ultra ii fs dna library prep kit  (New England Biolabs)


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    Name:
    NEBNext Ultra II FS DNA Library Prep Kit for Illumina
    Description:
    NEBNext Ultra II FS DNA Library Prep Kit for Illumina 96 rxns
    Catalog Number:
    e7805l
    Price:
    2400
    Size:
    96 rxns
    Category:
    DNA Template Preparation for PCR
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    Structured Review

    New England Biolabs ultra ii fs dna library prep kit
    NEBNext Ultra II FS DNA Library Prep Kit for Illumina
    NEBNext Ultra II FS DNA Library Prep Kit for Illumina 96 rxns
    https://www.bioz.com/result/ultra ii fs dna library prep kit/product/New England Biolabs
    Average 95 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    ultra ii fs dna library prep kit - by Bioz Stars, 2020-02
    95/100 stars

    Images

    1) Product Images from "A Fosmid-Based System for the Generation of Recombinant Cercopithecine Alphaherpesvirus 2 Encoding Reporter Genes"

    Article Title: A Fosmid-Based System for the Generation of Recombinant Cercopithecine Alphaherpesvirus 2 Encoding Reporter Genes

    Journal: Viruses

    doi: 10.3390/v11111026

    Cloning and characterization of CeHV-2 fosmids. ( a ) Scheme of CeHV-2 genome cloning. Viral DNA was isolated from virus particles, sheared, end-repaired and size fractionated on an agarose gel. Fractionated fragments were ligated into fosmid vector pCC1FOS (red) and packaged into phage lambda particles, which were then used to transduce cells of E. coli strain EPI300. Individual colonies were further characterized by colony PCR, end-sequencing, and restriction digest. ( b ) An overview of all fosmid clones that are characterized by colony PCR and end-sequencing. The genome of CeHV-2 is schematically represented on top, with U S regions drawn on both sides of the U L region. The direction of gene order, in the U L and U S regions, is indicated by arrows and inverted repeats are drawn as boxes. The positions of fosmid inserts are drawn as lines. The names of the fosmids and nucleotide positions of the insertions are given above the respective lines.
    Figure Legend Snippet: Cloning and characterization of CeHV-2 fosmids. ( a ) Scheme of CeHV-2 genome cloning. Viral DNA was isolated from virus particles, sheared, end-repaired and size fractionated on an agarose gel. Fractionated fragments were ligated into fosmid vector pCC1FOS (red) and packaged into phage lambda particles, which were then used to transduce cells of E. coli strain EPI300. Individual colonies were further characterized by colony PCR, end-sequencing, and restriction digest. ( b ) An overview of all fosmid clones that are characterized by colony PCR and end-sequencing. The genome of CeHV-2 is schematically represented on top, with U S regions drawn on both sides of the U L region. The direction of gene order, in the U L and U S regions, is indicated by arrows and inverted repeats are drawn as boxes. The positions of fosmid inserts are drawn as lines. The names of the fosmids and nucleotide positions of the insertions are given above the respective lines.

    Techniques Used: Clone Assay, Isolation, Agarose Gel Electrophoresis, Plasmid Preparation, Transduction, Polymerase Chain Reaction, Sequencing

    Related Articles

    Multiplexing:

    Article Title: In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi
    Article Snippet: The Illumina libraries were constructed for M . perstans and M . ozzardi using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs Inc., USA) as described by the manufacturer. .. A library was prepared from each time point then PCR amplified with a different index primer to enable multiplexing.

    Amplification:

    Article Title: In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi
    Article Snippet: The Illumina libraries were constructed for M . perstans and M . ozzardi using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs Inc., USA) as described by the manufacturer. .. A library was prepared from each time point then PCR amplified with a different index primer to enable multiplexing.

    Article Title: Genome Sequences of Six Cluster N Mycobacteriophages, Kevin1, Nenae, Parmesanjohn, ShrimpFriedEgg, Smurph, and SpongeBob, Isolated on Mycobacterium smegmatis mc2155
    Article Snippet: After purification and amplification of the phages, electron microscopy determined a Siphoviridae morphology for each of them. .. Briefly, sequencing libraries were prepared from genomic DNA (isolated by phenol-chloroform extraction) using an Ultra II FS kit (NEB) with dual-indexed barcoding and pooled with others for 48 total libraries run on an Illumina MiSeq instrument, yielding at least 482,600 single-end 150-base reads and at least 201-fold coverage for each genome.

