cdna fragments  (New England Biolabs)


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  • 93
    Name:
    NEBNext FFPE DNA Repair Mix
    Description:
    NEBNext FFPE DNA Repair Mix 96 rxns
    Catalog Number:
    m6630l
    Price:
    575
    Size:
    96 rxns
    Category:
    DNA Template Preparation for PCR
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    Structured Review

    New England Biolabs cdna fragments
    NEBNext FFPE DNA Repair Mix
    NEBNext FFPE DNA Repair Mix 96 rxns
    https://www.bioz.com/result/cdna fragments/product/New England Biolabs
    Average 93 stars, based on 45 article reviews
    Price from $9.99 to $1999.99
    cdna fragments - by Bioz Stars, 2020-04
    93/100 stars

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    Related Articles

    Amplification:

    Article Title: A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples
    Article Snippet: DNA was then repaired using the NEBNext® FFPE DNA Repair Mix, according the manufacturer’s protocol (New England Biolabs, Hitchin, UK). .. Library preparation was performed using the NEBNext® Ultra II™ DNA Library Prep Kit for Illumina® according to the manufacturer’s protocol for FFPE samples (New England Biolabs; half volumes of all reagents were used in the pilot experiment) and 10 cycles of library amplification, during which the library was indexed using custom PE1.0 (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′) and indexed reverse primer (5′-CAAGCAGAAGACGGCATACGAGAT CGTGAT GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′; index sequence underlined).

    Whole Genome Amplification:

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
    Article Snippet: NEB next FFPE repair The NEB Next FFPE Repair kit (NEB M6630, New England® Biolabs Inc) was used for repairing 150 ng of total DNA, according to the manufacturer’s protocol with a minor change of eluting DNA in 30 μL instead of 40 μL. .. A total of 10 μL of eluted DNA (total 50 ng of repaired DNA) was used for WGA using the Sigma WGA kit as described above.

    DNA Ligation:

    Article Title: The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
    Article Snippet: Four Oxford Nanopore Technologies (ONT) libraries were prepared using the Ligation Sequencing Kit 1D (SQK-LSK108 ONT), according to the manufacturer’s protocol 1D Genomic DNA by ligation (SQK-LSK108). .. A DNA Repair (NEBNext FFPE Repair Mix M6630) step as well as an End-repair and dA-tail step (NEBNext End repair / dA-tailing Module E7546) were then processed on 0.34 pmols of the sheared DNA sample, followed by ligation of sequencing adapters.

    Construct:

    Article Title: Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding
    Article Snippet: MinION Library Preparation and Sequencing Using the ligation methodology, a nanopore sequencing library was constructed using the ligation sequencing kit 1D (SQK-LSK108) and the native barcoding kit (EXP-NBD103) for 12 samples. .. Fragmented DNA was repaired and dA-tailed using the NEBNext FFPE DNA Repair Mix and NEBNext Ultra II End Repair/dA-Tailing Module (New England BioLabs).

    Incubation:

    Article Title: Sequencing of human genomes with nanopore technology
    Article Snippet: .. The sample was split into three 50 μl aliquots, each mixed with 6.5 μl of NEBNext FFPE DNA Repair Buffer, 2 μl of NEBNext FFPE DNA Repair Mix (New England Biolab, M6630), and 3.5 μl of nuclease-free water (NFW) and incubated at 20 °C for 15 min for DNA repair, re-pooled and cleaned up using a 0.8 × volume of AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions, with final elution in 30 μl of EB (10 mM Tris pH 8.0). .. The size of the sheared DNA was assessed using a TapeStation Genomic DNA system (Agilent).

    Article Title: The complex architecture and epigenomic impact of plant T-DNA insertions
    Article Snippet: Briefly, approximately 2 μg of purified DNA was repaired with NEBNext FFPE Repair Mix for 60 min at 20°C. .. Adapter mix (ONT, Oxford, UK) was added to the purified DNA along with Blunt/TA Ligase Master Mix (NEB) and incubated at 20°C for 30 min followed by 10 min at 65°C.

    Article Title: Picky Comprehensively Detects High Resolution Structural Variants in Nanopore Long Reads
    Article Snippet: Briefly, NEBNext FFPE RepairMix (NEB, M6630) was added to repair nicks in the DNA. .. 1 μL Hairpin Tether (HPT) was added to the reaction and incubated at room temperature for 15 minutes.

