ultratm dna library prep kit  (New England Biolabs)


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  • 99
    Name:
    NEBNext Ultra DNA Library Prep Kit for Illumina
    Description:
    NEBNext Ultra DNA Library Prep Kit for Illumina 96 rxns
    Catalog Number:
    E7370L
    Price:
    2076
    Size:
    96 rxns
    Category:
    DNA Template Preparation for PCR
    Score:
    85
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    Structured Review

    New England Biolabs ultratm dna library prep kit
    NEBNext Ultra DNA Library Prep Kit for Illumina
    NEBNext Ultra DNA Library Prep Kit for Illumina 96 rxns
    https://www.bioz.com/result/ultratm dna library prep kit/product/New England Biolabs
    Average 99 stars, based on 29 article reviews
    Price from $9.99 to $1999.99
    ultratm dna library prep kit - by Bioz Stars, 2019-10
    99/100 stars

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    Related Articles

    Clone Assay:

    Article Title: Complete Genome Sequence of a Human Cytomegalovirus Strain AD169 Bacterial Artificial Chromosome Clone
    Article Snippet: 400 ng of BAC DNA was used for library preparation using a NEBNext Ultra DNA sample preparation kit (NEB) according to the manufacturer’s recommendations. .. 400 ng of BAC DNA was used for library preparation using a NEBNext Ultra DNA sample preparation kit (NEB) according to the manufacturer’s recommendations.

    Centrifugation:

    Article Title: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae)
    Article Snippet: Problematic DNAs were cleaned with a QIAquick kit (QIAGEN, Valencia, California, USA); any DNAs too dilute for library preparation were concentrated by vacuum centrifugation. .. Libraries were prepared with 55.5 μL of sonicated DNA, using a NEBNext Ultra kit (New England Biolabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocols with the following modifications: size selection aimed for a 500–700-bp range (i.e., 30 μL AM XP beads [Beckman Coulter, Brea, California, USA] for the first size-selection step, and 15 μL for the second step), and PCR amplification mostly used six cycles (eight cycles for the herbarium specimen).

    Article Title: Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius
    Article Snippet: Bacteria from each individual colony were grown overnight in tryptic soy broth, pelleted by centrifugation at 5,000 × g for 10 min, and genomic DNA was extracted using the QIAamp Fast DNA stool minikit (Qiagen). .. Genomic DNA was used to construct a sequencing library employing a NEBNext Ultra DNA library prep kit (New England BioLabs, Ipswich, MA).

    Amplification:

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol. .. Cleanup of adaptor-ligated DNA was performed without size selection using a 1.0/1 ratio of SPRI beads/DNA.

    Article Title: Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA
    Article Snippet: NEBNext Ultra library preparation protocol consists of several enzymatic and two purification steps, one of which is used for size selection of library fragments. .. NEBNext Ultra library preparation protocol consists of several enzymatic and two purification steps, one of which is used for size selection of library fragments.

    Article Title: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae)
    Article Snippet: One microgram of clean genomic DNA in 60 μL was sonicated using a Covaris machine (model S220; Covaris, Woburn, Massachusetts, USA), aiming for fragment size of 500–700 bp. .. Libraries were prepared with 55.5 μL of sonicated DNA, using a NEBNext Ultra kit (New England Biolabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocols with the following modifications: size selection aimed for a 500–700-bp range (i.e., 30 μL AM XP beads [Beckman Coulter, Brea, California, USA] for the first size-selection step, and 15 μL for the second step), and PCR amplification mostly used six cycles (eight cycles for the herbarium specimen). .. Libraries were barcoded using NEBNext Multiplex oligos (New England Biolabs).

    Article Title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool‐ Seq data
    Article Snippet: An initial size selection was performed using AMPureXP beads (Beckman Coulter, CA, USA), either before the PCR step (for the two PCR‐based protocols), or at the end of the protocol (for the NEXTflex (−) protocol). .. The NEBNext Ultra (+) samples were amplified using Phusion Polymerase included in the NEBNext Ultra DNA Kit, and the NEBNext master mix samples using the master mix included into the TruSeqDNA LT Sample Prep Kit. .. Both PCR‐based protocols used the following cycling conditions: an initial denaturation step at 98 °C/30 s, followed by 10 cycles at 98 °C/10 s, 65 °C (Phusion polymerase) or 60 °C (TruSeq polymerase)/30 s, 72 °C/50 s and a final extension at 72 °C/7 min.

    Mass Spectrometry:

    Article Title: Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius
    Article Snippet: The remains of this animal were dated by an accelerator mass spectrometry (AMS) method at the Center for Isotope Research of Groningen University at 28,610 ± 110 years of age. .. Genomic DNA was used to construct a sequencing library employing a NEBNext Ultra DNA library prep kit (New England BioLabs, Ipswich, MA).

    Construct:

    Article Title: Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius
    Article Snippet: Bacteria from each individual colony were grown overnight in tryptic soy broth, pelleted by centrifugation at 5,000 × g for 10 min, and genomic DNA was extracted using the QIAamp Fast DNA stool minikit (Qiagen). .. Genomic DNA was used to construct a sequencing library employing a NEBNext Ultra DNA library prep kit (New England BioLabs, Ipswich, MA). .. Sequencing was performed on an Illumina MiSeq with the 301-cycle MiSeq reagent kit version 2, to achieve 150× average genome coverage.

    Electrophoresis:

    Article Title: Standardizing chromatin research: a simple and universal method for ChIP-seq
    Article Snippet: Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (E7370S, NEB). .. Subsequently adaptor-ligated DNA was enriched using 10 PCR cycles.

