mastermix  (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:
    Blunt TA Ligase Master Mix
    Description:
    Blunt TA Ligase Master Mix 250 rxns
    Catalog Number:
    M0367L
    Price:
    392
    Size:
    250 rxns
    Category:
    DNA Ligases
    Buy from Supplier


    Structured Review

    New England Biolabs mastermix
    Blunt TA Ligase Master Mix
    Blunt TA Ligase Master Mix 250 rxns
    https://www.bioz.com/result/mastermix/product/New England Biolabs
    Average 99 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    mastermix - by Bioz Stars, 2019-07
    99/100 stars

    Images

    Related Articles

    DNA Extraction:

    Article Title: Elucidating the diet of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing
    Article Snippet: Next, 100 µL of the mixture was used for DNA extraction similarly using DNAeasy Plant Mini Kit (Qiagen, Halden, Germany) instead of a stool-specific DNA extraction kit to improve the recovery of plant-derived DNA from faecal samples. .. The 20 µL PCR cocktail consists of 10 µL Q 5 Hot Start High-Fidelity 2× Master Mix (New England Biolab, Ipswich, MA, USA), 1 µL each of 10 µM forward and reverse primer, 1 µL gDNA and 7 µL nuclease-free water.

    Article Title: Discrete microfluidics for the isolation of circulating tumor cell subpopulations targeting fibroblast activation protein alpha and epithelial cell adhesion molecule
    Article Snippet: Cell lines of known KRAS genotype (HT29, wild-type and LS180—G12V) were secured from the Tissue Culture Facility at UNC. gDNA from the cell lines and CTCs was extracted using an Agencourt DNA isolation kit (Beckman–Coulter). .. PCR was performed with DNA in a total volume of 20 µl using Taq 2 × Master Mix (New England Biolabs, Ipswich, MA).

    Centrifugation:

    Article Title: BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis
    Article Snippet: Briefly, to prepare nuclei, respective mouse or human cells (1 × 105 ) were centrifuged at 500 g for 5 min, which was followed by a wash with ice-cold PBS and centrifugation at 500 g for 5 min. .. Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10–12 cycles.

    Amplification:

    Article Title: Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus
    Article Snippet: In order to generate sufficient amount of cDNAs for MinION library preparation, samples were amplified by endpoint PCR following the TeloPrime Kit’s manual. .. This step was followed by the 1D adapter ligation, which was carried out according to the 1D protocol, using the NEB Blunt/TA Ligase Master Mix (New England Biolabs).

    Article Title: High density genetic maps of St. Augustinegrass and applications to comparative genomic analysis and QTL mapping for turf quality traits
    Article Snippet: The reaction was stopped by incubation at 65 °C for 20 min. Barcoded adapters (containing unique barcode sequences, details in Additional file : Table S1) and a common-Y adapter were ligated to digested genomic DNA fragments at 22 °C overnight in 40 μL volume and stopped at 65 °C for 20 min. Then, 10 μL of each sample was pooled and cleaned up using QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany). .. After that, purified DNA was amplified using NEB MasterMix (New England BioLabs, Inc.; Ipswich, MA). .. PCR products were purified and size-selected using GeneRead Size Selection Kit (QIAGEN, Hilden, Germany) to remove adapter dimers and small fragments ( < 150 bp).

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Adaptors were ligated to the digested DNA by adding 0.9 ng of each of the barcoded and common adaptors with 400 U T4 DNA ligase (NEB) in ligase buffer, the amount of adaptor being previously determined by titration ( ). .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. The PCR was initiated at 72°C for 5 min, followed by 98°C for 30 s, then 18 cycles of 98°C for 10 s, 65°C for 30 s, 72°C for 30 s, finishing with 72°C for 5 min. Amplified libraries were checked by electrophoresis in an agarose gel to ensure they had successfully amplified.

    Article Title: Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults
    Article Snippet: With the calculated concentration, we aliquotted the appropriate volume of each library to introduce 4M molecules into the subsequent amplification step. .. Following ddPCR quantification, 4M molecules for each library were amplified using Q5 High-Fidelity 2 × Master Mix (New England Biolabs) using 1 μM P5/P7 primers ( ) in a 50 μl reaction under the following conditions: 98 °C for 30 s; 16 cycles of 98 °C for 10 s, 66 °C for 30 s, 72 °C for 30 s; 72 °C for 2 min; 4 °C hold. .. The PCR reaction was purified using the modified Ampure bead clean up.

    Article Title: Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
    Article Snippet: A second round of end repair and dA-tailing was performed on 500 ng of enriched, amplified PCR product using SureSelectXT reagents as described above, but without purification after dA-tailing. .. In detail, dA-tailed sample, blunt/TA ligase master mix (#M0367, NEB), tethered adapter mix and hairpin adapters (ONT) were incubated for 10 min at room temperature in protein LoBind tubes (#0030108116, Eppendorf) for ligation.

    Article Title: Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
    Article Snippet: To achieve the 1 μg of DNA needed for the Oxford Nanopore library prep, the full-length cDNA product was split into five aliquots and amplified for 13 cycles with KAPA Hifi Readymix 2 × (KAPA) using the ISPCR or multiplex cellular index primers. .. Ligation reaction was performed using Blunt/TA ligase master mix (NEB).

    Article Title: Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
    Article Snippet: Adapter ligation and tethering was then carried out with 20 µL ofAdapter Mix (ONT) and 50 µLof NEB Blunt/TA ligation Master Mix (New England Biolabs). .. Each R9 flow cell was primed with 1,000 µLof a mixture of Fuel Mix (ONT) and nuclease-free water.

    Article Title: Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes, et al. Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes
    Article Snippet: PCR amplification of the internal transcribed spacer region 2 (ITS2) was carried out on the individual samples using the ITS3 and ITS4 primers (White, Bruns, Lee, & Taylor, ). .. The PCR reaction mix contained 25 μl of Q5® High‐Fidelity 2× Master Mix (New England Biolabs), 2.5 μl each of the ITS3 and ITS4 primer, 2 μl of genomic DNA and 18 μl of nuclease‐free water.

    Article Title: Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
    Article Snippet: Briefly, the protocols comprise DNA end-repair and dA-tailing (NEBNext Ultra II End Repair/dA-Tailing Module, New England Biolabs (NEB), Ipswich, MA, USA) followed by purification using AMPure XP solid phase reversible immobilisation (SPRI) beads (Beckman Coulter, High Wycombe, UK); Sequencing adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by additional SPRI bead purification. .. For the samples with insufficient DNA requiring PCR amplification, additional steps between end-repair and sequencing adapter ligation included; PCR adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by SPRI bead purification; PCR amplification (Phusion High Fidelity PCR Master Mix, NEB) with 18 cycles (samples 229 and 249) or 24 cycles (samples 506 and 509) followed by additional SPRI bead purification. .. Samples were sequenced on FLO-MIN105 (v.R9) (sample 229) or FLO-MIN106 (v.R9.4) (all other samples) SpotON flowcells.