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: The recommended SQK-LSK109 protocol for library preparation for PromethION (ONT) sequencing was followed with slight increases in all enzymatic incubation times and during elution. .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Sequencing of human genomes with nanopore technology
    Article Snippet: .. The sample was split into three 50 μl aliquots, each mixed with 6.5 μl of NEBNext FFPE DNA Repair Buffer, 2 μl of NEBNext FFPE DNA Repair Mix (New England Biolab, M6630), and 3.5 μl of nuclease-free water (NFW) and incubated at 20 °C for 15 min for DNA repair, re-pooled and cleaned up using a 0.8 × volume of AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions, with final elution in 30 μl of EB (10 mM Tris pH 8.0). .. The size of the sheared DNA was assessed using a TapeStation Genomic DNA system (Agilent).

    Article Title: The complex architecture and epigenomic impact of plant T-DNA insertions
    Article Snippet: .. Briefly, approximately 2 μg of purified DNA was repaired with NEBNext FFPE Repair Mix for 60 min at 20°C. .. The DNA was purified with 0.5X Ampure XP beads (Beckman Coulter, Brea).

    Article Title: Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding
    Article Snippet: .. Fragmented DNA was repaired and dA-tailed using the NEBNext FFPE DNA Repair Mix and NEBNext Ultra II End Repair/dA-Tailing Module (New England BioLabs). .. An individual barcode was added to dA-tailed DNA by using the NEB Blunt/TA Ligase Master Mix (New England BioLabs).

    Article Title: A robust targeted sequencing approach for low input and variable quality DNA from clinical samples
    Article Snippet: .. In the cases where the TOMA repair was replaced by NEB repair (NEBNext FFPE DNA Repair Mix, NEB, Ipswich, MA), the same amount of DNA as for other repair treatments were repaired using the NEB kit following the manufacturer’s recommendations. .. The repaired DNA was then purified using the TOMA purification protocol using 2 volumes of sREP+ beads, resuspended in 40 μl elution buffer, and processed starting from the kinase step.

    Article Title: Picky Comprehensively Detects High Resolution Structural Variants in Nanopore Long Reads
    Article Snippet: .. Briefly, NEBNext FFPE RepairMix (NEB, M6630) was added to repair nicks in the DNA. .. Then end-repair and dA-tailing were performed using NEBNext Ultra II End-Repair/dA-tailing Module (NEB, E7546).

    Article Title: Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
    Article Snippet: .. NEB next FFPE repair The NEB Next FFPE Repair kit (NEB M6630, New England® Biolabs Inc) was used for repairing 150 ng of total DNA, according to the manufacturer’s protocol with a minor change of eluting DNA in 30 μL instead of 40 μL. .. A total of 10 μL of eluted DNA (total 50 ng of repaired DNA) was used for WGA using the Sigma WGA kit as described above.

    Article Title: Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines
    Article Snippet: .. DNA repair was performed using NEBNext FFPE Repair Mix (M6630, NEB). .. End-prep was performed using a NEBNext End repair/dA-tailing Module (E7546, NEB) and end-prepped DNAs were purified using Agencourt AMPure XP beads (Beckman Coulter).

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    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: The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
    Article Snippet: .. A DNA Repair (NEBNext FFPE Repair Mix M6630) step as well as an End-repair and dA-tail step (NEBNext End repair / dA-tailing Module E7546) were then processed on 0.34 pmols of the sheared DNA sample, followed by ligation of sequencing adapters. .. Then 0.07 pmols of library were loaded onto an R9.5 flow cell containing at least 800 active pores and run for 48 hr, on a MinION sequencer (ONT) and sequenced by the Minknow ONT software (v1.7.10 or v1.7.14).

    Article Title: A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples
    Article Snippet: .. DNA was then repaired using the NEBNext® FFPE DNA Repair Mix, according the manufacturer’s protocol (New England Biolabs, Hitchin, UK). .. Library preparation was performed using the NEBNext® Ultra II™ DNA Library Prep Kit for Illumina® according to the manufacturer’s protocol for FFPE samples (New England Biolabs; half volumes of all reagents were used in the pilot experiment) and 10 cycles of library amplification, during which the library was indexed using custom PE1.0 (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′) and indexed reverse primer (5′-CAAGCAGAAGACGGCATACGAGAT CGTGAT GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′; index sequence underlined).

    Flow Cytometry:

    Article Title: Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines
    Article Snippet: DNA repair was performed using NEBNext FFPE Repair Mix (M6630, NEB). .. Libraries were then purified using MyOne C1 beads (65001, Thermo Fisher Scientific) and sequenced for 48 hours by MinION Mk 1B with the SpotON Flow Cell (FLO-MIN106, R9.4 version for 2D; FLO-MIN107, R9.5 version for 1D and 1D2 , Oxford Nanopore Technologies).