    Article Title: Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development
    Article Snippet: Whole genome sequencing, SNP profile analysis, and TIDAL analysis Genomic DNA libraries were prepared using NEB Ultra II FS kit E7805. .. Library PCR amplification was also carried out as per manual instructions for six cycles and purified using one round of AmpureXP beads addition at 0.9X volume.

    Construct:

    Article Title: In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi
    Article Snippet: .. The Illumina libraries were constructed for M . perstans and M . ozzardi using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs Inc., USA) as described by the manufacturer. ..

    Article Title: SMURF-seq: efficient copy number profiling on long-read sequencers
    Article Snippet: .. DNA from SK-BR-3 cells was used to construct WGS library with the NEBNext UltraII FS DNA Library Prep Kit (NEB, Cat. no. E7805) following the manufacturer’s instructions. .. After library quality and quantity assessment with Qubit 3.0 HS dsDNA assay and BioAnalyzer HS dsDNA assay (Agilent), libraries were sequenced on HiSeq 2500 (Illumina) with single-end 130 cycles mode.

    Article Title: A Fosmid-Based System for the Generation of Recombinant Cercopithecine Alphaherpesvirus 2 Encoding Reporter Genes
    Article Snippet: Next-Generation Sequencing and Assembly Library preparation of fosmid-DNA was performed using the NEBnext Ultra II FS DNA Library Prep Kit (New England BioLabs, Ipswich, MA, USA) following the manufacturer’s protocol for < 100 ng DNA input (30–46 ng input amount). .. Sequence annotations were transferred from the reference vector constructs using Geneious Prime (Biomatters, Auckland, New Zealand).

    Incubation:

    Article Title: Genome Sequences of Six Cluster N Mycobacteriophages, Kevin1, Nenae, Parmesanjohn, ShrimpFriedEgg, Smurph, and SpongeBob, Isolated on Mycobacterium smegmatis mc2155
    Article Snippet: Soil samples were placed in 7H9 medium with the host and incubated for 3 days at 37°C, and supernatants were sterile filtered for testing on host lawns. .. Briefly, sequencing libraries were prepared from genomic DNA (isolated by phenol-chloroform extraction) using an Ultra II FS kit (NEB) with dual-indexed barcoding and pooled with others for 48 total libraries run on an Illumina MiSeq instrument, yielding at least 482,600 single-end 150-base reads and at least 201-fold coverage for each genome.

    Article Title: Complete Genome Sequences of Mycobacteriophages Candle, Schatzie, Sumter, and Waleliano
    Article Snippet: Sumter and Waleliano were enriched with the host bacterium in addition to incubation in 7H9 medium. .. The NEBNext Ultra II FS kit (New England BioLabs, Ipswich, MA) with dual-indexed barcoding was used to build DNA libraries, which were then pooled for sequencing.

    Article Title: Complete Genome Sequence of Bartonella bacilliformis Strain KC584 (ATCC 35686)
    Article Snippet: For short-read WGS, B. bacilliformis strain KC584 was streaked out from cryostock on Columbia blood agar (Becton, Dickinson, Heidelberg, Germany) and incubated for 4 days at 28°C. .. A short-read sequencing library was generated utilizing a NEBNext Ultra II FS DNA library prep kit (NEB, Ipswich, MA, USA).

    Article Title: Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica
    Article Snippet: After incubation at 55°C for 48 h, a single colony was used for genomic DNA extraction with a Wizard genomic DNA purification kit (Promega, Madison, USA), and the DNA was then quantified using a Qubit fluorometer (Thermo Fisher Scientific, Waltham, USA). .. A NEBNext Ultra II FS DNA library kit (New England Biolabs, Ipswich, USA) was used to prepare a paired-end 300-bp library, which was sequenced on an Illumina MiSeq system.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Ultra-deep massively parallel sequencing with unique molecular identifier tagging achieves comparable performance to droplet digital PCR for detection and quantification of circulating tumor DNA from lung cancer patients
    Article Snippet: .. For genomic DNA from FFPE, libraries were prepared from 2 ng of cfDNA using the NEBNext Ultra II FS DNA library prep kit (New England Biolabs, USA) following the manufacturer’s instructions. .. Similar to ctDNA libraries, FFPE libraries were pooled before hybridization with the xGen Lockdown probes and sequencing in the Illumina NextSeq 550 system.