    Article Title: BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis
    Article Snippet: Directly following transposition, the sample was purified using a Qiagen MinElute kit. .. Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10–12 cycles. .. The libraries were then purified using a Qiagen PCR cleanup kit.

    DNA Ligation:

    Article Title: Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
    Article Snippet: Samples 259, 312, 335, 352 and 354 were prepared using the 1D genomic DNA by ligation protocol (SQK-LSK108) (ONT). .. For the samples with insufficient DNA requiring PCR amplification, additional steps between end-repair and sequencing adapter ligation included; PCR adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by SPRI bead purification; PCR amplification (Phusion High Fidelity PCR Master Mix, NEB) with 18 cycles (samples 229 and 249) or 24 cycles (samples 506 and 509) followed by additional SPRI bead purification.

    Construct:

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions.

    Incubation:

    Article Title: High density genetic maps of St. Augustinegrass and applications to comparative genomic analysis and QTL mapping for turf quality traits
    Article Snippet: The reaction was stopped by incubation at 65 °C for 20 min. Barcoded adapters (containing unique barcode sequences, details in Additional file : Table S1) and a common-Y adapter were ligated to digested genomic DNA fragments at 22 °C overnight in 40 μL volume and stopped at 65 °C for 20 min. Then, 10 μL of each sample was pooled and cleaned up using QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany). .. After that, purified DNA was amplified using NEB MasterMix (New England BioLabs, Inc.; Ipswich, MA).

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Adaptors were ligated to the digested DNA by adding 0.9 ng of each of the barcoded and common adaptors with 400 U T4 DNA ligase (NEB) in ligase buffer, the amount of adaptor being previously determined by titration ( ). .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. The PCR was initiated at 72°C for 5 min, followed by 98°C for 30 s, then 18 cycles of 98°C for 10 s, 65°C for 30 s, 72°C for 30 s, finishing with 72°C for 5 min. Amplified libraries were checked by electrophoresis in an agarose gel to ensure they had successfully amplified.

    Article Title: Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
    Article Snippet: Instead, leader/hairpin ligation and sample clean-up were performed according to the ONT protocols for kit SQK-MAP003 (used in the M. tb strain H37Rv experiments only) or SQK-MAP004. .. In detail, dA-tailed sample, blunt/TA ligase master mix (#M0367, NEB), tethered adapter mix and hairpin adapters (ONT) were incubated for 10 min at room temperature in protein LoBind tubes (#0030108116, Eppendorf) for ligation. .. Libraries processed according to the ONT SQK-MAP003 protocol were cleaned up with AMPure XP beads; those made according to the SQK-MAP004 method were purified using Dynabeads for His-Tag isolation and pulldown (#10103D, Life Technologies) ( ).

    Article Title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus
    Article Snippet: Sequencing adapters, provided with the Ligation Sequencing Kit 1D (R9.4) (SQK-LSK108, ONT), were ligated to the dA-tailed nucleic acids. .. End-prepped DNA (30 µl) was mixed with 20 µl adapter mix (AMX, ONT) and 50 µl Blunt/TA Ligation Master Mix (New England Biolabs) in a total reaction volume of 100 µl and incubated at room temperature for 10 min. .. The sequencing library, containing double-stranded DNA with adapters ligated to the 3′ ends, was then purified using 40 µl AMPure XP beads.

    Formalin-fixed Paraffin-Embedded:

    Article Title: De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing
    Article Snippet: The sheared DNA was repaired using the FFPE Repair Mix, according to the manufacturer’s instructions (New England Biolabs). .. The adaptor and hairpin adapter were ligated using Blunt/TA Ligase Master Mix (New England Biolabs).

    Modification:

    Article Title: Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults
    Article Snippet: Following ddPCR quantification, 4M molecules for each library were amplified using Q5 High-Fidelity 2 × Master Mix (New England Biolabs) using 1 μM P5/P7 primers ( ) in a 50 μl reaction under the following conditions: 98 °C for 30 s; 16 cycles of 98 °C for 10 s, 66 °C for 30 s, 72 °C for 30 s; 72 °C for 2 min; 4 °C hold. .. The PCR reaction was purified using the modified Ampure bead clean up.

    Article Title: Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
    Article Snippet: Samples 229, 249, 506 and 509 had insufficient DNA for this protocol so were prepared using either a PCR-based protocol for low input genomic DNA with modified primers (DP006_revB_14Aug2015), followed by rapid sequencing adapter ligation (ONT) (sample 229) or the 1D low input genomic DNA with PCR protocol (SQK-LSK108) (ONT) (samples 249, 506 and 509). .. For the samples with insufficient DNA requiring PCR amplification, additional steps between end-repair and sequencing adapter ligation included; PCR adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by SPRI bead purification; PCR amplification (Phusion High Fidelity PCR Master Mix, NEB) with 18 cycles (samples 229 and 249) or 24 cycles (samples 506 and 509) followed by additional SPRI bead purification.

    Hybridization:

    Article Title: Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
    Article Snippet: In detail, dA-tailed sample, blunt/TA ligase master mix (#M0367, NEB), tethered adapter mix and hairpin adapters (ONT) were incubated for 10 min at room temperature in protein LoBind tubes (#0030108116, Eppendorf) for ligation. .. In detail, dA-tailed sample, blunt/TA ligase master mix (#M0367, NEB), tethered adapter mix and hairpin adapters (ONT) were incubated for 10 min at room temperature in protein LoBind tubes (#0030108116, Eppendorf) for ligation.

    Electroporation:

    Article Title: Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress
    Article Snippet: Simultaneous deletion of two genes during one electroporation round was made by the same protocol, but using 50–100 bp flanking primers with or without PT-bonds as listed in , and by mixing the different PCR products prior to electroporation. .. Integration of cassettes and removal of resistant markers was verified by colony PCR using OneTaq 2× Master Mix (New England Biolabs, Ipswich, MA), according to manufactures instructions. pSIJ8 were cured from the cells by growing them at 37 °C.

    Flow Cytometry:

    Article Title: Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris
    Article Snippet: End-repaired DNA was then A-tailed using the NEB Blunt/TA-ligase master mix (New England Biolabs, Ipswich, USA). .. Read event data were base-called by the software Metrichor (v2.39.3).

    Article Title: Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus
    Article Snippet: This step was followed by the 1D adapter ligation, which was carried out according to the 1D protocol, using the NEB Blunt/TA Ligase Master Mix (New England Biolabs). .. This step was followed by the 1D adapter ligation, which was carried out according to the 1D protocol, using the NEB Blunt/TA Ligase Master Mix (New England Biolabs).