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    Article Title: The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
    Article Snippet: A DNA Repair (NEBNext FFPE Repair Mix M6630) step as well as an End-repair and dA-tail step (NEBNext End repair / dA-tailing Module E7546) were then processed on 0.34 pmols of the sheared DNA sample, followed by ligation of sequencing adapters. .. Then 0.07 pmols of library were loaded onto an R9.5 flow cell containing at least 800 active pores and run for 48 hr, on a MinION sequencer (ONT) and sequenced by the Minknow ONT software (v1.7.10 or v1.7.14).

    Ligation:

    Article Title: The complex architecture and epigenomic impact of plant T-DNA insertions
    Article Snippet: The purified DNA was prepared for sequencing with the Ligation Sequencing Kit 1D (SQK-LSK108, ONT, Oxford, UK) sequencing kit protocol. .. Briefly, approximately 2 μg of purified DNA was repaired with NEBNext FFPE Repair Mix for 60 min at 20°C.

    Article Title: Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding
    Article Snippet: MinION Library Preparation and Sequencing Using the ligation methodology, a nanopore sequencing library was constructed using the ligation sequencing kit 1D (SQK-LSK108) and the native barcoding kit (EXP-NBD103) for 12 samples. .. Fragmented DNA was repaired and dA-tailed using the NEBNext FFPE DNA Repair Mix and NEBNext Ultra II End Repair/dA-Tailing Module (New England BioLabs).

    Article Title: A robust targeted sequencing approach for low input and variable quality DNA from clinical samples
    Article Snippet: In the cases where the TOMA repair was replaced by NEB repair (NEBNext FFPE DNA Repair Mix, NEB, Ipswich, MA), the same amount of DNA as for other repair treatments were repaired using the NEB kit following the manufacturer’s recommendations. .. After DNA repair, DNA concentrations were measured via ddPCR as described and an appropriate amount of DNA was used as input to ligation.

    Article Title: Picky Comprehensively Detects High Resolution Structural Variants in Nanopore Long Reads
    Article Snippet: Briefly, NEBNext FFPE RepairMix (NEB, M6630) was added to repair nicks in the DNA. .. For 2D libraries (WTD01-WTD13), we prepared the ligation reaction as below: 38 μL water (DNA), 10 μL Adapter Mix (AMX), 2 μL Hairpin Adapter (HPA) and 50 μL Blunt/TA Ligase Master Mix (New England Biolabs, M0367).

    Article Title: Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines
    Article Snippet: DNA repair was performed using NEBNext FFPE Repair Mix (M6630, NEB). .. Adapter ligation and tether attachment were conducted using the NEBNext Blunt/TA Ligase Master Mix (M0367S, NEB) and Ligation Sequencing Kit SQK-LSK208 for 2D, SQK-LSK108 for 1D and SQK-LSK308 for 1D2 .

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    Article Title: The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
    Article Snippet: .. A DNA Repair (NEBNext FFPE Repair Mix M6630) step as well as an End-repair and dA-tail step (NEBNext End repair / dA-tailing Module E7546) were then processed on 0.34 pmols of the sheared DNA sample, followed by ligation of sequencing adapters. .. Then 0.07 pmols of library were loaded onto an R9.5 flow cell containing at least 800 active pores and run for 48 hr, on a MinION sequencer (ONT) and sequenced by the Minknow ONT software (v1.7.10 or v1.7.14).

    DNA Sequencing:

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    Sequencing:

    Article Title: The complex architecture and epigenomic impact of plant T-DNA insertions
    Article Snippet: Paragraph title: ONT library prep and sequencing ... Briefly, approximately 2 μg of purified DNA was repaired with NEBNext FFPE Repair Mix for 60 min at 20°C.

    Article Title: Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding
    Article Snippet: Paragraph title: MinION Library Preparation and Sequencing ... Fragmented DNA was repaired and dA-tailed using the NEBNext FFPE DNA Repair Mix and NEBNext Ultra II End Repair/dA-Tailing Module (New England BioLabs).

    Article Title: A robust targeted sequencing approach for low input and variable quality DNA from clinical samples
    Article Snippet: Briefly, to select the set of targeting sequences, a melting temperature compatible with the annealing temperature was selected to delineate candidate primers considering the annealing buffer composition, and sequences were scored with an empirical scheme that accounted for both intrinsic features of the primer sequence, such as G + C content, homopolymers, and secondary structure, as well as genomic features such as the presence of SNPs identified within the dbSNP database, relative target position, the anticipated contribution to ROI coverage, and the predicted specificity of the primer across the genome. .. In the cases where the TOMA repair was replaced by NEB repair (NEBNext FFPE DNA Repair Mix, NEB, Ipswich, MA), the same amount of DNA as for other repair treatments were repaired using the NEB kit following the manufacturer’s recommendations.