    Mass Spectrometry:

    Article Title: Discovery and Characterization of Bacteriophage LuckyBarnes
    Article Snippet: We report here the characterization of a new bacteriophage, LuckyBarnes, which was isolated from soil collected in D’Iberville, MS, using enrichment with Brevibacterium iodinum ATCC 15728 in a peptone yeast calcium (PYCa) medium. .. Phage DNA was isolated using the Wizard DNA cleanup kit (Promega) and used to prepare a library with a NEBNext Ultra II FS kit (New England BioLabs), which was then sequenced on an Illumina MiSeq instrument with MiSeq v3 chemistry.

    Hybridization:

    Article Title: Ultra-deep massively parallel sequencing with unique molecular identifier tagging achieves comparable performance to droplet digital PCR for detection and quantification of circulating tumor DNA from lung cancer patients
    Article Snippet: For genomic DNA from FFPE, libraries were prepared from 2 ng of cfDNA using the NEBNext Ultra II FS DNA library prep kit (New England Biolabs, USA) following the manufacturer’s instructions. .. Similar to ctDNA libraries, FFPE libraries were pooled before hybridization with the xGen Lockdown probes and sequencing in the Illumina NextSeq 550 system.

    Electron Microscopy:

    Article Title: Genome Sequences of Six Cluster N Mycobacteriophages, Kevin1, Nenae, Parmesanjohn, ShrimpFriedEgg, Smurph, and SpongeBob, Isolated on Mycobacterium smegmatis mc2155
    Article Snippet: After purification and amplification of the phages, electron microscopy determined a Siphoviridae morphology for each of them. .. Briefly, sequencing libraries were prepared from genomic DNA (isolated by phenol-chloroform extraction) using an Ultra II FS kit (NEB) with dual-indexed barcoding and pooled with others for 48 total libraries run on an Illumina MiSeq instrument, yielding at least 482,600 single-end 150-base reads and at least 201-fold coverage for each genome.

    RAST Test:

    Article Title: Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica
    Article Snippet: A NEBNext Ultra II FS DNA library kit (New England Biolabs, Ipswich, USA) was used to prepare a paired-end 300-bp library, which was sequenced on an Illumina MiSeq system. .. The assembled scaffolds were quality checked with CheckM and RefineM , and the coding DNA sequences (CDSs) were predicted and annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) tool ( ) and the Rapid Annotations using Subsystems Technology (RAST) server ( ).

    Ligation:

    Article Title: PCR-free whole exome sequencing: Cost-effective and efficient in detecting rare mutations
    Article Snippet: .. PCR-free library preparation of DNA sheared enzymatically, followed by adaptor ligation using NEBNext Ultra II FS DNA Library Prep Kit (PCRfree-Frag) Using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (NEB, MA, USA), 2 μg DNA was fragmented by DNA Fragmentase at 37°C for 15 min, followed by end repair, A-tailing, and adaptor ligation according to the manufacturer’s instructions, except that the ligation condition used was 4°C for 4 h to maximize the efficiency of adaptor ligation ( ). .. Target enrichment with SureSelect XT Human All Exon V5 kit Input DNA amount for hybridization with the V5 kit was changed from 500 ng to 3000 ng for each library preparation method ( ).

    Article Title: Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development
    Article Snippet: Whole genome sequencing, SNP profile analysis, and TIDAL analysis Genomic DNA libraries were prepared using NEB Ultra II FS kit E7805. .. Briefly, 500 ng of genomic DNA ( > 10 kb) was fragmented at 37°C for 12 min, followed by adaptor ligation and loop excision according to kit manual protocol.

    Generated:

    Article Title: SMURF-seq: efficient copy number profiling on long-read sequencers
    Article Snippet: DNA from SK-BR-3 cells was used to construct WGS library with the NEBNext UltraII FS DNA Library Prep Kit (NEB, Cat. no. E7805) following the manufacturer’s instructions. .. The reads were mapped with BWA-MEM using the default parameters, PCR duplicates were removed, and CNV profiles were generated using exactly the same method as used for SMURF-seq reads.

    Article Title: Discovery and Characterization of Bacteriophage LuckyBarnes
    Article Snippet: Phage DNA was isolated using the Wizard DNA cleanup kit (Promega) and used to prepare a library with a NEBNext Ultra II FS kit (New England BioLabs), which was then sequenced on an Illumina MiSeq instrument with MiSeq v3 chemistry. .. The sequence run generated 1.42 million 150-bp single-end reads that were assembled in Newbler v.2.9 , with default parameters, to give a 50,774-bp contig with 3,954-fold coverage and a G+C content of 61.9%.