    Article Title: Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
    Article Snippet: Ligation reaction was performed using Blunt/TA ligase master mix (NEB). .. Ligation reaction was performed using Blunt/TA ligase master mix (NEB).

    Article Title: Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
    Article Snippet: Adapter ligation and tethering was then carried out with 20 µL ofAdapter Mix (ONT) and 50 µLof NEB Blunt/TA ligation Master Mix (New England Biolabs). .. The adapter ligated DNA library was then purified with AMPure beads, followed by the addition of Adapter Bead binding buffer (ONT), and finally eluted in 15 µLof Elution Buffer (ONT).

    Article Title: BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis
    Article Snippet: The nuclei pellet was resuspended in the transposase reaction mix (25 μL 2X Tagment buffer, 2.5 μL Tagment DNA enzyme (Illumina, FC-121-1030) and 22.5 μL nuclease-free water). .. Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10–12 cycles.

    Positive Control:

    Article Title: Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
    Article Snippet: Barcode DNA products were pooled with 5 µLof DNA CS (a positive control provided by ONT) and an end-repair was performed (NEB-Next Ultra II End-prep reaction buffer and enzyme mix, New England Biolabs), then purified using AMPure XP beads. .. Adapter ligation and tethering was then carried out with 20 µL ofAdapter Mix (ONT) and 50 µLof NEB Blunt/TA ligation Master Mix (New England Biolabs).

    Ligation:

    Article Title: Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus
    Article Snippet: The Ligation Sequencing kit (SQK-LSK108, ONT) and NEBNext End repair / dA-tailing Module (New England Biolabs) was used to repair the cDNA ends. .. This step was followed by the 1D adapter ligation, which was carried out according to the 1D protocol, using the NEB Blunt/TA Ligase Master Mix (New England Biolabs). .. We used barcoding for the better in silico identification of the transcripts’ ends.

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Adaptors were ligated to the digested DNA by adding 0.9 ng of each of the barcoded and common adaptors with 400 U T4 DNA ligase (NEB) in ligase buffer, the amount of adaptor being previously determined by titration ( ). .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. The PCR was initiated at 72°C for 5 min, followed by 98°C for 30 s, then 18 cycles of 98°C for 10 s, 65°C for 30 s, 72°C for 30 s, finishing with 72°C for 5 min. Amplified libraries were checked by electrophoresis in an agarose gel to ensure they had successfully amplified.

    Article Title: Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response
    Article Snippet: DNA was end-prepped using NEB Prep enzyme mix, end-repair reaction buffer (10X), and 30 ng of DNA for each samples, then held at 30 degrees Celsius for 30 minutes and then at 65 degrees Celsius for 30 minutes. .. Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes. .. The adaptor-ligated DNA was cleaned up using AMPure XP beads to remove any unwanted ligated products.

    Article Title: Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
    Article Snippet: Instead, leader/hairpin ligation and sample clean-up were performed according to the ONT protocols for kit SQK-MAP003 (used in the M. tb strain H37Rv experiments only) or SQK-MAP004. .. In detail, dA-tailed sample, blunt/TA ligase master mix (#M0367, NEB), tethered adapter mix and hairpin adapters (ONT) were incubated for 10 min at room temperature in protein LoBind tubes (#0030108116, Eppendorf) for ligation. .. Libraries processed according to the ONT SQK-MAP003 protocol were cleaned up with AMPure XP beads; those made according to the SQK-MAP004 method were purified using Dynabeads for His-Tag isolation and pulldown (#10103D, Life Technologies) ( ).

    Article Title: Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
    Article Snippet: The single cDNA or multiplex product was further end-repaired and dA-tailed using NEBNext Ultra End Repair/dA tailing mix (NEB), and adaptor ligated using the sequencing adaptors provided by ONT (HP Adaptor/Adaptor Mix). .. Ligation reaction was performed using Blunt/TA ligase master mix (NEB). .. Reactions were then enriched using Dynabeads MyOne C1 Streptavidin (Life Technologies) to capture molecules that contain the HP Adaptor.

    Article Title: First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans)
    Article Snippet: The library was blunt-ended and A-tailed with NEB Ultra II End prep module, and purified using 1× AMpure XP. .. Adapter ligation was then performed using Blunt-TA ligase master mix (NEB) and proprietary ONT “1D” adapters containing a preloaded motor protein. .. The library was purified using 0.4× Ampure XP, washed with buffer WB (ONT), and eluted with elution buffer EB (ONT), which contains a tether molecule that directs library molecules toward the nanopore membrane surface.

    Article Title: Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization
    Article Snippet: A total of 500 ng of PCR-product was then A-tailed (NEB), cleaned using Ampure, quantified and diluted to 0.2 pmols (220 bp average length). .. Ligation of hairpin and leader adapters (Oxford Nanopore Genomic DNA Sequencing Kit NSK-007) was performed using Blunt/TA ligase master mix (NEB) and was followed by attachment of a biotinylated tether molecule, which when bound specifically to the hairpin adapter, is enriched for using a Streptavidin bead pull-down (Dynabeads MyOne C1). .. Prepared libraries were sequenced on an R9 flowcell for 48 h. For analysis, we extracted the fasta sequences and timestamps of the reads with poretools blasted against the known sequences for on- and off-target E. rostratum probes ( ).

    Article Title: Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
    Article Snippet: Barcode DNA products were pooled with 5 µLof DNA CS (a positive control provided by ONT) and an end-repair was performed (NEB-Next Ultra II End-prep reaction buffer and enzyme mix, New England Biolabs), then purified using AMPure XP beads. .. Adapter ligation and tethering was then carried out with 20 µL ofAdapter Mix (ONT) and 50 µLof NEB Blunt/TA ligation Master Mix (New England Biolabs). .. The adapter ligated DNA library was then purified with AMPure beads, followed by the addition of Adapter Bead binding buffer (ONT), and finally eluted in 15 µLof Elution Buffer (ONT).

    Article Title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus
    Article Snippet: Sequencing adapters, provided with the Ligation Sequencing Kit 1D (R9.4) (SQK-LSK108, ONT), were ligated to the dA-tailed nucleic acids. .. End-prepped DNA (30 µl) was mixed with 20 µl adapter mix (AMX, ONT) and 50 µl Blunt/TA Ligation Master Mix (New England Biolabs) in a total reaction volume of 100 µl and incubated at room temperature for 10 min. .. The sequencing library, containing double-stranded DNA with adapters ligated to the 3′ ends, was then purified using 40 µl AMPure XP beads.

    Article Title: De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing
    Article Snippet: Then, prior to ligation, the DNA was again cleaned by extraction using a ratio of 1:1 Ampure XP beads to DNA. .. The adaptor and hairpin adapter were ligated using Blunt/TA Ligase Master Mix (New England Biolabs).