    Article Title: Picky Comprehensively Detects High Resolution Structural Variants in Nanopore Long Reads
    Article Snippet: Paragraph title: Nanopore long read sequencing ... Briefly, NEBNext FFPE RepairMix (NEB, M6630) was added to repair nicks in the DNA.

    Article Title: Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines
    Article Snippet: Paragraph title: Validation by physical long-read sequencing of MinION ... DNA repair was performed using NEBNext FFPE Repair Mix (M6630, NEB).

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: Paragraph title: Whole genome sequencing (WGS) ... In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

    Article Title: The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
    Article Snippet: .. A DNA Repair (NEBNext FFPE Repair Mix M6630) step as well as an End-repair and dA-tail step (NEBNext End repair / dA-tailing Module E7546) were then processed on 0.34 pmols of the sheared DNA sample, followed by ligation of sequencing adapters. .. Then 0.07 pmols of library were loaded onto an R9.5 flow cell containing at least 800 active pores and run for 48 hr, on a MinION sequencer (ONT) and sequenced by the Minknow ONT software (v1.7.10 or v1.7.14).

    Article Title: A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples
    Article Snippet: DNA was then repaired using the NEBNext® FFPE DNA Repair Mix, according the manufacturer’s protocol (New England Biolabs, Hitchin, UK). .. Library preparation was performed using the NEBNext® Ultra II™ DNA Library Prep Kit for Illumina® according to the manufacturer’s protocol for FFPE samples (New England Biolabs; half volumes of all reagents were used in the pilot experiment) and 10 cycles of library amplification, during which the library was indexed using custom PE1.0 (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′) and indexed reverse primer (5′-CAAGCAGAAGACGGCATACGAGAT CGTGAT GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′; index sequence underlined).

    Sonication:

    Article Title: A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples
    Article Snippet: WGS library preparation—standard protocol Good quality FFPE DNA was sonicated using the Covaris M220 focused ultrasonicator to an average fragment size of 300 bp; poor and very poor quality samples did not require further fragmentation ( ). .. DNA was then repaired using the NEBNext® FFPE DNA Repair Mix, according the manufacturer’s protocol (New England Biolabs, Hitchin, UK).

    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.

    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 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.

    Purification:

    Article Title: The complex architecture and epigenomic impact of plant T-DNA insertions
    Article Snippet: .. Briefly, approximately 2 μg of purified DNA was repaired with NEBNext FFPE Repair Mix for 60 min at 20°C. .. The DNA was purified with 0.5X Ampure XP beads (Beckman Coulter, Brea).

    Article Title: A robust targeted sequencing approach for low input and variable quality DNA from clinical samples
    Article Snippet: In the cases where the TOMA repair was replaced by NEB repair (NEBNext FFPE DNA Repair Mix, NEB, Ipswich, MA), the same amount of DNA as for other repair treatments were repaired using the NEB kit following the manufacturer’s recommendations. .. The repaired DNA was then purified using the TOMA purification protocol using 2 volumes of sREP+ beads, resuspended in 40 μl elution buffer, and processed starting from the kinase step.

    Article Title: Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines
    Article Snippet: DNA repair was performed using NEBNext FFPE Repair Mix (M6630, NEB). .. End-prep was performed using a NEBNext End repair/dA-tailing Module (E7546, NEB) and end-prepped DNAs were purified using Agencourt AMPure XP beads (Beckman Coulter).

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences. .. The final library (100 fmol) was loaded on a PromethION flow cell with 8021 active pores at the start, following the default protocol for PromethION DNA sequencing.

    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 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.

    Article Title: A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples
    Article Snippet: DNA was then repaired using the NEBNext® FFPE DNA Repair Mix, according the manufacturer’s protocol (New England Biolabs, Hitchin, UK). .. The library was purified and quantified using the same methods as described for DDAT.

    Plasmid Preparation:

    Article Title: Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast
    Article Snippet: Nanopore sequencing of library construction To enrich for the penicillin pathway assembly DNA and remove assembly vector backbone DNA, the multigene assembly library was digested with EcoRI and AlwNI. .. 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.

