end repair module  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Name:
    NEBNext End Repair Reaction Buffer
    Description:
    NEBNext End Repair Reaction Buffer 2 0 ml
    Catalog Number:
    B6052S
    Price:
    41
    Size:
    2 0 ml
    Category:
    Buffers
    Score:
    85
    Buy from Supplier


    Structured Review

    New England Biolabs end repair module
    NEBNext End Repair Reaction Buffer
    NEBNext End Repair Reaction Buffer 2 0 ml
    https://www.bioz.com/result/end repair module/product/New England Biolabs
    Average 99 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    end repair module - by Bioz Stars, 2019-11
    99/100 stars

    Images

    Related Articles

    Amplification:

    Article Title: SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)
    Article Snippet: Next 25 μL of NEBNext® End Repair Module (New England Biolabs) master mix, containing 5 μl of NEBNext End Repair Reaction Buffer (10X) and 2.5 μl of NEBNext End Repair Enzyme Mix (10,000 units/ml T4 PNK; 3,000 units/ml T4 DNA Polymerase), were added to the biotinylated beads. .. Next 25 μL of NEBNext® End Repair Module (New England Biolabs) master mix, containing 5 μl of NEBNext End Repair Reaction Buffer (10X) and 2.5 μl of NEBNext End Repair Enzyme Mix (10,000 units/ml T4 PNK; 3,000 units/ml T4 DNA Polymerase), were added to the biotinylated beads.

    Article Title: Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana
    Article Snippet: Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation. .. Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation.

    Synthesized:

    Article Title: Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana
    Article Snippet: The second-strand cDNA was synthesized using buffer, dNTPs, RNase H, and DNA polymerase I, followed by AMPure XP bead purification. .. Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation.

    Article Title: Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription
    Article Snippet: Second strand cDNA was synthesized with Second Strand Synthesis Enzyme Mix in the kit and purified. .. After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer. .. Each purification was conducted using Ampure XP beads (Beckman).

    Construct:

    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. .. End repair was performed using the NEBNext End Repair Module (E6050, NEB, Hitchin, Hertfordshire, UK) by mixing 1.0 μg DNA dissolved in 10 μl 1× TE buffer, 5 μl Quality Control DNA CS, 10 μl 10× NEBNext End Repair Reaction buffer and 5 μl NEBNext End Repair Enzyme Mix in a total reaction volume of 100 μl.

    Article Title: Past climate changes, population dynamics and the origin of Bison in Europe
    Article Snippet: Dual barcoded libraries for Illumina sequencing were constructed in the dedicated ancient DNA facility at the Jacques Monod Institute (Paris, France) using a double-stranded procedure previously described [ , ]. .. Prior to library preparation, uracil residues were removed through treatment with 1.5 units/30 μL reaction volume of USER Enzyme (New England Biolabs, Ipswich, MA) for 60 min at 37 °C in NEBNext End Repair buffer (New England Biolabs).

    Article Title: Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription
    Article Snippet: Isolated poly-A tailed RNAs were used to construct an RNAseq library using NEBNext Ultra RNA library prep kit for illumina (NEB). .. After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer.

    Real-time Polymerase Chain Reaction:

    Article Title: Two-step Crosslinking for Analysis of Protein-Chromatin Interactions
    Article Snippet: Illumina Genome Analyzer II system and associated equipment, reagents, kits, and software. .. Prepare the following reaction mix: ChIP enriched, qPCR verified DNA (42.5ul) NEBNext End Repair Reaction Buffer (5ul) NEBNext End Repair Enzyme Mix (2.5ul) The total volume should be 50ul. .. Purify DNA on QIAquick column and elute in 42ul elution buffer.

    Incubation:

    Article Title: SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)
    Article Snippet: Next 10 μL of Dynabeads® MyOne™ Streptavidin C1 (10 μg/μL), previously washed three times with 50 μL of 2X Binding and Washing (B & W) Buffer (10 mM Tris-HCl pH 7.5; 1 mM EDTA, 2 M NaCl), were added to each sample and resuspended in 20 μL of 2X B & W. Samples were incubated for 30 min at room temperature in rotation in order to capture the biotinylated fragments. .. Next 25 μL of NEBNext® End Repair Module (New England Biolabs) master mix, containing 5 μl of NEBNext End Repair Reaction Buffer (10X) and 2.5 μl of NEBNext End Repair Enzyme Mix (10,000 units/ml T4 PNK; 3,000 units/ml T4 DNA Polymerase), were added to the biotinylated beads.

    Article Title: Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
    Article Snippet: End repair was performed using the NEBNext End Repair Module (E6050, NEB, Hitchin, Hertfordshire, UK) by mixing 1.0 μg DNA dissolved in 10 μl 1× TE buffer, 5 μl Quality Control DNA CS, 10 μl 10× NEBNext End Repair Reaction buffer and 5 μl NEBNext End Repair Enzyme Mix in a total reaction volume of 100 μl. .. The reaction was incubated for 20 min at 24 °C in a G-Storm GS1 (G-Storm) thermal cycler without heated lid.

    Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing
    Article Snippet: The NEBNext DNA Library Prep Master Mix Set for Illumina separates the filling-in step from dA-tailing reaction. .. Using the MspI fragmented DNA (40–85 μL) described above, the NEBNext End Repair Reaction Buffer (10X; 10 μL), and the NEBNext End Repair Enzyme Mix (5 μL), we incubated the solution (final volume of 100 μl) at 20°C for 30 minutes. .. After incubation, the reaction mixture was diluted to 200 μL with dH2 O.

    Article Title: MIRA-seq for DNA methylation analysis of CpG islands
    Article Snippet: Genomic DNA was sonicated to an average fragment size of 100–300 bp using a sonicator. .. For DNA end repair, we incubated 0.5–2 μg sonicated genomic DNA in 1× NEB end repair reaction buffer by adding 5 μl of NEB End Repair Enzyme mix (New England Biolabs, MA, USA) in a volume of 100 μl. .. The DNA was purified using QIAquick PCR purification kit (Qiagen) and eluted with 50 μl of water.