    Article Title: Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes, et al. Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes
    Article Snippet: The PCR reaction mix contained 25 μl of Q5® High‐Fidelity 2× Master Mix (New England Biolabs), 2.5 μl each of the ITS3 and ITS4 primer, 2 μl of genomic DNA and 18 μl of nuclease‐free water. .. Amplicon libraries were prepared using 200 ng of each PCR product and the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® with dual indexing (barcoding).

    Article Title: Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
    Article Snippet: Briefly, the protocols comprise DNA end-repair and dA-tailing (NEBNext Ultra II End Repair/dA-Tailing Module, New England Biolabs (NEB), Ipswich, MA, USA) followed by purification using AMPure XP solid phase reversible immobilisation (SPRI) beads (Beckman Coulter, High Wycombe, UK); Sequencing adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by additional SPRI bead purification. .. For the samples with insufficient DNA requiring PCR amplification, additional steps between end-repair and sequencing adapter ligation included; PCR adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by SPRI bead purification; PCR amplification (Phusion High Fidelity PCR Master Mix, NEB) with 18 cycles (samples 229 and 249) or 24 cycles (samples 506 and 509) followed by additional SPRI bead purification. .. Samples were sequenced on FLO-MIN105 (v.R9) (sample 229) or FLO-MIN106 (v.R9.4) (all other samples) SpotON flowcells.

    Generated:

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions.

    DNA Sequencing:

    Article Title: Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response
    Article Snippet: Using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB #E7370S/L), DNA sequencing libraries were prepared for the mononucleosomally-sized and subnucleosomal-sized fragments for each sample. .. Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes.

    Article Title: Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization
    Article Snippet: A total of 500 ng of PCR-product was then A-tailed (NEB), cleaned using Ampure, quantified and diluted to 0.2 pmols (220 bp average length). .. Ligation of hairpin and leader adapters (Oxford Nanopore Genomic DNA Sequencing Kit NSK-007) was performed using Blunt/TA ligase master mix (NEB) and was followed by attachment of a biotinylated tether molecule, which when bound specifically to the hairpin adapter, is enriched for using a Streptavidin bead pull-down (Dynabeads MyOne C1). .. Prepared libraries were sequenced on an R9 flowcell for 48 h. For analysis, we extracted the fasta sequences and timestamps of the reads with poretools blasted against the known sequences for on- and off-target E. rostratum probes ( ).

    Polymerase Chain Reaction:

    Article Title: Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus
    Article Snippet: In order to generate sufficient amount of cDNAs for MinION library preparation, samples were amplified by endpoint PCR following the TeloPrime Kit’s manual. .. This step was followed by the 1D adapter ligation, which was carried out according to the 1D protocol, using the NEB Blunt/TA Ligase Master Mix (New England Biolabs).

    Article Title: High density genetic maps of St. Augustinegrass and applications to comparative genomic analysis and QTL mapping for turf quality traits
    Article Snippet: The reaction was stopped by incubation at 65 °C for 20 min. Barcoded adapters (containing unique barcode sequences, details in Additional file : Table S1) and a common-Y adapter were ligated to digested genomic DNA fragments at 22 °C overnight in 40 μL volume and stopped at 65 °C for 20 min. Then, 10 μL of each sample was pooled and cleaned up using QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany). .. After that, purified DNA was amplified using NEB MasterMix (New England BioLabs, Inc.; Ipswich, MA).

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Adaptors were ligated to the digested DNA by adding 0.9 ng of each of the barcoded and common adaptors with 400 U T4 DNA ligase (NEB) in ligase buffer, the amount of adaptor being previously determined by titration ( ). .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. The PCR was initiated at 72°C for 5 min, followed by 98°C for 30 s, then 18 cycles of 98°C for 10 s, 65°C for 30 s, 72°C for 30 s, finishing with 72°C for 5 min. Amplified libraries were checked by electrophoresis in an agarose gel to ensure they had successfully amplified.

    Article Title: Recapitulation of premature aging with iPSCs from Hutchinson-Gilford progeria syndrome
    Article Snippet: Primer sequences to amplify exon 11 of the LMNA gene are listed in . .. 50 μl PCR reactions using 3 ng genomic DNA templates, 100 nM of the forward and reverse primers with 25 μl Taq 2× Master Mix (NEB) was performed at 94°C for 2 min, 34 cycles of 94°C 30 s, 55.5°C for 40 s, and 72°C for 40 s, and finally 72°C for 3 min. Products were purified with 0.9× volume of AMPure beads (Agencourt). .. Amplicons were sequenced by capillary Sanger sequencing (Genewiz).

    Article Title: Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress
    Article Snippet: Removal of antibiotic markers was done at 30 °C in LB by inducing FLP with 50 mM L-rhamnose (final concentration) at an OD~0.1–0.4 for 4–6 h prior to plating unless otherwise stated. .. Integration of cassettes and removal of resistant markers was verified by colony PCR using OneTaq 2× Master Mix (New England Biolabs, Ipswich, MA), according to manufactures instructions. pSIJ8 were cured from the cells by growing them at 37 °C. .. Seven genes encoding the following proteins: Rfe (involved in enterobacterial common antigen (ECA) and O-antigen LPS biosynthesis), PtsP (part of the nitrogen phosphotransferase system, PTSNtr ), YobF (a small protein with no known function), EvgS (the sensor kinase of the EvgSA two component signal transduction system), YciW (a predicted oxidoreductase), AckA (acetate kinase, catalyzing reversible conversion of acetyl phosphate and acetate) and TypA (a member of the ribosome-binding GTPase family), were selected for combinatorial gene deletions (4–7 deletions) based on results from a previous study .

    Article Title: Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response
    Article Snippet: Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes. .. Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes.

    Article Title: Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults
    Article Snippet: Following ddPCR quantification, 4M molecules for each library were amplified using Q5 High-Fidelity 2 × Master Mix (New England Biolabs) using 1 μM P5/P7 primers ( ) in a 50 μl reaction under the following conditions: 98 °C for 30 s; 16 cycles of 98 °C for 10 s, 66 °C for 30 s, 72 °C for 30 s; 72 °C for 2 min; 4 °C hold. .. One-hundred microlitres of beads were washed twice with ddH2 O and replaced with 100 μl of the modified PEG solution described above.

    Article Title: Elucidating the diet of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing
    Article Snippet: PCR reaction was performed using IlluM_rbcLF and IlluM_rbcLR. .. The 20 µL PCR cocktail consists of 10 µL Q 5 Hot Start High-Fidelity 2× Master Mix (New England Biolab, Ipswich, MA, USA), 1 µL each of 10 µM forward and reverse primer, 1 µL gDNA and 7 µL nuclease-free water. .. All reactions were performed in a Veriti® 96-Well Fast Thermal Cycler with the following protocol: initial denaturation for 30 s at 98 °C, 25 cycles of 10 s at 98 °C, 30 s at 55 °C and 10 s at 65 °C, with a final 1 min extension at 65 °C.