    Incubation:

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: Second strand synthesis was performed using a custom reaction (20 μl first strand cDNA, 10 μl × 10 thermopol buffer, 1 ml × 100 BSA, 3 ml 10 mM dNTPs, 0.5 μl RnaseH, 1 μl Taq polymerase, 0.1 μl Pfu polymerase, 64.4 ml H2 O) which was incubated in a thermocycler under the following conditions: 37 °C 5 min, 65 °C 1 min, 72 °C 30 min) followed by SPRI purification (beads/DNA ratio 1.8/1). .. Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol.

    Expressing:

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: The libraries were prepared using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (E7370L), size-selected and multiplexed before paired-end sequencing on the HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina) in the Wellcome Trust Centre for Human Genetics. .. For transcription inhibition, HeLa cells were treated with 50 μM 5,6-dichlorobenzimidazole riboside (DRB; Sigma, D1916) for 5 h, as described ( ).

    Modification:

    Article Title: Personalized identification of tumor-associated immunogenic neoepitopes in hepatocellular carcinoma in complete remission after sorafenib treatment
    Article Snippet: Library preparation, capture, sequencing, and bioinformatics analysis were performed by IntegraGen, Evry, France. .. Genomic DNA was captured using SureSelect Human All Exon v4 + UTR - 70 Mb (Agilent) according to manufacturer’s instruction and protocols without modification except for library preparation which was performed using NEBNext Ultra kit (New England Biolabs). .. Pooled capture-enriched DNA samples were then sequenced by paired-end 75 bases massively parallel sequencing on HiSeq 2000 (Illumina).

    Derivative Assay:

    Article Title: Complete Genome Sequences of Two Bordetella hinzii Strains Isolated from Humans
    Article Snippet: Here, we report the complete genome sequences of two clinically derived B. hinzii strains from the culture collection at the Centers for Disease Control and Prevention. .. Libraries were prepared for PacBio sequencing using the SMRTbell template prep kit 1.0 and polymerase binding kit P4, while HiSeq libraries were prepared using the NEBNext Ultra library prep kit (New England BioLabs, Ipswich, MA).

    Hybridization:

    Article Title: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae)
    Article Snippet: Libraries were prepared with 55.5 μL of sonicated DNA, using a NEBNext Ultra kit (New England Biolabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocols with the following modifications: size selection aimed for a 500–700-bp range (i.e., 30 μL AM XP beads [Beckman Coulter, Brea, California, USA] for the first size-selection step, and 15 μL for the second step), and PCR amplification mostly used six cycles (eight cycles for the herbarium specimen). .. Libraries were prepared with 55.5 μL of sonicated DNA, using a NEBNext Ultra kit (New England Biolabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocols with the following modifications: size selection aimed for a 500–700-bp range (i.e., 30 μL AM XP beads [Beckman Coulter, Brea, California, USA] for the first size-selection step, and 15 μL for the second step), and PCR amplification mostly used six cycles (eight cycles for the herbarium specimen).

    Transfection:

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: Paragraph title: Cell cultures, transfections and library preparations. ... The libraries were prepared using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (E7370L), size-selected and multiplexed before paired-end sequencing on the HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina) in the Wellcome Trust Centre for Human Genetics.

    Gas Chromatography:

    Article Title: Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq
    Article Snippet: A high IQR was observed for the NEBNext Ultra isolates, suggesting that this library prep method does not provide a uniform coverage; a more uniform coverage is seen with the TruSeq Nano-prepared genomes. .. This was also evident when genome coverage was plotted against percentage GC content ( ): coverage dropped more severely at high AT regions for isolates prepared with the NEBNext Ultra kit, however, both kits performed equally poorly at regions with high GC content. .. Gaps in coverage, defined as any bases or regions of the genomes that are sequenced with less than 15% read depth, provide a meaningful way to look at non-uniform sequence coverage.

    Ligation:

    Article Title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool‐ Seq data
    Article Snippet: End repair, A‐tailing and ligation were performed according to the suppliers' protocols except that the adapters for the NEBNext DNA (+) libraries were taken from the TruSeq DNA LT Sample Prep Kit (FC‐121‐2001). .. The NEBNext Ultra (+) samples were amplified using Phusion Polymerase included in the NEBNext Ultra DNA Kit, and the NEBNext master mix samples using the master mix included into the TruSeqDNA LT Sample Prep Kit.

    Article Title: Standardizing chromatin research: a simple and universal method for ChIP-seq
    Article Snippet: Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (E7370S, NEB). .. Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (E7370S, NEB).

    Affinity Magnetic Separation:

    Article Title: Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius
    Article Snippet: The remains of this animal were dated by an accelerator mass spectrometry (AMS) method at the Center for Isotope Research of Groningen University at 28,610 ± 110 years of age. .. Genomic DNA was used to construct a sequencing library employing a NEBNext Ultra DNA library prep kit (New England BioLabs, Ipswich, MA).

    Generated:

    Article Title: Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy
    Article Snippet: Then, the mixed PCR products were purified with the EZNA Gel Extraction Kit (Omega, United States). .. Sequencing libraries were generated using the NEBNext® UltraTM DNA Library Prep Kit for Illumina® sequencing (New England Biolabs, United States) following the manufacturer’s recommendations, and index codes were added. .. The library quality was assessed on a Qubit@ 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system.

    Article Title: Interferon lambda protects the female reproductive tract against Zika virus infection
    Article Snippet: Briefly, libraries were prepared with the Ultra Library Preparation kit (New England BioLabs), and quality was determined using the Qubit assay (Thermo Scientific) and Agilent 2100 Bioanalyzer. .. Briefly, libraries were prepared with the Ultra Library Preparation kit (New England BioLabs), and quality was determined using the Qubit assay (Thermo Scientific) and Agilent 2100 Bioanalyzer.