    Article Title: Past climate changes, population dynamics and the origin of Bison in Europe
    Article Snippet: Prior to library preparation, uracil residues were removed through treatment with 1.5 units/30 μL reaction volume of USER Enzyme (New England Biolabs, Ipswich, MA) for 60 min at 37 °C in NEBNext End Repair buffer (New England Biolabs). .. End-repaired DNA was purified on MinElute columns using the Qiagen Gel extraction protocol, and DNA was eluted twice, each with 16 μL of γ-irradiated H2 O [ ].

    Article Title: Personalized genomic analyses for cancer mutation discovery and interpretation
    Article Snippet: Purified, fragmented DNA was mixed with 36 μl of H2 O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix [cat# E6050, New England BioLabs (NEB)]. .. Purified, fragmented DNA was mixed with 36 μl of H2 O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix [cat# E6050, New England BioLabs (NEB)].

    Article Title: CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network
    Article Snippet: Purified, fragmented DNA was mixed with 36 μl of H2O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix (cat# E6050, NEB). .. Purified, fragmented DNA was mixed with 36 μl of H2O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix (cat# E6050, NEB).

    Article Title: Elucidating the pathogenesis of synchronous and metachronous tumors in a woman with endometrioid carcinomas using a whole-exome sequencing approach
    Article Snippet: Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050). .. Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050).

    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: In brief, DNA fragmented using the Covaris S2 in 50 μL was used for NEBNext End Prep, followed by an immediate adaptor ligation step with a 1.5 μM diluted adaptor. .. Clean-up of adaptor-ligated DNA without size selection was carried out followed by PCR amplification with eight cycles and ten cycles for 20 ng and 5 ng input, respectively.

    Article Title: Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq
    Article Snippet: We employed the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370S) to prepare a standard NGS library, with slight modification. .. Briefly, end preparation was performed in a reaction containing 18.5 μl of recovered DNA, 2.17 μl of NEBNext End Repair Reaction Buffer and 1 μl of NEBNext End Prep Enzyme Mix, with incubation for 30 min at 20 °C and 30 min at 65 °C. .. Then, 5 μl of Blunt/TA Ligase Master Mix, 0.33 μl of NEBNext Ligation Enhancer and 0.17 μl of barcode adaptor (Bioo Scientific, NEXTflex DNA Barcodes, 514102) were added to the mixture, followed by incubation at 20 °C for 30 min.

    Article Title: Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription
    Article Snippet: Second strand cDNA was synthesized with Second Strand Synthesis Enzyme Mix in the kit and purified. .. After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer. .. Each purification was conducted using Ampure XP beads (Beckman).

    Article Title: Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas
    Article Snippet: Purified, fragmented DNA was mixed with 40 μl of water, 10 μl of End-Repair Reaction buffer and 5 μl of End-Repair Enzyme Mix (E6050, NEB). .. Purified, fragmented DNA was mixed with 40 μl of water, 10 μl of End-Repair Reaction buffer and 5 μl of End-Repair Enzyme Mix (E6050, NEB).

    Article Title: Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients
    Article Snippet: Purified, fragmented DNA was mixed with 36 μl of H20, 10 μl of End-Repair Reaction Buffer, 5 μl of End-Repair Enzyme Mix (cat# E6050, NEB, Ipswich, MA). .. Purified, fragmented DNA was mixed with 36 μl of H20, 10 μl of End-Repair Reaction Buffer, 5 μl of End-Repair Enzyme Mix (cat# E6050, NEB, Ipswich, MA).

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: This was repeated after subsequent end repair and DA-tailing reactions with the respective modules supplied by New England Biolabs (Ipswich, MA, USA) (NEBNext™ DNA Sample Prep Reagent Set 1: E6000), following the manufacturer’s instructions. .. To ligate sequencing adaptors, a 50 μl reaction mixture containing the sample was set with addition of 25 μl of 2× DNA T4 ligase buffer (New England Biolabs, Inc.), 4 μl 4 μM Illumina paired-end duplex adaptors (Integrated DNA Technologies, Coralville, IA, USA) and 2 μl T4 DNA ligase.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Personalized genomic analyses for cancer mutation discovery and interpretation
    Article Snippet: In brief, DNA was extracted from frozen or FFPE tissue, along with matched blood or saliva samples using the Qiagen DNA FFPE Tissue Kit or Qiagen DNA Blood Mini Kit (Qiagen). .. Purified, fragmented DNA was mixed with 36 μl of H2 O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix [cat# E6050, New England BioLabs (NEB)].

    Article Title: Elucidating the pathogenesis of synchronous and metachronous tumors in a woman with endometrioid carcinomas using a whole-exome sequencing approach
    Article Snippet: Briefly, gDNA was extracted from frozen or FFPE tissue with matched saliva samples by using the QIAGEN DNA FFPE tissue kit or QIAGEN DNA blood mini kit (QIAGEN). .. Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050).

    Article Title: Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients
    Article Snippet: In brief, DNA was extracted from frozen or formalin-fixed paraffin-embedded tissue, along with matched blood or saliva samples using the Qiagen DNA formalin-fixed paraffin-embedded tissue kit or Qiagen DNA blood mini kit (Qiagen, CA). .. Purified, fragmented DNA was mixed with 36 μl of H20, 10 μl of End-Repair Reaction Buffer, 5 μl of End-Repair Enzyme Mix (cat# E6050, NEB, Ipswich, MA).

    Expressing:

    Article Title: Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription
    Article Snippet: After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer. .. After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer.

    Modification:

    Article Title: Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq
    Article Snippet: We employed the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370S) to prepare a standard NGS library, with slight modification. .. Briefly, end preparation was performed in a reaction containing 18.5 μl of recovered DNA, 2.17 μl of NEBNext End Repair Reaction Buffer and 1 μl of NEBNext End Prep Enzyme Mix, with incubation for 30 min at 20 °C and 30 min at 65 °C.