    Article Title: Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
    Article Snippet: A second round of end repair and dA-tailing was performed on 500 ng of enriched, amplified PCR product using SureSelectXT reagents as described above, but without purification after dA-tailing. .. In detail, dA-tailed sample, blunt/TA ligase master mix (#M0367, NEB), tethered adapter mix and hairpin adapters (ONT) were incubated for 10 min at room temperature in protein LoBind tubes (#0030108116, Eppendorf) for ligation.

    Article Title: Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization
    Article Snippet: A total of 500 ng of PCR-product was then A-tailed (NEB), cleaned using Ampure, quantified and diluted to 0.2 pmols (220 bp average length). .. Ligation of hairpin and leader adapters (Oxford Nanopore Genomic DNA Sequencing Kit NSK-007) was performed using Blunt/TA ligase master mix (NEB) and was followed by attachment of a biotinylated tether molecule, which when bound specifically to the hairpin adapter, is enriched for using a Streptavidin bead pull-down (Dynabeads MyOne C1).

    Article Title: Discrete microfluidics for the isolation of circulating tumor cell subpopulations targeting fibroblast activation protein alpha and epithelial cell adhesion molecule
    Article Snippet: Cell lines of known KRAS genotype (HT29, wild-type and LS180—G12V) were secured from the Tissue Culture Facility at UNC. gDNA from the cell lines and CTCs was extracted using an Agencourt DNA isolation kit (Beckman–Coulter). .. PCR was performed with DNA in a total volume of 20 µl using Taq 2 × Master Mix (New England Biolabs, Ipswich, MA). .. PCR cocktails consisted of 2 µl of primers, 10 µl Taq 2× Master Mix, 6 µl nuclease free water and 2 µl gDNA.

    Article Title: Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
    Article Snippet: DNA library preparation was carried out according to the 1D PCR barcoding amplicons SQK-LSK108 protocol (ONT). .. Adapter ligation and tethering was then carried out with 20 µL ofAdapter Mix (ONT) and 50 µLof NEB Blunt/TA ligation Master Mix (New England Biolabs).

    Article Title: Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes, et al. Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes
    Article Snippet: PCR amplification of the internal transcribed spacer region 2 (ITS2) was carried out on the individual samples using the ITS3 and ITS4 primers (White, Bruns, Lee, & Taylor, ). .. The PCR reaction mix contained 25 μl of Q5® High‐Fidelity 2× Master Mix (New England Biolabs), 2.5 μl each of the ITS3 and ITS4 primer, 2 μl of genomic DNA and 18 μl of nuclease‐free water. .. The cycling program was 98°C 30 s, {98°C 10 s, 63°C 30 s, 72°C 30 s} for 32 cycles, 72°C 2 min.

    Article Title: Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
    Article Snippet: Briefly, the protocols comprise DNA end-repair and dA-tailing (NEBNext Ultra II End Repair/dA-Tailing Module, New England Biolabs (NEB), Ipswich, MA, USA) followed by purification using AMPure XP solid phase reversible immobilisation (SPRI) beads (Beckman Coulter, High Wycombe, UK); Sequencing adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by additional SPRI bead purification. .. For the samples with insufficient DNA requiring PCR amplification, additional steps between end-repair and sequencing adapter ligation included; PCR adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by SPRI bead purification; PCR amplification (Phusion High Fidelity PCR Master Mix, NEB) with 18 cycles (samples 229 and 249) or 24 cycles (samples 506 and 509) followed by additional SPRI bead purification. .. Samples were sequenced on FLO-MIN105 (v.R9) (sample 229) or FLO-MIN106 (v.R9.4) (all other samples) SpotON flowcells.

    Article Title: BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis
    Article Snippet: Directly following transposition, the sample was purified using a Qiagen MinElute kit. .. Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10–12 cycles. .. The libraries were then purified using a Qiagen PCR cleanup kit.

    Sonication:

    Article Title: Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
    Article Snippet: Libraries were prepared for sequencing on an Oxford Nanopore MinION (Oxford Nanopore Technologies (ONT)) using genomic DNA previously extracted from sonication fluid samples [ ]. .. For the samples with insufficient DNA requiring PCR amplification, additional steps between end-repair and sequencing adapter ligation included; PCR adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by SPRI bead purification; PCR amplification (Phusion High Fidelity PCR Master Mix, NEB) with 18 cycles (samples 229 and 249) or 24 cycles (samples 506 and 509) followed by additional SPRI bead purification.

    Binding Assay:

    Article Title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus
    Article Snippet: A deoxyadenosine was ligated to the 3′-end of double-stranded nucleic acids to allow binding of complimentary sequencing adapters. .. End-prepped DNA (30 µl) was mixed with 20 µl adapter mix (AMX, ONT) and 50 µl Blunt/TA Ligation Master Mix (New England Biolabs) in a total reaction volume of 100 µl and incubated at room temperature for 10 min.

    Molecular Weight:

    Article Title: De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing
    Article Snippet: In short, high molecular weight DNA was sheared with a g-TUBE (Covaris) to an average fragment length of 20 kbp. .. The adaptor and hairpin adapter were ligated using Blunt/TA Ligase Master Mix (New England Biolabs).

    Multiplexing:

    Article Title: Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
    Article Snippet: Ligation reaction was performed using Blunt/TA ligase master mix (NEB). .. Single-cell libraries were either sequenced solely on one (Cell1 and Cell2) or two (Cell3) separate MinION R7.3 flow cells and ran on the 48 h 2D protocol.

    Magnetic Beads:

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Adaptors were ligated to the digested DNA by adding 0.9 ng of each of the barcoded and common adaptors with 400 U T4 DNA ligase (NEB) in ligase buffer, the amount of adaptor being previously determined by titration ( ). .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. The PCR was initiated at 72°C for 5 min, followed by 98°C for 30 s, then 18 cycles of 98°C for 10 s, 65°C for 30 s, 72°C for 30 s, finishing with 72°C for 5 min. Amplified libraries were checked by electrophoresis in an agarose gel to ensure they had successfully amplified.

    Mutagenesis:

    Article Title: Recapitulation of premature aging with iPSCs from Hutchinson-Gilford progeria syndrome
    Article Snippet: Paragraph title: Mutation validation ... 50 μl PCR reactions using 3 ng genomic DNA templates, 100 nM of the forward and reverse primers with 25 μl Taq 2× Master Mix (NEB) was performed at 94°C for 2 min, 34 cycles of 94°C 30 s, 55.5°C for 40 s, and 72°C for 40 s, and finally 72°C for 3 min. Products were purified with 0.9× volume of AMPure beads (Agencourt).