    Article Title: Complete Genome Sequences of Two Bordetella hinzii Strains Isolated from Humans
    Article Snippet: Libraries were prepared for PacBio sequencing using the SMRTbell template prep kit 1.0 and polymerase binding kit P4, while HiSeq libraries were prepared using the NEBNext Ultra library prep kit (New England BioLabs, Ipswich, MA). .. Libraries were prepared for PacBio sequencing using the SMRTbell template prep kit 1.0 and polymerase binding kit P4, while HiSeq libraries were prepared using the NEBNext Ultra library prep kit (New England BioLabs, Ipswich, MA).

    Article Title: Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition
    Article Snippet: Then, mixture PCR products were purified with GeneJET Gel Extraction Kit (Thermo Scientific). .. Sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added. .. The library quality was assessed on the Qubit @ 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system.

    DNA Sequencing:

    Article Title: Draft Genome Sequence of a Pseudomonas aeruginosa Strain Able To Decompose N,N-Dimethyl Formamide
    Article Snippet: Genome sequencing was performed at CapitalBio Technology using Illumina technology with a DNA sequencing (DNA-seq) paired-end protocol. .. A library was prepared with the NEBNext Ultra DNA library prep kit for Illumina, and the instrument used for sequencing was HiSeq 2500.

    Polymerase Chain Reaction:

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol. .. Cleanup of adaptor-ligated DNA was performed without size selection using a 1.0/1 ratio of SPRI beads/DNA.

    Article Title: Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA
    Article Snippet: NEBNext Ultra library preparation protocol consists of several enzymatic and two purification steps, one of which is used for size selection of library fragments. .. NEBNext Ultra library preparation protocol consists of several enzymatic and two purification steps, one of which is used for size selection of library fragments.

    Article Title: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae)
    Article Snippet: One microgram of clean genomic DNA in 60 μL was sonicated using a Covaris machine (model S220; Covaris, Woburn, Massachusetts, USA), aiming for fragment size of 500–700 bp. .. Libraries were prepared with 55.5 μL of sonicated DNA, using a NEBNext Ultra kit (New England Biolabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocols with the following modifications: size selection aimed for a 500–700-bp range (i.e., 30 μL AM XP beads [Beckman Coulter, Brea, California, USA] for the first size-selection step, and 15 μL for the second step), and PCR amplification mostly used six cycles (eight cycles for the herbarium specimen). .. Libraries were barcoded using NEBNext Multiplex oligos (New England Biolabs).

    Article Title: Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition
    Article Snippet: Then, mixture PCR products were purified with GeneJET Gel Extraction Kit (Thermo Scientific). .. Sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added.

    Article Title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool‐ Seq data
    Article Snippet: An initial size selection was performed using AMPureXP beads (Beckman Coulter, CA, USA), either before the PCR step (for the two PCR‐based protocols), or at the end of the protocol (for the NEXTflex (−) protocol). .. The NEBNext Ultra (+) samples were amplified using Phusion Polymerase included in the NEBNext Ultra DNA Kit, and the NEBNext master mix samples using the master mix included into the TruSeqDNA LT Sample Prep Kit.

    Article Title: Standardizing chromatin research: a simple and universal method for ChIP-seq
    Article Snippet: Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (E7370S, NEB). .. Following adaptor ligation (1.5 μM), size selection was omitted and adaptor-ligated DNA was directly purified using AMPure XP beads (Beckman Coulter).

    Sonication:

    Article Title: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae)
    Article Snippet: One microgram of clean genomic DNA in 60 μL was sonicated using a Covaris machine (model S220; Covaris, Woburn, Massachusetts, USA), aiming for fragment size of 500–700 bp. .. Libraries were prepared with 55.5 μL of sonicated DNA, using a NEBNext Ultra kit (New England Biolabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocols with the following modifications: size selection aimed for a 500–700-bp range (i.e., 30 μL AM XP beads [Beckman Coulter, Brea, California, USA] for the first size-selection step, and 15 μL for the second step), and PCR amplification mostly used six cycles (eight cycles for the herbarium specimen). .. Libraries were barcoded using NEBNext Multiplex oligos (New England Biolabs).

    Binding Assay:

    Article Title: Complete Genome Sequences of Two Bordetella hinzii Strains Isolated from Humans
    Article Snippet: Genomic DNA was isolated with the Gentra Puregene yeast/bacteria kit (Qiagen, Valencia, CA). .. Libraries were prepared for PacBio sequencing using the SMRTbell template prep kit 1.0 and polymerase binding kit P4, while HiSeq libraries were prepared using the NEBNext Ultra library prep kit (New England BioLabs, Ipswich, MA). .. PacBio sequencing reads were filtered and assembled de novo using the Hierarchical Genome Assembly Process algorithm (HGAP) version 3.

    ChIP-sequencing:

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: Paragraph title: Chromatin immunoprecipitation sequencing ... Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol.

    DNA Extraction:

    Article Title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool‐ Seq data
    Article Snippet: Paragraph title: DNA extraction and library preparation ... The NEBNext Ultra (+) samples were amplified using Phusion Polymerase included in the NEBNext Ultra DNA Kit, and the NEBNext master mix samples using the master mix included into the TruSeqDNA LT Sample Prep Kit.

    Fluorescence:

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol. .. For the PCR amplification of libraries, 0.5 μl of × 100 Syber Green was added to each reaction and the PCR amplification was performed on a LightCycler 480 (Roche) using the following cycling conditions: initial denaturation (98 °C, 30 s) followed by 9–12 cycles (98 °C, 10 s; 65 °C, 30 s; 72 °C, 30 s).