    Flow Cytometry:

    Article Title: Mapping targets for small nucleolar RNAs in yeast
    Article Snippet: 750 μl PE buffer was then added to the column and the column centrifuged as above, then the flow-through discarded. .. 10x NEBNext End Repair Reaction Buffer and 3 μl NEBNext End Prep Enzyme Mix were added to the thawed purified double stranded cDNA.

    Ancient DNA Assay:

    Article Title: Past climate changes, population dynamics and the origin of Bison in Europe
    Article Snippet: Ancient DNA extracts were quantified on a Qubit 2.0 Fluorimeter (Thermo Fisher Scientific, Waltham, MA). .. Prior to library preparation, uracil residues were removed through treatment with 1.5 units/30 μL reaction volume of USER Enzyme (New England Biolabs, Ipswich, MA) for 60 min at 37 °C in NEBNext End Repair buffer (New England Biolabs).

    other:

    Article Title: Genome-wide Mapping of Protein-DNA Interactions on Nascent Chromatin
    Article Snippet: Add 3 μl reaction buffer and 3 μl NEB End Repair Enzyme Mix to the bead suspension.

    Polymerase Chain Reaction:

    Article Title: Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology
    Article Snippet: Then 5 µl of DNA CS (Oxford Nanopore, SQK-MAP004), 10 µl of 10× NEBNext End Repair Reaction Buffer, and 5 µl of NEBNext End Repair Enzyme Mix were added to the size-selected DNA fragment and mixed by gently pipetting. .. Then 5 µl of DNA CS (Oxford Nanopore, SQK-MAP004), 10 µl of 10× NEBNext End Repair Reaction Buffer, and 5 µl of NEBNext End Repair Enzyme Mix were added to the size-selected DNA fragment and mixed by gently pipetting.

    Article Title: SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)
    Article Snippet: Next 25 μL of NEBNext® End Repair Module (New England Biolabs) master mix, containing 5 μl of NEBNext End Repair Reaction Buffer (10X) and 2.5 μl of NEBNext End Repair Enzyme Mix (10,000 units/ml T4 PNK; 3,000 units/ml T4 DNA Polymerase), were added to the biotinylated beads. .. Next 25 μL of NEBNext® End Repair Module (New England Biolabs) master mix, containing 5 μl of NEBNext End Repair Reaction Buffer (10X) and 2.5 μl of NEBNext End Repair Enzyme Mix (10,000 units/ml T4 PNK; 3,000 units/ml T4 DNA Polymerase), were added to the biotinylated beads.

    Article Title: Mapping targets for small nucleolar RNAs in yeast
    Article Snippet: Samples were then purified using a QIAquick PCR purification kit as follows: 5 volumes of PB buffer were added to 1 volume of PCR reaction and mixed. .. 10x NEBNext End Repair Reaction Buffer and 3 μl NEBNext End Prep Enzyme Mix were added to the thawed purified double stranded cDNA.

    Article Title: Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana
    Article Snippet: Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation. .. Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation.

    Article Title: Personalized genomic analyses for cancer mutation discovery and interpretation
    Article Snippet: To remove fragments smaller than 150 bp, DNA was purified using Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1.0:0.9 of polymerase chain reaction (PCR) product to beads twice and washed using 70% ethanol per the manufacturer’s instructions. .. Purified, fragmented DNA was mixed with 36 μl of H2 O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix [cat# E6050, New England BioLabs (NEB)].

    Article Title: CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network
    Article Snippet: To remove fragments smaller than 150bp, DNA was purified using Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1.0 to 0.9 of PCR product to beads twice and washed using 70% ethanol per the manufacturer's instructions. .. Purified, fragmented DNA was mixed with 36 μl of H2O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix (cat# E6050, NEB).

    Article Title: Elucidating the pathogenesis of synchronous and metachronous tumors in a woman with endometrioid carcinomas using a whole-exome sequencing approach
    Article Snippet: To remove fragments smaller than 150 bp, we purified the DNA twice by using Agencourt AMPure XP beads (Beckman Coulter) at a ratio of 1.0 to 0.9 of PCR product to beads and washed it with 70% ethanol according to the manufacturer's instructions. .. Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050).

    Article Title: Sequencing of Ebola Virus Genomes Using Nanopore Technology
    Article Snippet: Several discrete bands should be visible, corresponding to the various PCR product lengths (strong band at ~2.1 kb, moderate band at ~2.7 kb, weak bands at 1.3, 3.4, and 4.0 kb). .. Combine 80 μl of pooled, purified PCR products from step C9 and 5 μl DNA CS, add 10 μl 10x NEBNext end repair buffer and 5 μl NEBNext end repair enzyme mix, mix by pipetting, incubate at RT for 30 min. Clean up with 180 μl Agencourt beads as described in section C, but use 300 μl EtOH for washing, add 30 μl elution buffer, take off 25 μl eluate, put in PCR tube. .. Add 3 μl 10x NEBNext dA-tailing buffer and 2 μl NEBNext dA-tailing enzyme mix, incubate for 30 min at 37 °C.

    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: In brief, DNA fragmented using the Covaris S2 in 50 μL was used for NEBNext End Prep, followed by an immediate adaptor ligation step with a 1.5 μM diluted adaptor. .. Clean-up of adaptor-ligated DNA without size selection was carried out followed by PCR amplification with eight cycles and ten cycles for 20 ng and 5 ng input, respectively.

    Article Title: Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq
    Article Snippet: Briefly, end preparation was performed in a reaction containing 18.5 μl of recovered DNA, 2.17 μl of NEBNext End Repair Reaction Buffer and 1 μl of NEBNext End Prep Enzyme Mix, with incubation for 30 min at 20 °C and 30 min at 65 °C. .. The product was purified with 0.8 × AMPure XP beads.

    Article Title: Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription
    Article Snippet: Second strand cDNA was synthesized with Second Strand Synthesis Enzyme Mix in the kit and purified. .. After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer. .. Each purification was conducted using Ampure XP beads (Beckman).