    Size-exclusion Chromatography:

    Article Title: Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
    Article Snippet: The ligated DNA was amplified using Long Amp Taq 2x Master mix (#M0287, NEB) and ONT PCR primers with the following program: 95 °C 3 min; 15–18 cycles of 95 °C 15 sec, 62 °C 15 sec, 65 °C 10 min; 65 °C 20 min; 4 °C hold. .. In detail, dA-tailed sample, blunt/TA ligase master mix (#M0367, NEB), tethered adapter mix and hairpin adapters (ONT) were incubated for 10 min at room temperature in protein LoBind tubes (#0030108116, Eppendorf) for ligation.

    Purification:

    Article Title: Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris
    Article Snippet: Purified gDNAs were stored at 4°C until library preparation. .. End-repaired DNA was then A-tailed using the NEB Blunt/TA-ligase master mix (New England Biolabs, Ipswich, USA).

    Article Title: High density genetic maps of St. Augustinegrass and applications to comparative genomic analysis and QTL mapping for turf quality traits
    Article Snippet: The reaction was stopped by incubation at 65 °C for 20 min. Barcoded adapters (containing unique barcode sequences, details in Additional file : Table S1) and a common-Y adapter were ligated to digested genomic DNA fragments at 22 °C overnight in 40 μL volume and stopped at 65 °C for 20 min. Then, 10 μL of each sample was pooled and cleaned up using QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany). .. After that, purified DNA was amplified using NEB MasterMix (New England BioLabs, Inc.; Ipswich, MA). .. PCR products were purified and size-selected using GeneRead Size Selection Kit (QIAGEN, Hilden, Germany) to remove adapter dimers and small fragments ( < 150 bp).

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Adaptors were ligated to the digested DNA by adding 0.9 ng of each of the barcoded and common adaptors with 400 U T4 DNA ligase (NEB) in ligase buffer, the amount of adaptor being previously determined by titration ( ). .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. The PCR was initiated at 72°C for 5 min, followed by 98°C for 30 s, then 18 cycles of 98°C for 10 s, 65°C for 30 s, 72°C for 30 s, finishing with 72°C for 5 min. Amplified libraries were checked by electrophoresis in an agarose gel to ensure they had successfully amplified.

    Article Title: Recapitulation of premature aging with iPSCs from Hutchinson-Gilford progeria syndrome
    Article Snippet: Primer sequences to amplify exon 11 of the LMNA gene are listed in . .. 50 μl PCR reactions using 3 ng genomic DNA templates, 100 nM of the forward and reverse primers with 25 μl Taq 2× Master Mix (NEB) was performed at 94°C for 2 min, 34 cycles of 94°C 30 s, 55.5°C for 40 s, and 72°C for 40 s, and finally 72°C for 3 min. Products were purified with 0.9× volume of AMPure beads (Agencourt). .. Amplicons were sequenced by capillary Sanger sequencing (Genewiz).

    Article Title: Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults
    Article Snippet: Following ddPCR quantification, 4M molecules for each library were amplified using Q5 High-Fidelity 2 × Master Mix (New England Biolabs) using 1 μM P5/P7 primers ( ) in a 50 μl reaction under the following conditions: 98 °C for 30 s; 16 cycles of 98 °C for 10 s, 66 °C for 30 s, 72 °C for 30 s; 72 °C for 2 min; 4 °C hold. .. One-hundred microlitres of beads were washed twice with ddH2 O and replaced with 100 μl of the modified PEG solution described above.

    Article Title: Elucidating the diet of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing
    Article Snippet: The 20 µL PCR cocktail consists of 10 µL Q 5 Hot Start High-Fidelity 2× Master Mix (New England Biolab, Ipswich, MA, USA), 1 µL each of 10 µM forward and reverse primer, 1 µL gDNA and 7 µL nuclease-free water. .. The 20 µL PCR cocktail consists of 10 µL Q 5 Hot Start High-Fidelity 2× Master Mix (New England Biolab, Ipswich, MA, USA), 1 µL each of 10 µM forward and reverse primer, 1 µL gDNA and 7 µL nuclease-free water.

    Article Title: Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
    Article Snippet: A second round of end repair and dA-tailing was performed on 500 ng of enriched, amplified PCR product using SureSelectXT reagents as described above, but without purification after dA-tailing. .. In detail, dA-tailed sample, blunt/TA ligase master mix (#M0367, NEB), tethered adapter mix and hairpin adapters (ONT) were incubated for 10 min at room temperature in protein LoBind tubes (#0030108116, Eppendorf) for ligation.

    Article Title: First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans)
    Article Snippet: The library was blunt-ended and A-tailed with NEB Ultra II End prep module, and purified using 1× AMpure XP. .. Adapter ligation was then performed using Blunt-TA ligase master mix (NEB) and proprietary ONT “1D” adapters containing a preloaded motor protein.

    Article Title: Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization
    Article Snippet: PCR product was purified using Ampure XP (Agencourt), and quantified using a Qubit dsDNA HS Assay kit (Thermo Fisher). .. Ligation of hairpin and leader adapters (Oxford Nanopore Genomic DNA Sequencing Kit NSK-007) was performed using Blunt/TA ligase master mix (NEB) and was followed by attachment of a biotinylated tether molecule, which when bound specifically to the hairpin adapter, is enriched for using a Streptavidin bead pull-down (Dynabeads MyOne C1).

    Article Title: Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
    Article Snippet: Barcode DNA products were pooled with 5 µLof DNA CS (a positive control provided by ONT) and an end-repair was performed (NEB-Next Ultra II End-prep reaction buffer and enzyme mix, New England Biolabs), then purified using AMPure XP beads. .. Adapter ligation and tethering was then carried out with 20 µL ofAdapter Mix (ONT) and 50 µLof NEB Blunt/TA ligation Master Mix (New England Biolabs).

    Article Title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus
    Article Snippet: Fifty microliters of (un)amplified DNA were mixed with 7 µl Ultra II End-Prep Reaction Buffer (New England Biolabs) and 3 µl Ultra II End-prep enzyme mix (New England Biolabs), and incubated at 20 °C for 5 min and 65 °C for 5 min. Next, nucleic acids were purified using 60 µl AMPure XP Beads and eluted in 31 µl nuclease-free water. .. End-prepped DNA (30 µl) was mixed with 20 µl adapter mix (AMX, ONT) and 50 µl Blunt/TA Ligation Master Mix (New England Biolabs) in a total reaction volume of 100 µl and incubated at room temperature for 10 min.