    Mutagenesis:

    Article Title: Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers
    Article Snippet: Personalized tumor mutation profiles were identified for each patient’s tumor by either whole exome sequencing (WES) or a targeted gene sequencing approach. .. Whole-genome libraries were prepared from gDNA using the NEBNext DNA Library Prep kit (New England Biolabs, Ipswich, MA), enriched to whole exome libraries using the SeqCap EZ Human Exome Library v3.0 capture system (Roche NimbleGen, Madison, WI), covering approximately 64 Mb of the genome where variants can be called; paired-end sequencing (2x100 nt reads) was done on Illumina HiSeq 2500 (Illumina, San Diego, CA) in either High Output or Rapid Run mode.

    Isolation:

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: For library preparations, total RNA was used to isolate intact poly(A)+ RNA with the NEBNext poly(A) mRNA magnetic isolation module (E7490L), employing the Human/mouse/rat Ribo-Zero™ rRNA Removal Kit (Cambio/Epicentre) according to manufacturers’ recommendations. .. The libraries were prepared using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (E7370L), size-selected and multiplexed before paired-end sequencing on the HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina) in the Wellcome Trust Centre for Human Genetics.

    Article Title: Complete Genome Sequences of Two Bordetella hinzii Strains Isolated from Humans
    Article Snippet: Genomic DNA was isolated with the Gentra Puregene yeast/bacteria kit (Qiagen, Valencia, CA). .. Libraries were prepared for PacBio sequencing using the SMRTbell template prep kit 1.0 and polymerase binding kit P4, while HiSeq libraries were prepared using the NEBNext Ultra library prep kit (New England BioLabs, Ipswich, MA).

    Article Title: Complete Genome Sequence of a Human Cytomegalovirus Strain AD169 Bacterial Artificial Chromosome Clone
    Article Snippet: In the present study, AD169-BAC DNA was isolated from the Escherichia coli strain DH10B, purified using a Nucleobond Xtra-Midi column (Macherey-Nagel) following the manufacturer’s instructions, and resuspended in 10 mM Tris-HCl, pH 8.0. .. 400 ng of BAC DNA was used for library preparation using a NEBNext Ultra DNA sample preparation kit (NEB) according to the manufacturer’s recommendations.

    Flow Cytometry:

    Article Title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool‐ Seq data
    Article Snippet: End repair, A‐tailing and ligation were performed according to the suppliers' protocols except that the adapters for the NEBNext DNA (+) libraries were taken from the TruSeq DNA LT Sample Prep Kit (FC‐121‐2001). .. The NEBNext Ultra (+) samples were amplified using Phusion Polymerase included in the NEBNext Ultra DNA Kit, and the NEBNext master mix samples using the master mix included into the TruSeqDNA LT Sample Prep Kit.

    Purification:

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: Second strand synthesis was performed using a custom reaction (20 μl first strand cDNA, 10 μl × 10 thermopol buffer, 1 ml × 100 BSA, 3 ml 10 mM dNTPs, 0.5 μl RnaseH, 1 μl Taq polymerase, 0.1 μl Pfu polymerase, 64.4 ml H2 O) which was incubated in a thermocycler under the following conditions: 37 °C 5 min, 65 °C 1 min, 72 °C 30 min) followed by SPRI purification (beads/DNA ratio 1.8/1). .. Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol. .. Since for all samples, the input amount of DNA was below 100 ng; the adaptors were diluted 1:10 in sterile water before adaptor ligation.

    Article Title: Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements
    Article Snippet: After RNase A treatment, DNA was purified by phenol chloroform extraction followed by ethanol precipitation. .. Sequencing libraries for both ChIP and mono-nucleosomes were prepared using NEB Library Prep Kit and Bioo multiplex adapter for Illumina, and then sequenced by paired-end sequencing.

    Article Title: Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA
    Article Snippet: The integrity of all genomic DNA samples was evaluated using agarose gels and their quantity measured with PicoGreen reagents on a Qubit 2.0 instrument. .. NEBNext Ultra library preparation protocol consists of several enzymatic and two purification steps, one of which is used for size selection of library fragments. .. Genomic DNA samples were sheared in 55 μ L of TLE buffer (10 mM Tris, 0.1 mM EDTA, pH 8) using Covaris E220 with the following settings: duty cycle 10%, intensity 5, cycle 200, and time 100 sec. After shearing, two enzymatic steps (end preparation and adapter ligation) are performed in the same tube, followed by size selection of the library fragments using a double AMPure cleanup.

    Article Title: Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition
    Article Snippet: Then, mixture PCR products were purified with GeneJET Gel Extraction Kit (Thermo Scientific). .. Sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added.

    Article Title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool‐ Seq data
    Article Snippet: Purification steps within the NEBNext DNA (+) protocol were performed using Qiagen columns (Qiagen, Hilden, Germany). .. The NEBNext Ultra (+) samples were amplified using Phusion Polymerase included in the NEBNext Ultra DNA Kit, and the NEBNext master mix samples using the master mix included into the TruSeqDNA LT Sample Prep Kit.

    Article Title: Complete Genome Sequence of a Human Cytomegalovirus Strain AD169 Bacterial Artificial Chromosome Clone
    Article Snippet: In the present study, AD169-BAC DNA was isolated from the Escherichia coli strain DH10B, purified using a Nucleobond Xtra-Midi column (Macherey-Nagel) following the manufacturer’s instructions, and resuspended in 10 mM Tris-HCl, pH 8.0. .. 400 ng of BAC DNA was used for library preparation using a NEBNext Ultra DNA sample preparation kit (NEB) according to the manufacturer’s recommendations.