    Article Title: Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas
    Article Snippet: Purified, fragmented DNA was mixed with 40 μl of water, 10 μl of End-Repair Reaction buffer and 5 μl of End-Repair Enzyme Mix (E6050, NEB). .. Purified, fragmented DNA was mixed with 40 μl of water, 10 μl of End-Repair Reaction buffer and 5 μl of End-Repair Enzyme Mix (E6050, NEB).

    Article Title: Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients
    Article Snippet: To remove fragments smaller than 150 bp, DNA was purified using Agencourt AMPure XP beads (Beckman Coulter, IN) in a ratio of 1.0 to 0.9 of PCR product to beads twice and washed using 70% ethanol as per the manufacturer's instructions. .. Purified, fragmented DNA was mixed with 36 μl of H20, 10 μl of End-Repair Reaction Buffer, 5 μl of End-Repair Enzyme Mix (cat# E6050, NEB, Ipswich, MA).

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: This was repeated after subsequent end repair and DA-tailing reactions with the respective modules supplied by New England Biolabs (Ipswich, MA, USA) (NEBNext™ DNA Sample Prep Reagent Set 1: E6000), following the manufacturer’s instructions. .. This was repeated after subsequent end repair and DA-tailing reactions with the respective modules supplied by New England Biolabs (Ipswich, MA, USA) (NEBNext™ DNA Sample Prep Reagent Set 1: E6000), following the manufacturer’s instructions.

    Sonication:

    Article Title: MIRA-seq for DNA methylation analysis of CpG islands
    Article Snippet: Genomic DNA was sonicated to an average fragment size of 100–300 bp using a sonicator. .. For DNA end repair, we incubated 0.5–2 μg sonicated genomic DNA in 1× NEB end repair reaction buffer by adding 5 μl of NEB End Repair Enzyme mix (New England Biolabs, MA, USA) in a volume of 100 μl. .. The DNA was purified using QIAquick PCR purification kit (Qiagen) and eluted with 50 μl of water.

    Binding Assay:

    Article Title: SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)
    Article Snippet: Next 10 μL of Dynabeads® MyOne™ Streptavidin C1 (10 μg/μL), previously washed three times with 50 μL of 2X Binding and Washing (B & W) Buffer (10 mM Tris-HCl pH 7.5; 1 mM EDTA, 2 M NaCl), were added to each sample and resuspended in 20 μL of 2X B & W. Samples were incubated for 30 min at room temperature in rotation in order to capture the biotinylated fragments. .. Next 25 μL of NEBNext® End Repair Module (New England Biolabs) master mix, containing 5 μl of NEBNext End Repair Reaction Buffer (10X) and 2.5 μl of NEBNext End Repair Enzyme Mix (10,000 units/ml T4 PNK; 3,000 units/ml T4 DNA Polymerase), were added to the biotinylated beads.

    Article Title: Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas
    Article Snippet: To remove fragments of < 150 bp, DNA was mixed with 25 μl of 5× Phusion HF buffer, 416 μl of double-distilled water and 84 μl of NT binding buffer and loaded onto a NucleoSpin column (636972, Clontech). .. Purified, fragmented DNA was mixed with 40 μl of water, 10 μl of End-Repair Reaction buffer and 5 μl of End-Repair Enzyme Mix (E6050, NEB).

    DNA Extraction:

    Article Title: Elucidating the pathogenesis of synchronous and metachronous tumors in a woman with endometrioid carcinomas using a whole-exome sequencing approach
    Article Snippet: Genomic DNA isolation, library construction, exome and targeted capture, next-generation sequencing, and bioinformatics analyses of tumor and normal samples were performed at Personal Genome Diagnostics. .. Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050).

    Nucleic Acid Electrophoresis:

    Article Title: Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology
    Article Snippet: Then 2 μl of DNA was used for a 2% gel electrophoresis to confirm fragment size. .. Then 5 µl of DNA CS (Oxford Nanopore, SQK-MAP004), 10 µl of 10× NEBNext End Repair Reaction Buffer, and 5 µl of NEBNext End Repair Enzyme Mix were added to the size-selected DNA fragment and mixed by gently pipetting.

    RNA Sequencing Assay:

    Article Title: Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription
    Article Snippet: Paragraph title: RNA-seq and data analysis ... After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer.

    Magnetic Beads:

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: After the DNA was fragmented it was cleaned and concentrated with a 1:1 ratio of Ampure XP magnetic beads. .. This was repeated after subsequent end repair and DA-tailing reactions with the respective modules supplied by New England Biolabs (Ipswich, MA, USA) (NEBNext™ DNA Sample Prep Reagent Set 1: E6000), following the manufacturer’s instructions.

    Isolation:

    Article Title: Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription
    Article Snippet: Isolated poly-A tailed RNAs were incubated at 94°C for 15 min for fragmentation. .. After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer.

    Size-exclusion Chromatography:

    Article Title: SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)
    Article Snippet: Next 25 μL of NEBNext® End Repair Module (New England Biolabs) master mix, containing 5 μl of NEBNext End Repair Reaction Buffer (10X) and 2.5 μl of NEBNext End Repair Enzyme Mix (10,000 units/ml T4 PNK; 3,000 units/ml T4 DNA Polymerase), were added to the biotinylated beads. .. The biotinylated fragments from each library were amplified in 50 μl volumes containing 25 ng DNA fragments, 1X GoTaq® Green Master Mix (Promega) and 25 pmol each of the following primers: Library PCR Primer 1, 5′ -CCACTACGCCTCCGCTTTCCTCTCTATG-3 ′ and Library PCR Primer 2, 5′ -CTGCCCCGGGTTCCTCATTCT-3′ [ ].