    Article Title: Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
    Article Snippet: Briefly, the protocols comprise DNA end-repair and dA-tailing (NEBNext Ultra II End Repair/dA-Tailing Module, New England Biolabs (NEB), Ipswich, MA, USA) followed by purification using AMPure XP solid phase reversible immobilisation (SPRI) beads (Beckman Coulter, High Wycombe, UK); Sequencing adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by additional SPRI bead purification. .. For the samples with insufficient DNA requiring PCR amplification, additional steps between end-repair and sequencing adapter ligation included; PCR adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by SPRI bead purification; PCR amplification (Phusion High Fidelity PCR Master Mix, NEB) with 18 cycles (samples 229 and 249) or 24 cycles (samples 506 and 509) followed by additional SPRI bead purification. .. Samples were sequenced on FLO-MIN105 (v.R9) (sample 229) or FLO-MIN106 (v.R9.4) (all other samples) SpotON flowcells.

    Article Title: BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis
    Article Snippet: Directly following transposition, the sample was purified using a Qiagen MinElute kit. .. Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10–12 cycles. .. The libraries were then purified using a Qiagen PCR cleanup kit.

    Sequencing:

    Article Title: Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris
    Article Snippet: Paragraph title: gDNA extraction for MinION sequencing ... End-repaired DNA was then A-tailed using the NEB Blunt/TA-ligase master mix (New England Biolabs, Ipswich, USA).

    Article Title: Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus
    Article Snippet: Paragraph title: Cap selection, cDNA synthesis and sequencing ... This step was followed by the 1D adapter ligation, which was carried out according to the 1D protocol, using the NEB Blunt/TA Ligase Master Mix (New England Biolabs).

    Article Title: High density genetic maps of St. Augustinegrass and applications to comparative genomic analysis and QTL mapping for turf quality traits
    Article Snippet: After that, purified DNA was amplified using NEB MasterMix (New England BioLabs, Inc.; Ipswich, MA). .. After that, purified DNA was amplified using NEB MasterMix (New England BioLabs, Inc.; Ipswich, MA).

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions.

    Article Title: Recapitulation of premature aging with iPSCs from Hutchinson-Gilford progeria syndrome
    Article Snippet: 50 μl PCR reactions using 3 ng genomic DNA templates, 100 nM of the forward and reverse primers with 25 μl Taq 2× Master Mix (NEB) was performed at 94°C for 2 min, 34 cycles of 94°C 30 s, 55.5°C for 40 s, and 72°C for 40 s, and finally 72°C for 3 min. Products were purified with 0.9× volume of AMPure beads (Agencourt). .. Amplicons were sequenced by capillary Sanger sequencing (Genewiz).

    Article Title: Elucidating the diet of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing
    Article Snippet: Prior to primer synthesis, partial Illumina adapter sequences were added to the 5′ end of the designed primers, rbcL-357F and rbcL-556R, to allow barcoding and sequencing on the Illumina platform. .. The 20 µL PCR cocktail consists of 10 µL Q 5 Hot Start High-Fidelity 2× Master Mix (New England Biolab, Ipswich, MA, USA), 1 µL each of 10 µM forward and reverse primer, 1 µL gDNA and 7 µL nuclease-free water.

    Article Title: Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
    Article Snippet: Paragraph title: Nanopore library preparation, sequencing and analysis. ... In detail, dA-tailed sample, blunt/TA ligase master mix (#M0367, NEB), tethered adapter mix and hairpin adapters (ONT) were incubated for 10 min at room temperature in protein LoBind tubes (#0030108116, Eppendorf) for ligation.

    Article Title: Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
    Article Snippet: The single cDNA or multiplex product was further end-repaired and dA-tailed using NEBNext Ultra End Repair/dA tailing mix (NEB), and adaptor ligated using the sequencing adaptors provided by ONT (HP Adaptor/Adaptor Mix). .. Ligation reaction was performed using Blunt/TA ligase master mix (NEB).

    Article Title: Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
    Article Snippet: Paragraph title: MinION sequencing ... Adapter ligation and tethering was then carried out with 20 µL ofAdapter Mix (ONT) and 50 µLof NEB Blunt/TA ligation Master Mix (New England Biolabs).

    Article Title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus
    Article Snippet: Sequencing adapters, provided with the Ligation Sequencing Kit 1D (R9.4) (SQK-LSK108, ONT), were ligated to the dA-tailed nucleic acids. .. End-prepped DNA (30 µl) was mixed with 20 µl adapter mix (AMX, ONT) and 50 µl Blunt/TA Ligation Master Mix (New England Biolabs) in a total reaction volume of 100 µl and incubated at room temperature for 10 min.

    Article Title: De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing
    Article Snippet: Paragraph title: MinION library preparation, sequencing and quality control ... The adaptor and hairpin adapter were ligated using Blunt/TA Ligase Master Mix (New England Biolabs).

    Article Title: Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices
    Article Snippet: Briefly, the protocols comprise DNA end-repair and dA-tailing (NEBNext Ultra II End Repair/dA-Tailing Module, New England Biolabs (NEB), Ipswich, MA, USA) followed by purification using AMPure XP solid phase reversible immobilisation (SPRI) beads (Beckman Coulter, High Wycombe, UK); Sequencing adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by additional SPRI bead purification. .. For the samples with insufficient DNA requiring PCR amplification, additional steps between end-repair and sequencing adapter ligation included; PCR adapter ligation (Blunt/TA Ligase Master Mix, NEB) followed by SPRI bead purification; PCR amplification (Phusion High Fidelity PCR Master Mix, NEB) with 18 cycles (samples 229 and 249) or 24 cycles (samples 506 and 509) followed by additional SPRI bead purification. .. Samples were sequenced on FLO-MIN105 (v.R9) (sample 229) or FLO-MIN106 (v.R9.4) (all other samples) SpotON flowcells.

    Article Title: BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis
    Article Snippet: Paragraph title: Assay of transposase-accessible chromatin using sequencing ... Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10–12 cycles.

    Polyacrylamide Gel Electrophoresis:

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: The PCR primers were PAGE (polyacrylamide gel electrophoresis) purified from Integrated DNA Technologies (Coralville, IA, United States). .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions.

    Staining:

    Article Title: Discrete microfluidics for the isolation of circulating tumor cell subpopulations targeting fibroblast activation protein alpha and epithelial cell adhesion molecule
    Article Snippet: PCR was performed with DNA in a total volume of 20 µl using Taq 2 × Master Mix (New England Biolabs, Ipswich, MA). .. PCR was performed with DNA in a total volume of 20 µl using Taq 2 × Master Mix (New England Biolabs, Ipswich, MA).

    IA:

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: The PCR primers were PAGE (polyacrylamide gel electrophoresis) purified from Integrated DNA Technologies (Coralville, IA, United States). .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions.

    Titration:

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Adaptors were ligated to the digested DNA by adding 0.9 ng of each of the barcoded and common adaptors with 400 U T4 DNA ligase (NEB) in ligase buffer, the amount of adaptor being previously determined by titration ( ). .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions.