    Article Title: Complete Genome Sequence of GD1108, a Moderate-Virulence Strain of Human-Associated ST398 Methicillin-Susceptible Staphylococcus aureus
    Article Snippet: The genome was generated from the hybrid assembly of PacBio and Illumina sequencing reads. .. The library was prepared using the NEBNext Ultra II FS DNA fragment library kit, and then 600 cycle MiSeq v3 sequencing was done.

    Article Title: Complete Genome Sequence of Bartonella bacilliformis Strain KC584 (ATCC 35686)
    Article Snippet: .. A short-read sequencing library was generated utilizing a NEBNext Ultra II FS DNA library prep kit (NEB, Ipswich, MA, USA). .. Sequencing was carried out on a MiSeq sequencer using v2 chemistry.

    other:

    Article Title: A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments
    Article Snippet: We thank New England Biolabs for providing NEBNext Ultra II FS DNA Library Prep Kit before it was commercially available.

    Imaging:

    Article Title: Complete Genome Sequences of Mycobacteriophages Candle, Schatzie, Sumter, and Waleliano
    Article Snippet: Imaging with a transmission electron microscope showed that all four phages belong to the family Siphoviridae, given the noncontractile tails, which ranged from 142.0 to 335.29 nm long, and with isometric heads ranging from 42.0 to 83.3 nm. .. The NEBNext Ultra II FS kit (New England BioLabs, Ipswich, MA) with dual-indexed barcoding was used to build DNA libraries, which were then pooled for sequencing.

    Transmission Assay:

    Article Title: Discovery and Characterization of Bacteriophage LuckyBarnes
    Article Snippet: Transmission electron microscopy of LuckyBarnes revealed a 50-nm capsid and a 250-nm-long flexible tail ( ). .. Phage DNA was isolated using the Wizard DNA cleanup kit (Promega) and used to prepare a library with a NEBNext Ultra II FS kit (New England BioLabs), which was then sequenced on an Illumina MiSeq instrument with MiSeq v3 chemistry.

    Article Title: Complete Genome Sequences of Mycobacteriophages Candle, Schatzie, Sumter, and Waleliano
    Article Snippet: Imaging with a transmission electron microscope showed that all four phages belong to the family Siphoviridae, given the noncontractile tails, which ranged from 142.0 to 335.29 nm long, and with isometric heads ranging from 42.0 to 83.3 nm. .. The NEBNext Ultra II FS kit (New England BioLabs, Ipswich, MA) with dual-indexed barcoding was used to build DNA libraries, which were then pooled for sequencing.

    Sequencing:

    Article Title: In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi
    Article Snippet: Paragraph title: Illumina library construction and sequencing ... The Illumina libraries were constructed for M . perstans and M . ozzardi using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs Inc., USA) as described by the manufacturer.

    Article Title: Genome Sequence of Mycobacterium Phage LilHazelnut
    Article Snippet: .. A NEBNext Ultra II FS kit with dual-indexed barcoding was used to prepare a sequencing library from genomic DNA. .. This library plus those from 47 other phages were pooled and run on an Illumina MiSeq instrument.

    Article Title: Discovery and Characterization of Bacteriophage LuckyBarnes
    Article Snippet: Phage DNA was isolated using the Wizard DNA cleanup kit (Promega) and used to prepare a library with a NEBNext Ultra II FS kit (New England BioLabs), which was then sequenced on an Illumina MiSeq instrument with MiSeq v3 chemistry. .. The sequence run generated 1.42 million 150-bp single-end reads that were assembled in Newbler v.2.9 , with default parameters, to give a 50,774-bp contig with 3,954-fold coverage and a G+C content of 61.9%.

    Article Title: A Fosmid-Based System for the Generation of Recombinant Cercopithecine Alphaherpesvirus 2 Encoding Reporter Genes
    Article Snippet: Next-Generation Sequencing and Assembly Library preparation of fosmid-DNA was performed using the NEBnext Ultra II FS DNA Library Prep Kit (New England BioLabs, Ipswich, MA, USA) following the manufacturer’s protocol for < 100 ng DNA input (30–46 ng input amount). .. The quality was controlled using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and the libraries were subsequently sequenced on an Illumina MiSeq (Illumina, San Diego, CA, USA) with a 600v3 sequencing kit (2 × 300 bp paired-end reads).