    Article Title: Sequencing of Ebola Virus Genomes Using Nanopore Technology
    Article Snippet: Combine 80 μl of pooled, purified PCR products from step C9 and 5 μl DNA CS, add 10 μl 10x NEBNext end repair buffer and 5 μl NEBNext end repair enzyme mix, mix by pipetting, incubate at RT for 30 min. Clean up with 180 μl Agencourt beads as described in section C, but use 300 μl EtOH for washing, add 30 μl elution buffer, take off 25 μl eluate, put in PCR tube. .. Combine 80 μl of pooled, purified PCR products from step C9 and 5 μl DNA CS, add 10 μl 10x NEBNext end repair buffer and 5 μl NEBNext end repair enzyme mix, mix by pipetting, incubate at RT for 30 min. Clean up with 180 μl Agencourt beads as described in section C, but use 300 μl EtOH for washing, add 30 μl elution buffer, take off 25 μl eluate, put in PCR tube.

    Purification:

    Article Title: Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology
    Article Snippet: Purified DNA (3 μl) was saved for NanoDrop quantification. .. Then 5 µl of DNA CS (Oxford Nanopore, SQK-MAP004), 10 µl of 10× NEBNext End Repair Reaction Buffer, and 5 µl of NEBNext End Repair Enzyme Mix were added to the size-selected DNA fragment and mixed by gently pipetting.

    Article Title: SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)
    Article Snippet: The ligation products were purified using one volume of Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions and solubilized in 50 μL of 1X Low TE (10 mM Tris-HCl, 0.1 mM EDTA). .. Next 25 μL of NEBNext® End Repair Module (New England Biolabs) master mix, containing 5 μl of NEBNext End Repair Reaction Buffer (10X) and 2.5 μl of NEBNext End Repair Enzyme Mix (10,000 units/ml T4 PNK; 3,000 units/ml T4 DNA Polymerase), were added to the biotinylated beads.

    Article Title: Mapping targets for small nucleolar RNAs in yeast
    Article Snippet: The column was then transferred to a fresh 1.5 ml Eppendorf, 58 μl 10 mM Tris pH7.8 pipetted into the centre of the column and the column left to stand for 1 min. .. 10x NEBNext End Repair Reaction Buffer and 3 μl NEBNext End Prep Enzyme Mix were added to the thawed purified double stranded cDNA. .. 15 μl Blunt/TA Ligase Master Mix and 1.5μM NEBNext Multiplex Adapter were added directly to the End Prep reaction mix along with nuclease-free water to make a total volume of 83.5 μl.

    Article Title: Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana
    Article Snippet: The second-strand cDNA was synthesized using buffer, dNTPs, RNase H, and DNA polymerase I, followed by AMPure XP bead purification. .. Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation.

    Article Title: MIRA-seq for DNA methylation analysis of CpG islands
    Article Snippet: For DNA end repair, we incubated 0.5–2 μg sonicated genomic DNA in 1× NEB end repair reaction buffer by adding 5 μl of NEB End Repair Enzyme mix (New England Biolabs, MA, USA) in a volume of 100 μl. .. For DNA end repair, we incubated 0.5–2 μg sonicated genomic DNA in 1× NEB end repair reaction buffer by adding 5 μl of NEB End Repair Enzyme mix (New England Biolabs, MA, USA) in a volume of 100 μl.

    Article Title: Past climate changes, population dynamics and the origin of Bison in Europe
    Article Snippet: Prior to library preparation, uracil residues were removed through treatment with 1.5 units/30 μL reaction volume of USER Enzyme (New England Biolabs, Ipswich, MA) for 60 min at 37 °C in NEBNext End Repair buffer (New England Biolabs). .. Prior to library preparation, uracil residues were removed through treatment with 1.5 units/30 μL reaction volume of USER Enzyme (New England Biolabs, Ipswich, MA) for 60 min at 37 °C in NEBNext End Repair buffer (New England Biolabs).

    Article Title: Personalized genomic analyses for cancer mutation discovery and interpretation
    Article Snippet: To remove fragments smaller than 150 bp, DNA was purified using Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1.0:0.9 of polymerase chain reaction (PCR) product to beads twice and washed using 70% ethanol per the manufacturer’s instructions. .. Purified, fragmented DNA was mixed with 36 μl of H2 O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix [cat# E6050, New England BioLabs (NEB)]. .. The 100-μl end-repair mixture was incubated at 20°C for 30 min and purified using Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1.0:1.25 of PCR product to beads and washed using 70% ethanol per the manufacturer’s instructions.

    Article Title: CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network
    Article Snippet: To remove fragments smaller than 150bp, DNA was purified using Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1.0 to 0.9 of PCR product to beads twice and washed using 70% ethanol per the manufacturer's instructions. .. Purified, fragmented DNA was mixed with 36 μl of H2O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix (cat# E6050, NEB). .. The 100 μl end-repair mixture was incubated at 20°C for 30 min, and purified using Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1.0 to 1.25 of PCR product to beads and washed using 70% ethanol per the manufacturer's instructions.

    Article Title: Elucidating the pathogenesis of synchronous and metachronous tumors in a woman with endometrioid carcinomas using a whole-exome sequencing approach
    Article Snippet: To remove fragments smaller than 150 bp, we purified the DNA twice by using Agencourt AMPure XP beads (Beckman Coulter) at a ratio of 1.0 to 0.9 of PCR product to beads and washed it with 70% ethanol according to the manufacturer's instructions. .. Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050). .. The 100-µl end-repair mixture was incubated for 30 min at 20°C, purified with Agencourt AMPure XP beads (Beckman Coulter) at a ratio of 1.0 to 1.25 of PCR product to beads, and washed with 70% ethanol per the manufacturer's instructions.

