Coulter) in a ratio of 1:1 volume of beads per sample and eluted in 30 µl of nuclease-free water (Sigma).

    Multiplex Assay:

    Article Title: Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform
    Article Snippet: Paragraph title: Rapid multiplex MinION Sequencing library preparation ... ∼0.5 pmole of fragmented gDNA (165 ng ∼500-bp DNA) was subjected to a 30 µL end-repair/dA-tailing reaction using the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, Cat. E7546L) as detailed above with addition of 3 mM dATP after 5min incubation at 20°, followed by 5 min incubation at 65°.

    Selection:

    Article Title: Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
    Article Snippet: These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA. .. These results were then compared to those obtained with a library preparation without prior WGA using an NEBNext Ultra II paired-end kit, which requires a very small amount of input DNA.

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: This panel was designed for the low-flow study to create a selection of possible candidate genes for overgrowth on the basis of the genes/pathways already known to be involved in this phenotype. .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Article Title: Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform
    Article Snippet: ∼0.5 pmole of fragmented gDNA (165 ng ∼500-bp DNA) was subjected to a 30 µL end-repair/dA-tailing reaction using the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, Cat. E7546L) as detailed above with addition of 3 mM dATP after 5min incubation at 20°, followed by 5 min incubation at 65°. .. ∼0.5 pmole of fragmented gDNA (165 ng ∼500-bp DNA) was subjected to a 30 µL end-repair/dA-tailing reaction using the NEBNext Ultra II End Repair/dA-Tailing Module (NEB, Cat. E7546L) as detailed above with addition of 3 mM dATP after 5min incubation at 20°, followed by 5 min incubation at 65°.

    Agarose Gel Electrophoresis:

    Article Title: Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast
    Article Snippet: Restriction digest products ranging from 5,616 to 6,117 bp were isolated by agarose gel electrophoresis and purified using a QIAquick gel extraction kit (Qiagen). .. The repaired DNA was recovered using Agincourt AMPure XP beads (A63880, Beckman Coulter), washed twice in 200 μl 70% ethanol and eluted in 46 μl dH2 O. DNA was then dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (E7546, New England Biolabs) according to the manufacturer's instructions and recovered using Agincourt AMPure XP beads as before, eluting in 30 μl dH2 O.

    Concentration Assay:

    Article Title: Complete Genome Sequence Reveals Evolutionary Dynamics of an Emerging and Variant Pathovar of Xanthomonas euvesicatoria
    Article Snippet: Purification of the genomic DNA was again performed with AMPure beads to ensure the concentration remains > 1 µg (in 45 µl). .. DNA end repair was performed using NEBNext Ultra II End repair/dA-Tailing Module (NEB, Ipswich) and again Ampure XP beads (Beckman Coulter) were used to perform the cleanup.

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB). .. Ligation products were purified and size selected using 0.8× Agencourt AMPure XP beads.

    Article Title: The use of Oxford Nanopore native barcoding for complete genome assembly
    Article Snippet: DNA from an overnight culture was extracted using the Qiagen Genomic Tip 500/G Kit, following the manufacturer's instructions, except lysozyme was replaced with lysostaphin to a final concentration of 200 μg/ml. .. The NEBNext Ultra II End Repair/dA Tailing kit (E7546S, NEB) was used to prepare 1000 ng of sheared genomic DNA (1000 ng DNA in 50 μl nuclease free water, 7 μl of Ultra II End-Prep Buffer, 3 μl Ultra II End-Prep Enzyme Mix in a total volume of 60 μl).

    Gel Extraction:

    Article Title: Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast
    Article Snippet: Restriction digest products ranging from 5,616 to 6,117 bp were isolated by agarose gel electrophoresis and purified using a QIAquick gel extraction kit (Qiagen). .. The repaired DNA was recovered using Agincourt AMPure XP beads (A63880, Beckman Coulter), washed twice in 200 μl 70% ethanol and eluted in 46 μl dH2 O. DNA was then dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (E7546, New England Biolabs) according to the manufacturer's instructions and recovered using Agincourt AMPure XP beads as before, eluting in 30 μl dH2 O.

    Variant Assay:

    Article Title: Mosaic RAS/MAPK variants cause sporadic vascular malformations which respond to targeted therapy
    Article Snippet: Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB). .. Amplicons were 3′ adenylated using the NebNext Ultra II End Repair/dA Tailing Module (NEB), followed by the NextFlex DNA Barcode adapter (Bio Scientific) ligation using the NebNext Ultra II ligation module (NEB).

    Nanopore Sequencing:

    Article Title: Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast
    Article Snippet: Paragraph title: Nanopore sequencing of library construction ... The repaired DNA was recovered using Agincourt AMPure XP beads (A63880, Beckman Coulter), washed twice in 200 μl 70% ethanol and eluted in 46 μl dH2 O. DNA was then dA-tailed using NEBNext Ultra II End Repair/dA-Tailing Module (E7546, New England Biolabs) according to the manufacturer's instructions and recovered using Agincourt AMPure XP beads as before, eluting in 30 μl dH2 O.

    Article Title: Forensic SNP Genotyping using Nanopore MinION Sequencing
    Article Snippet: Paragraph title: Nanopore Sequencing ... End-repair was performed on 1.034 μg of the concatenated amplicons using the Ultra II End-Repair/dA-Tailing module (NEB, Ipswich, USA) according to the manufacturer’s instructions.

    Article Title: Rapid resistome mapping using nanopore sequencing
    Article Snippet: Paragraph title: Nanopore sequencing library preparation ... The NEBNext Ultra II End Repair/dA Tailing module (E7546S, NEB, USA) was used to prepare 1000 ng of the functionally selected DNA.

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