    Article Title: Standardizing chromatin research: a simple and universal method for ChIP-seq
    Article Snippet: Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (E7370S, NEB). .. Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (E7370S, NEB).

    Sequencing:

    Article Title: Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy
    Article Snippet: Then, the mixed PCR products were purified with the EZNA Gel Extraction Kit (Omega, United States). .. Sequencing libraries were generated using the NEBNext® UltraTM DNA Library Prep Kit for Illumina® sequencing (New England Biolabs, United States) following the manufacturer’s recommendations, and index codes were added. .. The library quality was assessed on a Qubit@ 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system.

    Article Title: Personalized identification of tumor-associated immunogenic neoepitopes in hepatocellular carcinoma in complete remission after sorafenib treatment
    Article Snippet: Paragraph title: Whole exome sequencing ... Genomic DNA was captured using SureSelect Human All Exon v4 + UTR - 70 Mb (Agilent) according to manufacturer’s instruction and protocols without modification except for library preparation which was performed using NEBNext Ultra kit (New England Biolabs).

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: Second strand synthesis was performed using a custom reaction (20 μl first strand cDNA, 10 μl × 10 thermopol buffer, 1 ml × 100 BSA, 3 ml 10 mM dNTPs, 0.5 μl RnaseH, 1 μl Taq polymerase, 0.1 μl Pfu polymerase, 64.4 ml H2 O) which was incubated in a thermocycler under the following conditions: 37 °C 5 min, 65 °C 1 min, 72 °C 30 min) followed by SPRI purification (beads/DNA ratio 1.8/1). .. Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol. .. Since for all samples, the input amount of DNA was below 100 ng; the adaptors were diluted 1:10 in sterile water before adaptor ligation.

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: For library preparations, total RNA was used to isolate intact poly(A)+ RNA with the NEBNext poly(A) mRNA magnetic isolation module (E7490L), employing the Human/mouse/rat Ribo-Zero™ rRNA Removal Kit (Cambio/Epicentre) according to manufacturers’ recommendations. .. The libraries were prepared using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (E7370L), size-selected and multiplexed before paired-end sequencing on the HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina) in the Wellcome Trust Centre for Human Genetics. .. For transcription inhibition, HeLa cells were treated with 50 μM 5,6-dichlorobenzimidazole riboside (DRB; Sigma, D1916) for 5 h, as described ( ).

    Article Title: Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak
    Article Snippet: Paragraph title: Whole Genome Sequencing and SNP Detection and Confirmation ... One microgram of DNA from M. tuberculosis was used to prepare libraries for Next-Generation Sequencing (NGS) according to the manufacturer’s instruction using Illumina Genomic Sample pre kits (Illumina, Inc, San Diego, CA) or New England Biolabs library preparation kits (Ipswich, MA 01938-2723).

    Article Title: Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements
    Article Snippet: Finally, DNA fragments of ∼147 bp were size-selected with an E-gel system (Invitrogen). .. Sequencing libraries for both ChIP and mono-nucleosomes were prepared using NEB Library Prep Kit and Bioo multiplex adapter for Illumina, and then sequenced by paired-end sequencing. .. In order to profile occupancy, coordinates of mapped reads were shifted toward the center of the insert DNA by a distance equal to half of the insert size, then reads were counted in bins of 5 bp.

    Article Title: Complete Genome Sequences of Two Bordetella hinzii Strains Isolated from Humans
    Article Snippet: Genomic DNA was isolated with the Gentra Puregene yeast/bacteria kit (Qiagen, Valencia, CA). .. Libraries were prepared for PacBio sequencing using the SMRTbell template prep kit 1.0 and polymerase binding kit P4, while HiSeq libraries were prepared using the NEBNext Ultra library prep kit (New England BioLabs, Ipswich, MA). .. PacBio sequencing reads were filtered and assembled de novo using the Hierarchical Genome Assembly Process algorithm (HGAP) version 3.

    Article Title: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae)
    Article Snippet: Libraries were prepared with 55.5 μL of sonicated DNA, using a NEBNext Ultra kit (New England Biolabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocols with the following modifications: size selection aimed for a 500–700-bp range (i.e., 30 μL AM XP beads [Beckman Coulter, Brea, California, USA] for the first size-selection step, and 15 μL for the second step), and PCR amplification mostly used six cycles (eight cycles for the herbarium specimen). .. Libraries were prepared with 55.5 μL of sonicated DNA, using a NEBNext Ultra kit (New England Biolabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocols with the following modifications: size selection aimed for a 500–700-bp range (i.e., 30 μL AM XP beads [Beckman Coulter, Brea, California, USA] for the first size-selection step, and 15 μL for the second step), and PCR amplification mostly used six cycles (eight cycles for the herbarium specimen).

    Article Title: Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition
    Article Snippet: Then, mixture PCR products were purified with GeneJET Gel Extraction Kit (Thermo Scientific). .. Sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added. .. The library quality was assessed on the Qubit @ 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system.

    Article Title: Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius
    Article Snippet: Bacteria from each individual colony were grown overnight in tryptic soy broth, pelleted by centrifugation at 5,000 × g for 10 min, and genomic DNA was extracted using the QIAamp Fast DNA stool minikit (Qiagen). .. Genomic DNA was used to construct a sequencing library employing a NEBNext Ultra DNA library prep kit (New England BioLabs, Ipswich, MA). .. Sequencing was performed on an Illumina MiSeq with the 301-cycle MiSeq reagent kit version 2, to achieve 150× average genome coverage.