    Article Title: Sequencing of Ebola Virus Genomes Using Nanopore Technology
    Article Snippet: Several discrete bands should be visible, corresponding to the various PCR product lengths (strong band at ~2.1 kb, moderate band at ~2.7 kb, weak bands at 1.3, 3.4, and 4.0 kb). .. Combine 80 μl of pooled, purified PCR products from step C9 and 5 μl DNA CS, add 10 μl 10x NEBNext end repair buffer and 5 μl NEBNext end repair enzyme mix, mix by pipetting, incubate at RT for 30 min. Clean up with 180 μl Agencourt beads as described in section C, but use 300 μl EtOH for washing, add 30 μl elution buffer, take off 25 μl eluate, put in PCR tube. .. Add 3 μl 10x NEBNext dA-tailing buffer and 2 μl NEBNext dA-tailing enzyme mix, incubate for 30 min at 37 °C.

    Article Title: Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq
    Article Snippet: Briefly, end preparation was performed in a reaction containing 18.5 μl of recovered DNA, 2.17 μl of NEBNext End Repair Reaction Buffer and 1 μl of NEBNext End Prep Enzyme Mix, with incubation for 30 min at 20 °C and 30 min at 65 °C. .. Briefly, end preparation was performed in a reaction containing 18.5 μl of recovered DNA, 2.17 μl of NEBNext End Repair Reaction Buffer and 1 μl of NEBNext End Prep Enzyme Mix, with incubation for 30 min at 20 °C and 30 min at 65 °C.

    Article Title: Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription
    Article Snippet: Second strand cDNA was synthesized with Second Strand Synthesis Enzyme Mix in the kit and purified. .. After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer. .. Each purification was conducted using Ampure XP beads (Beckman).

    Article Title: Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas
    Article Snippet: DNA was eluted in 45 μl of the elution buffer included in the kit. .. Purified, fragmented DNA was mixed with 40 μl of water, 10 μl of End-Repair Reaction buffer and 5 μl of End-Repair Enzyme Mix (E6050, NEB). .. The 100-μl end-repair mixture was incubated at 20 °C for 30 min, and DNA was purified with a PCR purification kit (28104, Qiagen) and eluted with 42 μl of elution buffer.

    Article Title: Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients
    Article Snippet: To remove fragments smaller than 150 bp, DNA was purified using Agencourt AMPure XP beads (Beckman Coulter, IN) in a ratio of 1.0 to 0.9 of PCR product to beads twice and washed using 70% ethanol as per the manufacturer's instructions. .. Purified, fragmented DNA was mixed with 36 μl of H20, 10 μl of End-Repair Reaction Buffer, 5 μl of End-Repair Enzyme Mix (cat# E6050, NEB, Ipswich, MA). .. The 100-μl end-repair mixture was incubated at 20 °C for 30 min, and purified using Agencourt AMPure XP beads (Beckman Coulter, IN) in a ratio of 1.0 to 1.25 of PCR product to beads and washed using 70% ethanol as per the manufacturer's instructions.

    Sequencing:

    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 ... End repair was performed using the NEBNext End Repair Module (E6050, NEB, Hitchin, Hertfordshire, UK) by mixing 1.0 μg DNA dissolved in 10 μl 1× TE buffer, 5 μl Quality Control DNA CS, 10 μl 10× NEBNext End Repair Reaction buffer and 5 μl NEBNext End Repair Enzyme Mix in a total reaction volume of 100 μl.

    Article Title: Mapping targets for small nucleolar RNAs in yeast
    Article Snippet: Paragraph title: RNA library preparation for Illumina sequencing ... 10x NEBNext End Repair Reaction Buffer and 3 μl NEBNext End Prep Enzyme Mix were added to the thawed purified double stranded cDNA.

    Article Title: Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana
    Article Snippet: Paragraph title: Library Preparation and Illumina Sequencing ... Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation.

    Article Title: MIRA-seq for DNA methylation analysis of CpG islands
    Article Snippet: Paragraph title: Ligation of Illumina deep sequencing linkers ... For DNA end repair, we incubated 0.5–2 μg sonicated genomic DNA in 1× NEB end repair reaction buffer by adding 5 μl of NEB End Repair Enzyme mix (New England Biolabs, MA, USA) in a volume of 100 μl.

    Article Title: Past climate changes, population dynamics and the origin of Bison in Europe
    Article Snippet: Dual barcoded libraries for Illumina sequencing were constructed in the dedicated ancient DNA facility at the Jacques Monod Institute (Paris, France) using a double-stranded procedure previously described [ , ]. .. Prior to library preparation, uracil residues were removed through treatment with 1.5 units/30 μL reaction volume of USER Enzyme (New England Biolabs, Ipswich, MA) for 60 min at 37 °C in NEBNext End Repair buffer (New England Biolabs).

    Article Title: Age-associated bimodal transcriptional drift reduces intergenic disparities in transcription
    Article Snippet: After end repair of the synthesized double-stranded DNAs using NEBNext End Prep Enzyme Mix in the condition of 20°C for 30 min and 65°C for 30 min, NEBNext Adaptor was added into the 3’ end adenylated DNA with Blunt/TA Ligase Master Mix and the mixture was incubated at 20°C for 15 min. DNA samples were enriched by 15 cycles of PCR reaction consisting of the purified ligates, NEBNext Q5 Hot Start HiFi PCR Master Mix 2X, and index primer. .. Enriched DNA fragments were purified and sequenced using NextSeq 500.

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: Paragraph title: Paired-end illumina sequencing ... This was repeated after subsequent end repair and DA-tailing reactions with the respective modules supplied by New England Biolabs (Ipswich, MA, USA) (NEBNext™ DNA Sample Prep Reagent Set 1: E6000), following the manufacturer’s instructions.

    Agarose Gel Electrophoresis:

    Article Title: Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana
    Article Snippet: Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation. .. Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation.

    Article Title: Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq
    Article Snippet: Briefly, end preparation was performed in a reaction containing 18.5 μl of recovered DNA, 2.17 μl of NEBNext End Repair Reaction Buffer and 1 μl of NEBNext End Prep Enzyme Mix, with incubation for 30 min at 20 °C and 30 min at 65 °C. .. PCR was performed in a reaction consisting of 24 μl of ligated DNA, 1 μl of NEXTflex Primer Mix (Bioo Scientific, 514102) and 25 μl of KAPA HiFi HotStart ReadyMix (2 × ) with the following cycling conditions: 98 °C for 45 s and 5–11 cycles of 98 °C for 15 s, 65 °C for 30 s and 72 °C for 1 min, with a final step at 72 °C for 4 min and holding at 4 °C.