    Software:

    Article Title: Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris
    Article Snippet: End-repaired DNA was then A-tailed using the NEB Blunt/TA-ligase master mix (New England Biolabs, Ipswich, USA). .. End-repaired DNA was then A-tailed using the NEB Blunt/TA-ligase master mix (New England Biolabs, Ipswich, USA).

    Article Title: Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
    Article Snippet: Adapter ligation and tethering was then carried out with 20 µL ofAdapter Mix (ONT) and 50 µLof NEB Blunt/TA ligation Master Mix (New England Biolabs). .. Then 12 µL of the amplicon library was diluted in 75 μL of running buffer with 35 µL RBF, 25.5 uL LLB, and 2.5 μL nuclease-free water and added to the flow cell via the SpotON sample port.

    Multiplex Assay:

    Article Title: Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response
    Article Snippet: Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes. .. Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes.

    Article Title: Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
    Article Snippet: The single cDNA or multiplex product was further end-repaired and dA-tailed using NEBNext Ultra End Repair/dA tailing mix (NEB), and adaptor ligated using the sequencing adaptors provided by ONT (HP Adaptor/Adaptor Mix). .. Ligation reaction was performed using Blunt/TA ligase master mix (NEB).

    Article Title: Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization
    Article Snippet: A second round of PCR (OneTaq, NEB) adding Oxford-specific barcodes was performed, allowing us to multiplex (although we chose not to in this case). .. Ligation of hairpin and leader adapters (Oxford Nanopore Genomic DNA Sequencing Kit NSK-007) was performed using Blunt/TA ligase master mix (NEB) and was followed by attachment of a biotinylated tether molecule, which when bound specifically to the hairpin adapter, is enriched for using a Streptavidin bead pull-down (Dynabeads MyOne C1).

    Article Title: Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes, et al. Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes
    Article Snippet: The PCR reaction mix contained 25 μl of Q5® High‐Fidelity 2× Master Mix (New England Biolabs), 2.5 μl each of the ITS3 and ITS4 primer, 2 μl of genomic DNA and 18 μl of nuclease‐free water. .. Amplicon libraries were prepared using 200 ng of each PCR product and the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® with dual indexing (barcoding).

    Selection:

    Article Title: Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus
    Article Snippet: Paragraph title: Cap selection, cDNA synthesis and sequencing ... This step was followed by the 1D adapter ligation, which was carried out according to the 1D protocol, using the NEB Blunt/TA Ligase Master Mix (New England Biolabs).

    Agarose Gel Electrophoresis:

    Article Title: Discrete microfluidics for the isolation of circulating tumor cell subpopulations targeting fibroblast activation protein alpha and epithelial cell adhesion molecule
    Article Snippet: PCR was performed with DNA in a total volume of 20 µl using Taq 2 × Master Mix (New England Biolabs, Ipswich, MA). .. PCR was performed with DNA in a total volume of 20 µl using Taq 2 × Master Mix (New England Biolabs, Ipswich, MA).

    Next-Generation Sequencing:

    Article Title: Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes, et al. Flower preferences and pollen transport networks for cavity‐nesting solitary bees: Implications for the design of agri‐environment schemes
    Article Snippet: Paragraph title: Next generation sequencing of pollen sample DNA ... The PCR reaction mix contained 25 μl of Q5® High‐Fidelity 2× Master Mix (New England Biolabs), 2.5 μl each of the ITS3 and ITS4 primer, 2 μl of genomic DNA and 18 μl of nuclease‐free water.

    Concentration Assay:

    Article Title: Genomic Selection for Ascochyta Blight Resistance in Pea
    Article Snippet: Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions. .. Ligation reactions were incubated at 22°C for 2 h then inactivated at 65°C for 30 min. Ligation products were purified using Ampclean magnetic beads (MAGBIO genomics, Gaithersburg, MD, United States), then amplified by PCR using Taq 2× mastermix (NEB), with 25 pmol of each primer, and 10 μl ligation products in 50 μl, in individual reactions.

    Article Title: Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress
    Article Snippet: Removal of antibiotic markers was done at 30 °C in LB by inducing FLP with 50 mM L-rhamnose (final concentration) at an OD~0.1–0.4 for 4–6 h prior to plating unless otherwise stated. .. Integration of cassettes and removal of resistant markers was verified by colony PCR using OneTaq 2× Master Mix (New England Biolabs, Ipswich, MA), according to manufactures instructions. pSIJ8 were cured from the cells by growing them at 37 °C.

    Lysis:

    Article Title: BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis
    Article Snippet: Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). .. Following purification, we amplified library fragments using Nextera PCR Primers (Illumina Nextera Index kit) and NEBnext PCR master mix (New England lab, 0541) for a total of 10–12 cycles.

    Nanopore Sequencing:

    Article Title: Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
    Article Snippet: Paragraph title: Nanopore sequencing ... Ligation reaction was performed using Blunt/TA ligase master mix (NEB).

    Article Title: First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans)
    Article Snippet: Paragraph title: Nanopore sequencing library construction and data preparation ... Adapter ligation was then performed using Blunt-TA ligase master mix (NEB) and proprietary ONT “1D” adapters containing a preloaded motor protein.

    Article Title: Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization
    Article Snippet: Paragraph title: Nanopore sequencing ... Ligation of hairpin and leader adapters (Oxford Nanopore Genomic DNA Sequencing Kit NSK-007) was performed using Blunt/TA ligase master mix (NEB) and was followed by attachment of a biotinylated tether molecule, which when bound specifically to the hairpin adapter, is enriched for using a Streptavidin bead pull-down (Dynabeads MyOne C1).

    Article Title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus
    Article Snippet: Paragraph title: Nanopore sequencing library preparation ... End-prepped DNA (30 µl) was mixed with 20 µl adapter mix (AMX, ONT) and 50 µl Blunt/TA Ligation Master Mix (New England Biolabs) in a total reaction volume of 100 µl and incubated at room temperature for 10 min.

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    New England Biolabs q5 high fidelity 2x master mix
    Q5 High Fidelity 2x Master Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 48 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/q5 high fidelity 2x master mix/product/New England Biolabs
    Average 99 stars, based on 48 article reviews
    Price from $9.99 to $1999.99
    q5 high fidelity 2x master mix - by Bioz Stars, 2019-07
    99/100 stars
      Buy from Supplier

    99
    New England Biolabs mastermix
    Mastermix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mastermix/product/New England Biolabs
    Average 99 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    mastermix - by Bioz Stars, 2019-07
    99/100 stars
      Buy from Supplier

    94
    New England Biolabs pcr amplification
    Pcr Amplification, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 77 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr amplification/product/New England Biolabs
    Average 94 stars, based on 77 article reviews
    Price from $9.99 to $1999.99
    pcr amplification - by Bioz Stars, 2019-07
    94/100 stars
      Buy from Supplier

    Image Search Results