    Software:

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: Additionally, the public genome data repository of Complete Genomics Inc. containing freely accessible WGS data of 69 individuals, 52 unrelated individuals (software version 1.10.0; http://www.completegenomics.com/public-data/ ) [ ], as well as WGS data from 427 individuals (157 unrelated) sequenced by Complete Genomics Inc. (software version 2.2.0) and distributed by the 1000 genome project [ ] were used for comparative purposes. .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

    Article Title: The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird
    Article Snippet: A DNA Repair (NEBNext FFPE Repair Mix M6630) step as well as an End-repair and dA-tail step (NEBNext End repair / dA-tailing Module E7546) were then processed on 0.34 pmols of the sheared DNA sample, followed by ligation of sequencing adapters. .. Then 0.07 pmols of library were loaded onto an R9.5 flow cell containing at least 800 active pores and run for 48 hr, on a MinION sequencer (ONT) and sequenced by the Minknow ONT software (v1.7.10 or v1.7.14).

    Multiplex Assay:

    Article Title: A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples
    Article Snippet: DNA was then repaired using the NEBNext® FFPE DNA Repair Mix, according the manufacturer’s protocol (New England Biolabs, Hitchin, UK). .. For the pilot experiment, the library was dual indexed using NEBNext® Multiplex Oligos for Illumina® (NEB).

    Selection:

    Article Title: Picky Comprehensively Detects High Resolution Structural Variants in Nanopore Long Reads
    Article Snippet: For libraries targeted at 12 Kb, size selection was performed for sheared fragments larger than 10 Kb using 0.75% agarose cassette (Sage Science, BLF7510) by Blue Pippin™ DNA Size Selection System. .. Briefly, NEBNext FFPE RepairMix (NEB, M6630) was added to repair nicks in the DNA.

    Agarose Gel Electrophoresis:

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: Prior to library preparation, the DNA was sheared to 35 kb using the Megaruptor (Diagenode, BE) and size selected to a minimal length of 6 kb on the BluePippin (Sage Science, MA, USA) using a High-pass protocol and the S1 external marker on a 0.75% agarose gel (Sage Science, USA). .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

    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 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.

    Ethanol Precipitation:

    Article Title: The complex architecture and epigenomic impact of plant T-DNA insertions
    Article Snippet: An ethanol precipitation was performed as before for 3 hours at 4°C, washed, and resuspended overnight in 350μL 1x TE buffer. .. Briefly, approximately 2 μg of purified DNA was repaired with NEBNext FFPE Repair Mix for 60 min at 20°C.

    Marker:

    Article Title: Sequencing of human genomes with nanopore technology
    Article Snippet: The sample was split into three 50 μl aliquots, each mixed with 6.5 μl of NEBNext FFPE DNA Repair Buffer, 2 μl of NEBNext FFPE DNA Repair Mix (New England Biolab, M6630), and 3.5 μl of nuclease-free water (NFW) and incubated at 20 °C for 15 min for DNA repair, re-pooled and cleaned up using a 0.8 × volume of AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions, with final elution in 30 μl of EB (10 mM Tris pH 8.0). .. To remove small, unwanted fragments of DNA, the sample was size-selected using a BluePippin™ gel cassette (BLF7510, Sage Science) using the 0.75% DF Marker S1 high-pass 6–10 kb vs3 cassette definition, with Range mode and BP start set at 6000 bp.

    Article Title: Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
    Article Snippet: Prior to library preparation, the DNA was sheared to 35 kb using the Megaruptor (Diagenode, BE) and size selected to a minimal length of 6 kb on the BluePippin (Sage Science, MA, USA) using a High-pass protocol and the S1 external marker on a 0.75% agarose gel (Sage Science, USA). .. In short, DNA template damage and ends were repaired in a combined step using NEBNext FFPE DNA Repair Mix and NEBNext Ultra II ER/dAT Module (New England Biolabs, USA) followed by AMPureXP (Beckman Coulter, CA, USA) bead purification and ligation of platform-specific adapter sequences.

    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 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.

    Nanopore Sequencing:

    Article Title: Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding
    Article Snippet: MinION Library Preparation and Sequencing Using the ligation methodology, a nanopore sequencing library was constructed using the ligation sequencing kit 1D (SQK-LSK108) and the native barcoding kit (EXP-NBD103) for 12 samples. .. Fragmented DNA was repaired and dA-tailed using the NEBNext FFPE DNA Repair Mix and NEBNext Ultra II End Repair/dA-Tailing Module (New England BioLabs).

    Article Title: Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast
    Article Snippet: Paragraph title: Nanopore sequencing of library construction ... 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.

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  • 90
    New England Biolabs cdna library solution
    Cdna Library Solution, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cdna library solution/product/New England Biolabs
    Average 90 stars, based on 1 article reviews
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    cdna library solution - by Bioz Stars, 2020-04
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