    Chromatin Immunoprecipitation:

    Article Title: Two-step Crosslinking for Analysis of Protein-Chromatin Interactions
    Article Snippet: Illumina Genome Analyzer II system and associated equipment, reagents, kits, and software. .. Prepare the following reaction mix: ChIP enriched, qPCR verified DNA (42.5ul) NEBNext End Repair Reaction Buffer (5ul) NEBNext End Repair Enzyme Mix (2.5ul) The total volume should be 50ul. .. Purify DNA on QIAquick column and elute in 42ul elution buffer.

    Selection:

    Article Title: Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq
    Article Snippet: Briefly, end preparation was performed in a reaction containing 18.5 μl of recovered DNA, 2.17 μl of NEBNext End Repair Reaction Buffer and 1 μl of NEBNext End Prep Enzyme Mix, with incubation for 30 min at 20 °C and 30 min at 65 °C. .. PCR was performed in a reaction consisting of 24 μl of ligated DNA, 1 μl of NEXTflex Primer Mix (Bioo Scientific, 514102) and 25 μl of KAPA HiFi HotStart ReadyMix (2 × ) with the following cycling conditions: 98 °C for 45 s and 5–11 cycles of 98 °C for 15 s, 65 °C for 30 s and 72 °C for 1 min, with a final step at 72 °C for 4 min and holding at 4 °C.

    Sample Prep:

    Article Title: Personalized genomic analyses for cancer mutation discovery and interpretation
    Article Snippet: Paragraph title: Sample preparation and next-generation sequencing ... Purified, fragmented DNA was mixed with 36 μl of H2 O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix [cat# E6050, New England BioLabs (NEB)].

    Article Title: CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network
    Article Snippet: Paragraph title: Sample preparation of SCC25 and SQ20B for next-generation sequencing ... Purified, fragmented DNA was mixed with 36 μl of H2O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix (cat# E6050, NEB).

    Article Title: Elucidating the pathogenesis of synchronous and metachronous tumors in a woman with endometrioid carcinomas using a whole-exome sequencing approach
    Article Snippet: Paragraph title: Sample Preparation and Next-Generation Sequencing ... Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050).

    Article Title: Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients
    Article Snippet: Paragraph title: Sample preparation and next-generation sequencing ... Purified, fragmented DNA was mixed with 36 μl of H20, 10 μl of End-Repair Reaction Buffer, 5 μl of End-Repair Enzyme Mix (cat# E6050, NEB, Ipswich, MA).

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: After the DNA was fragmented it was cleaned and concentrated with a 1:1 ratio of Ampure XP magnetic beads. .. This was repeated after subsequent end repair and DA-tailing reactions with the respective modules supplied by New England Biolabs (Ipswich, MA, USA) (NEBNext™ DNA Sample Prep Reagent Set 1: E6000), following the manufacturer’s instructions. .. To ligate sequencing adaptors, a 50 μl reaction mixture containing the sample was set with addition of 25 μl of 2× DNA T4 ligase buffer (New England Biolabs, Inc.), 4 μl 4 μM Illumina paired-end duplex adaptors (Integrated DNA Technologies, Coralville, IA, USA) and 2 μl T4 DNA ligase.

    Ethanol Precipitation:

    Article Title: BisQC: an operational pipeline for multiplexed bisulfite sequencing
    Article Snippet: Using the MspI fragmented DNA (40–85 μL) described above, the NEBNext End Repair Reaction Buffer (10X; 10 μL), and the NEBNext End Repair Enzyme Mix (5 μL), we incubated the solution (final volume of 100 μl) at 20°C for 30 minutes. .. After incubation, the reaction mixture was diluted to 200 μL with dH2 O.

    Next-Generation Sequencing:

    Article Title: Personalized genomic analyses for cancer mutation discovery and interpretation
    Article Snippet: Paragraph title: Sample preparation and next-generation sequencing ... Purified, fragmented DNA was mixed with 36 μl of H2 O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix [cat# E6050, New England BioLabs (NEB)].

    Article Title: CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network
    Article Snippet: Paragraph title: Sample preparation of SCC25 and SQ20B for next-generation sequencing ... Purified, fragmented DNA was mixed with 36 μl of H2O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix (cat# E6050, NEB).

    Article Title: Elucidating the pathogenesis of synchronous and metachronous tumors in a woman with endometrioid carcinomas using a whole-exome sequencing approach
    Article Snippet: Paragraph title: Sample Preparation and Next-Generation Sequencing ... Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050).

    Article Title: Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq
    Article Snippet: Paragraph title: Standard NGS library preparation ... Briefly, end preparation was performed in a reaction containing 18.5 μl of recovered DNA, 2.17 μl of NEBNext End Repair Reaction Buffer and 1 μl of NEBNext End Prep Enzyme Mix, with incubation for 30 min at 20 °C and 30 min at 65 °C.

    Article Title: Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients
    Article Snippet: Paragraph title: Sample preparation and next-generation sequencing ... Purified, fragmented DNA was mixed with 36 μl of H20, 10 μl of End-Repair Reaction Buffer, 5 μl of End-Repair Enzyme Mix (cat# E6050, NEB, Ipswich, MA).

    Ligation:

    Article Title: SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.)
    Article Snippet: The ligation products were purified using one volume of Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions and solubilized in 50 μL of 1X Low TE (10 mM Tris-HCl, 0.1 mM EDTA). .. Next 25 μL of NEBNext® End Repair Module (New England Biolabs) master mix, containing 5 μl of NEBNext End Repair Reaction Buffer (10X) and 2.5 μl of NEBNext End Repair Enzyme Mix (10,000 units/ml T4 PNK; 3,000 units/ml T4 DNA Polymerase), were added to the biotinylated beads.