    Article Title: Draft Genome Sequence of a Pseudomonas aeruginosa Strain Able To Decompose N,N-Dimethyl Formamide
    Article Snippet: Genome sequencing was performed at CapitalBio Technology using Illumina technology with a DNA sequencing (DNA-seq) paired-end protocol. .. A library was prepared with the NEBNext Ultra DNA library prep kit for Illumina, and the instrument used for sequencing was HiSeq 2500. .. The resulted 15 million reads were assembled with Velvet 1.1 ( ) and then refined with SEQuel version 1.0.2 ( ).

    Article Title: Epigenetic regulation of diacylglycerol kinase alpha promotes radiation-induced fibrosis
    Article Snippet: Paragraph title: ChIP sequencing ... DNA libraries were prepared from 2 to 5 ng of immunoprecipitated DNA using NEBNext Ultra DNA library Prep Kit (New England Biolabs).

    Article Title: Complete Genome Sequence of a Human Cytomegalovirus Strain AD169 Bacterial Artificial Chromosome Clone
    Article Snippet: The BAC clone containing the complete AD169var ATCC sequence was named AD169-BAC and was used for the construction of numerous HCMV mutants in many laboratories around the world. .. 400 ng of BAC DNA was used for library preparation using a NEBNext Ultra DNA sample preparation kit (NEB) according to the manufacturer’s recommendations.

    Article Title: Standardizing chromatin research: a simple and universal method for ChIP-seq
    Article Snippet: Fragment size distribution was analyzed by capillary electrophoresis (Agilent 2100 Bioanalyzer) using the High Sensitivity DNA ChIP kit (Agilent, 5067–4626). .. Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (E7370S, NEB). .. Starting amount of fragmented DNA varied between sub-nanograms and 2–5 ng.

    Cotransfection:

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: The libraries were prepared using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (E7370L), size-selected and multiplexed before paired-end sequencing on the HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina) in the Wellcome Trust Centre for Human Genetics. .. For transcription inhibition, HeLa cells were treated with 50 μM 5,6-dichlorobenzimidazole riboside (DRB; Sigma, D1916) for 5 h, as described ( ).

    Concentration Assay:

    Article Title: Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements
    Article Snippet: Then, micrococcal nuclease (MNase) was added at a concentration from 40 U-100 U for 10 min at 37°C. .. Sequencing libraries for both ChIP and mono-nucleosomes were prepared using NEB Library Prep Kit and Bioo multiplex adapter for Illumina, and then sequenced by paired-end sequencing.

    Agarose Gel Electrophoresis:

    Article Title: Draft Genome Sequence of a Pseudomonas aeruginosa Strain Able To Decompose N,N-Dimethyl Formamide
    Article Snippet: The quality and quantity of DNA were assayed using a K5500 microspectrophotometer (Kaiao) and agarose gel electrophoresis. .. A library was prepared with the NEBNext Ultra DNA library prep kit for Illumina, and the instrument used for sequencing was HiSeq 2500.

    Article Title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool‐ Seq data
    Article Snippet: The NEBNext Ultra (+) samples were amplified using Phusion Polymerase included in the NEBNext Ultra DNA Kit, and the NEBNext master mix samples using the master mix included into the TruSeqDNA LT Sample Prep Kit. .. Both PCR‐based protocols used the following cycling conditions: an initial denaturation step at 98 °C/30 s, followed by 10 cycles at 98 °C/10 s, 65 °C (Phusion polymerase) or 60 °C (TruSeq polymerase)/30 s, 72 °C/50 s and a final extension at 72 °C/7 min.

    Chromatin Immunoprecipitation:

    Article Title: Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements
    Article Snippet: Finally, DNA fragments of ∼147 bp were size-selected with an E-gel system (Invitrogen). .. Sequencing libraries for both ChIP and mono-nucleosomes were prepared using NEB Library Prep Kit and Bioo multiplex adapter for Illumina, and then sequenced by paired-end sequencing. .. In order to profile occupancy, coordinates of mapped reads were shifted toward the center of the insert DNA by a distance equal to half of the insert size, then reads were counted in bins of 5 bp.

    Article Title: Epigenetic regulation of diacylglycerol kinase alpha promotes radiation-induced fibrosis
    Article Snippet: Paragraph title: ChIP sequencing ... DNA libraries were prepared from 2 to 5 ng of immunoprecipitated DNA using NEBNext Ultra DNA library Prep Kit (New England Biolabs).

    Plasmid Preparation:

    Article Title: PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
    Article Snippet: The libraries were prepared using the NEBNext® Ultra DNA Library Prep Kit for Illumina® (E7370L), size-selected and multiplexed before paired-end sequencing on the HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina) in the Wellcome Trust Centre for Human Genetics. .. For transcription inhibition, HeLa cells were treated with 50 μM 5,6-dichlorobenzimidazole riboside (DRB; Sigma, D1916) for 5 h, as described ( ).

    Article Title: Complete Genome Sequence of a Human Cytomegalovirus Strain AD169 Bacterial Artificial Chromosome Clone
    Article Snippet: 400 ng of BAC DNA was used for library preparation using a NEBNext Ultra DNA sample preparation kit (NEB) according to the manufacturer’s recommendations. .. 400 ng of BAC DNA was used for library preparation using a NEBNext Ultra DNA sample preparation kit (NEB) according to the manufacturer’s recommendations.

    Software:

    Article Title: Interferon lambda protects the female reproductive tract against Zika virus infection
    Article Snippet: Briefly, libraries were prepared with the Ultra Library Preparation kit (New England BioLabs), and quality was determined using the Qubit assay (Thermo Scientific) and Agilent 2100 Bioanalyzer. .. Briefly, libraries were prepared with the Ultra Library Preparation kit (New England BioLabs), and quality was determined using the Qubit assay (Thermo Scientific) and Agilent 2100 Bioanalyzer.

    Article Title: Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition
    Article Snippet: Sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added. .. Sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added.

    Article Title: Draft Genome Sequence of Enterococcus faecium Strain 58m, Isolated from Intestinal Tract Content of a Woolly Mammoth, Mammuthus primigenius
    Article Snippet: Genomic DNA was used to construct a sequencing library employing a NEBNext Ultra DNA library prep kit (New England BioLabs, Ipswich, MA). .. The quality of the raw sequence data was checked using FastQC ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ).

    Multiplex Assay:

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: Second strand synthesis was performed using a custom reaction (20 μl first strand cDNA, 10 μl × 10 thermopol buffer, 1 ml × 100 BSA, 3 ml 10 mM dNTPs, 0.5 μl RnaseH, 1 μl Taq polymerase, 0.1 μl Pfu polymerase, 64.4 ml H2 O) which was incubated in a thermocycler under the following conditions: 37 °C 5 min, 65 °C 1 min, 72 °C 30 min) followed by SPRI purification (beads/DNA ratio 1.8/1). .. Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol. .. Since for all samples, the input amount of DNA was below 100 ng; the adaptors were diluted 1:10 in sterile water before adaptor ligation.

    Article Title: Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements
    Article Snippet: Finally, DNA fragments of ∼147 bp were size-selected with an E-gel system (Invitrogen). .. Sequencing libraries for both ChIP and mono-nucleosomes were prepared using NEB Library Prep Kit and Bioo multiplex adapter for Illumina, and then sequenced by paired-end sequencing. .. In order to profile occupancy, coordinates of mapped reads were shifted toward the center of the insert DNA by a distance equal to half of the insert size, then reads were counted in bins of 5 bp.

    Selection:

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol. .. Since for all samples, the input amount of DNA was below 100 ng; the adaptors were diluted 1:10 in sterile water before adaptor ligation.

    Article Title: Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA
    Article Snippet: The integrity of all genomic DNA samples was evaluated using agarose gels and their quantity measured with PicoGreen reagents on a Qubit 2.0 instrument. .. NEBNext Ultra library preparation protocol consists of several enzymatic and two purification steps, one of which is used for size selection of library fragments. .. Genomic DNA samples were sheared in 55 μ L of TLE buffer (10 mM Tris, 0.1 mM EDTA, pH 8) using Covaris E220 with the following settings: duty cycle 10%, intensity 5, cycle 200, and time 100 sec. After shearing, two enzymatic steps (end preparation and adapter ligation) are performed in the same tube, followed by size selection of the library fragments using a double AMPure cleanup.

    Article Title: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: A phylogenomic example from Heuchera (Saxifragaceae)
    Article Snippet: One microgram of clean genomic DNA in 60 μL was sonicated using a Covaris machine (model S220; Covaris, Woburn, Massachusetts, USA), aiming for fragment size of 500–700 bp. .. Libraries were prepared with 55.5 μL of sonicated DNA, using a NEBNext Ultra kit (New England Biolabs, Ipswich, Massachusetts, USA), following the manufacturer’s protocols with the following modifications: size selection aimed for a 500–700-bp range (i.e., 30 μL AM XP beads [Beckman Coulter, Brea, California, USA] for the first size-selection step, and 15 μL for the second step), and PCR amplification mostly used six cycles (eight cycles for the herbarium specimen). .. Libraries were barcoded using NEBNext Multiplex oligos (New England Biolabs).

    Article Title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool‐ Seq data
    Article Snippet: An initial size selection was performed using AMPureXP beads (Beckman Coulter, CA, USA), either before the PCR step (for the two PCR‐based protocols), or at the end of the protocol (for the NEXTflex (−) protocol). .. The NEBNext Ultra (+) samples were amplified using Phusion Polymerase included in the NEBNext Ultra DNA Kit, and the NEBNext master mix samples using the master mix included into the TruSeqDNA LT Sample Prep Kit.

    Article Title: Standardizing chromatin research: a simple and universal method for ChIP-seq
    Article Snippet: Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (E7370S, NEB). .. Sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep kit for Illumina (E7370S, NEB).

    Sample Prep:

    Article Title: The impact of library preparation protocols on the consistency of allele frequency estimates in Pool‐ Seq data
    Article Snippet: An initial size selection was performed using AMPureXP beads (Beckman Coulter, CA, USA), either before the PCR step (for the two PCR‐based protocols), or at the end of the protocol (for the NEXTflex (−) protocol). .. The NEBNext Ultra (+) samples were amplified using Phusion Polymerase included in the NEBNext Ultra DNA Kit, and the NEBNext master mix samples using the master mix included into the TruSeqDNA LT Sample Prep Kit. .. Both PCR‐based protocols used the following cycling conditions: an initial denaturation step at 98 °C/30 s, followed by 10 cycles at 98 °C/10 s, 65 °C (Phusion polymerase) or 60 °C (TruSeq polymerase)/30 s, 72 °C/50 s and a final extension at 72 °C/7 min.

    Article Title: Complete Genome Sequence of a Human Cytomegalovirus Strain AD169 Bacterial Artificial Chromosome Clone
    Article Snippet: In the present study, AD169-BAC DNA was isolated from the Escherichia coli strain DH10B, purified using a Nucleobond Xtra-Midi column (Macherey-Nagel) following the manufacturer’s instructions, and resuspended in 10 mM Tris-HCl, pH 8.0. .. 400 ng of BAC DNA was used for library preparation using a NEBNext Ultra DNA sample preparation kit (NEB) according to the manufacturer’s recommendations. .. Diluted libraries were paired-end sequenced (2 × 250 cycles) with an Illumina MiSeq sequencer generating 1.8 million paired reads.