    Article Title: Genome-Wide Identification of Circular RNAs in Arabidopsis thaliana
    Article Snippet: The second-strand cDNA was synthesized using buffer, dNTPs, RNase H, and DNA polymerase I, followed by AMPure XP bead purification. .. Third, the short fragments were further resolved with NEBNext End Repair Reaction Buffer and NEBNext Pre Enzyme Mix for end repair and poly (A) ligation. .. Subsequently, the fragments were connected with adapters, and then the second strand containing “U” was degraded using uracil-specific excision reagent (USER).

    Article Title: MIRA-seq for DNA methylation analysis of CpG islands
    Article Snippet: Paragraph title: Ligation of Illumina deep sequencing linkers ... For DNA end repair, we incubated 0.5–2 μg sonicated genomic DNA in 1× NEB end repair reaction buffer by adding 5 μl of NEB End Repair Enzyme mix (New England Biolabs, MA, USA) in a volume of 100 μl.

    Article Title: Past climate changes, population dynamics and the origin of Bison in Europe
    Article Snippet: The USER Enzyme, End-repair and adapter ligation mixtures were decontaminated using Ethidium monoazide [ ] to inactivate bovine DNA associated with BSA present in these reagents that could interfere with the final results. .. Prior to library preparation, uracil residues were removed through treatment with 1.5 units/30 μL reaction volume of USER Enzyme (New England Biolabs, Ipswich, MA) for 60 min at 37 °C in NEBNext End Repair buffer (New England Biolabs).

    Article Title: Personalized genomic analyses for cancer mutation discovery and interpretation
    Article Snippet: Purified, fragmented DNA was mixed with 36 μl of H2 O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix [cat# E6050, New England BioLabs (NEB)]. .. Purified, fragmented DNA was mixed with 36 μl of H2 O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix [cat# E6050, New England BioLabs (NEB)].

    Article Title: CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network
    Article Snippet: Purified, fragmented DNA was mixed with 36 μl of H2O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix (cat# E6050, NEB). .. Purified, fragmented DNA was mixed with 36 μl of H2O, 10 μl of End Repair Reaction Buffer, 5 μl of End Repair Enzyme Mix (cat# E6050, NEB).

    Article Title: Elucidating the pathogenesis of synchronous and metachronous tumors in a woman with endometrioid carcinomas using a whole-exome sequencing approach
    Article Snippet: Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050). .. Purified, fragmented DNA was mixed with 36 µl of H2 O, 10 µl of End Repair Reaction Buffer, and 5 µl of End Repair Enzyme Mix (NEB; cat# E6050).

    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: Library preparation was performed from MCC samples (n = 2) with 5 ng and 20 ng input, breast tumor samples (n = 4), and pre-cancerous breast lesions (papilloma) (n = 2) with 5 ng DNA input as described in the NEBNext® Ultra ™ II DNA Library Prep Kit (NEB E7645S/L, New England BioLabs ® Inc.) with several minor modifications. .. In brief, DNA fragmented using the Covaris S2 in 50 μL was used for NEBNext End Prep, followed by an immediate adaptor ligation step with a 1.5 μM diluted adaptor. .. Clean-up of adaptor-ligated DNA without size selection was carried out followed by PCR amplification with eight cycles and ten cycles for 20 ng and 5 ng input, respectively.

    Article Title: Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients
    Article Snippet: Purified, fragmented DNA was mixed with 36 μl of H20, 10 μl of End-Repair Reaction Buffer, 5 μl of End-Repair Enzyme Mix (cat# E6050, NEB, Ipswich, MA). .. Purified, fragmented DNA was mixed with 36 μl of H20, 10 μl of End-Repair Reaction Buffer, 5 μl of End-Repair Enzyme Mix (cat# E6050, NEB, Ipswich, MA).

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: This was repeated after subsequent end repair and DA-tailing reactions with the respective modules supplied by New England Biolabs (Ipswich, MA, USA) (NEBNext™ DNA Sample Prep Reagent Set 1: E6000), following the manufacturer’s instructions. .. To ligate sequencing adaptors, a 50 μl reaction mixture containing the sample was set with addition of 25 μl of 2× DNA T4 ligase buffer (New England Biolabs, Inc.), 4 μl 4 μM Illumina paired-end duplex adaptors (Integrated DNA Technologies, Coralville, IA, USA) and 2 μl T4 DNA ligase.

    Concentration Assay:

    Article Title: Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire
    Article Snippet: End repair was performed using the NEBNext End Repair Module (E6050, NEB, Hitchin, Hertfordshire, UK) by mixing 1.0 μg DNA dissolved in 10 μl 1× TE buffer, 5 μl Quality Control DNA CS, 10 μl 10× NEBNext End Repair Reaction buffer and 5 μl NEBNext End Repair Enzyme Mix in a total reaction volume of 100 μl. .. 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.

    Gel Extraction:

    Article Title: Past climate changes, population dynamics and the origin of Bison in Europe
    Article Snippet: Prior to library preparation, uracil residues were removed through treatment with 1.5 units/30 μL reaction volume of USER Enzyme (New England Biolabs, Ipswich, MA) for 60 min at 37 °C in NEBNext End Repair buffer (New England Biolabs). .. Prior to library preparation, uracil residues were removed through treatment with 1.5 units/30 μL reaction volume of USER Enzyme (New England Biolabs, Ipswich, MA) for 60 min at 37 °C in NEBNext End Repair buffer (New England Biolabs).

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars

  • 99
    New England Biolabs end repair module
    End Repair Module, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/end repair module/product/New England Biolabs
    Average 99 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    end repair module - by Bioz Stars, 2019-11
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs end repair enzyme mix
    End Repair Enzyme Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/end repair enzyme mix/product/New England Biolabs
    Average 99 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    end repair enzyme mix - by Bioz Stars, 2019-11
    99/100 stars
      Buy from Supplier

    Image Search Results