    In Vitro:

    Article Title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells
    Article Snippet: In vitro transcription was performed overnight using the RNAMaxx high yield kit (200339, Stratagene), and the resulting RNA was purified using SPRI beads (Agencourt AMPure XP, Beckman Coulter; beads/DNA ratio 1.8/1) followed by a reverse transcription (1 h, 42 °C; 10 min, 75 °C) using the T7-BpmI-oligo(A)14 primer and the Superscript III reverse transcription kit (18080044, Invitrogen). .. Resulting double-stranded DNA was then digested with BpmI for 2 h at 37 °C, purified again with SPRI beads (beads/DNA ratio 1.5/1) and eluted in 13 μl ddH2 O. Illumina sequencing libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB) and the NEBNext Multiplex-Oligos for Illumina (E7335, NEB) following the manufacturer’s protocol.

    Ethanol Precipitation:

    Article Title: Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements
    Article Snippet: After RNase A treatment, DNA was purified by phenol chloroform extraction followed by ethanol precipitation. .. Sequencing libraries for both ChIP and mono-nucleosomes were prepared using NEB Library Prep Kit and Bioo multiplex adapter for Illumina, and then sequenced by paired-end sequencing.

    Next-Generation Sequencing:

    Article Title: Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy
    Article Snippet: Paragraph title: Library Preparation and NGS Sequencing ... Sequencing libraries were generated using the NEBNext® UltraTM DNA Library Prep Kit for Illumina® sequencing (New England Biolabs, United States) following the manufacturer’s recommendations, and index codes were added.

    Article Title: Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak
    Article Snippet: DNA from M. tuberculosis isolates from the 9 persons with culture positive TB was extracted using standardized procedures from Lowenstein Jensen media (first subculture from the original liquid culture) in all cases except isolate E, in which DNA was extracted from the second subculture . .. One microgram of DNA from M. tuberculosis was used to prepare libraries for Next-Generation Sequencing (NGS) according to the manufacturer’s instruction using Illumina Genomic Sample pre kits (Illumina, Inc, San Diego, CA) or New England Biolabs library preparation kits (Ipswich, MA 01938-2723). .. The M. tuberculosis DNA libraries were sequenced on Genome Analyzer (Illumina, Inc, San Diego, CA) for WSG according to the manufacturer’s specifications.

    Article Title: A Fast Solution to NGS Library Prep with Low Nanogram DNA Input
    Article Snippet: By delivering massive DNA sequences at unprecedented speed and cost, NGS promises to make personalized medicine a reality in the foreseeable future. .. Our objective here was to overcome this challenge by developing NEBNext® Ultra DNA Library Prep Kit, a fast library preparation method.

    Immunoprecipitation:

    Article Title: Epigenetic regulation of diacylglycerol kinase alpha promotes radiation-induced fibrosis
    Article Snippet: Data were mapped to human genome (GRCHh37/hg19). .. DNA libraries were prepared from 2 to 5 ng of immunoprecipitated DNA using NEBNext Ultra DNA library Prep Kit (New England Biolabs). .. Sequencing was carried out at the Genomics and Proteomics Core Facility (German Cancer Research Center, Heidelberg, Germany).

    Magnetic Cell Separation:

    Article Title: Epigenetic regulation of diacylglycerol kinase alpha promotes radiation-induced fibrosis
    Article Snippet: DNA libraries were prepared from 2 to 5 ng of immunoprecipitated DNA using NEBNext Ultra DNA library Prep Kit (New England Biolabs). .. Sequencing was carried out at the Genomics and Proteomics Core Facility (German Cancer Research Center, Heidelberg, Germany).

    BAC Assay:

    Article Title: Complete Genome Sequence of a Human Cytomegalovirus Strain AD169 Bacterial Artificial Chromosome Clone
    Article Snippet: In the present study, AD169-BAC DNA was isolated from the Escherichia coli strain DH10B, purified using a Nucleobond Xtra-Midi column (Macherey-Nagel) following the manufacturer’s instructions, and resuspended in 10 mM Tris-HCl, pH 8.0. .. 400 ng of BAC DNA was used for library preparation using a NEBNext Ultra DNA sample preparation kit (NEB) according to the manufacturer’s recommendations. .. Diluted libraries were paired-end sequenced (2 × 250 cycles) with an Illumina MiSeq sequencer generating 1.8 million paired reads.

    Gel Extraction:

    Article Title: Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition
    Article Snippet: Then, mixture PCR products were purified with GeneJET Gel Extraction Kit (Thermo Scientific). .. Sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added.

    Variant Assay:

    Article Title: Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers
    Article Snippet: Whole-genome libraries were prepared from gDNA using the NEBNext DNA Library Prep kit (New England Biolabs, Ipswich, MA), enriched to whole exome libraries using the SeqCap EZ Human Exome Library v3.0 capture system (Roche NimbleGen, Madison, WI), covering approximately 64 Mb of the genome where variants can be called; paired-end sequencing (2x100 nt reads) was done on Illumina HiSeq 2500 (Illumina, San Diego, CA) in either High Output or Rapid Run mode. .. Based on experience, candidate somatic mutations were triaged for Taqman probe development if mutant allele fraction was ≥ 8% and passed manual review by inspecting raw read alignments in the IGV genome browser tool, then validated for final generation of probe by direct Sanger sequencing of tumor DNA and its paired peripheral blood mononuclear cell (PBMC) genomic DNA.

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    New England Biolabs ultratm ii fs dna library prep kit
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