    Article Title: Complete Genome Sequence of GD1108, a Moderate-Virulence Strain of Human-Associated ST398 Methicillin-Susceptible Staphylococcus aureus
    Article Snippet: .. The library was prepared using the NEBNext Ultra II FS DNA fragment library kit, and then 600 cycle MiSeq v3 sequencing was done. .. A sheared large-insert PacBio library was prepared at the Genome Quebec Innovation Centre in Montreal, Canada, using Covaris g-TUBEs and the SMRTbell template prep kit 1.0.

    Article Title: Complete Genome Sequences of Mycobacteriophages Candle, Schatzie, Sumter, and Waleliano
    Article Snippet: .. The NEBNext Ultra II FS kit (New England BioLabs, Ipswich, MA) with dual-indexed barcoding was used to build DNA libraries, which were then pooled for sequencing. .. Sequencing was performed at the Pittsburgh Bacteriophage Institute using an Illumina MiSeq platform.

    Article Title: Complete Genome Sequence of Bartonella bacilliformis Strain KC584 (ATCC 35686)
    Article Snippet: .. A short-read sequencing library was generated utilizing a NEBNext Ultra II FS DNA library prep kit (NEB, Ipswich, MA, USA). .. Sequencing was carried out on a MiSeq sequencer using v2 chemistry.

    Article Title: Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica
    Article Snippet: Here, we present the draft genome sequence of Geobacillus sp. strain LEMMJ02, isolated from Antarctic volcano sediment collected near a fumarole (500 g of sediment from 0 to 5 cm deep; environmental temperature, 100°C) in Fumarole Bay, Deception Island (62°58′2.7″S; 60°42′36.4″W). .. A NEBNext Ultra II FS DNA library kit (New England Biolabs, Ipswich, USA) was used to prepare a paired-end 300-bp library, which was sequenced on an Illumina MiSeq system.

    Article Title: Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development
    Article Snippet: .. Whole genome sequencing, SNP profile analysis, and TIDAL analysis Genomic DNA libraries were prepared using NEB Ultra II FS kit E7805. .. Briefly, 500 ng of genomic DNA ( > 10 kb) was fragmented at 37°C for 12 min, followed by adaptor ligation and loop excision according to kit manual protocol.

    Article Title: Ultra-deep massively parallel sequencing with unique molecular identifier tagging achieves comparable performance to droplet digital PCR for detection and quantification of circulating tumor DNA from lung cancer patients
    Article Snippet: Paragraph title: Ultra-deep massively parallel sequencing with unique molecular identifier tagging ... For genomic DNA from FFPE, libraries were prepared from 2 ng of cfDNA using the NEBNext Ultra II FS DNA library prep kit (New England Biolabs, USA) following the manufacturer’s instructions.

    DNA Extraction:

    Article Title: Genome Sequence of Mycobacterium Phage LilHazelnut
    Article Snippet: Genomic DNA was isolated from LilHazelnut lysates with a Wizard DNA extraction kit (Promega). .. A NEBNext Ultra II FS kit with dual-indexed barcoding was used to prepare a sequencing library from genomic DNA.

    Article Title: Genome Sequences of Three Microbacterium Phages Isolated from Flowers
    Article Snippet: .. Phage DNA was isolated from phage lysates using the Wizard DNA extraction kit (Promega), and then sequencing libraries were prepared using an NEB Ultra II FS kit and run on an Illumina MiSeq platform, yielding at least 100,000 single-end 150-base reads for each genome. ..

    Article Title: Complete Genome Sequence of Bartonella bacilliformis Strain KC584 (ATCC 35686)
    Article Snippet: The QIAamp DNA minikit (Qiagen, Hilden, Germany) was used for genomic DNA isolation. .. A short-read sequencing library was generated utilizing a NEBNext Ultra II FS DNA library prep kit (NEB, Ipswich, MA, USA).

    Article Title: Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica
    Article Snippet: After incubation at 55°C for 48 h, a single colony was used for genomic DNA extraction with a Wizard genomic DNA purification kit (Promega, Madison, USA), and the DNA was then quantified using a Qubit fluorometer (Thermo Fisher Scientific, Waltham, USA). .. A NEBNext Ultra II FS DNA library kit (New England Biolabs, Ipswich, USA) was used to prepare a paired-end 300-bp library, which was sequenced on an Illumina MiSeq system.

    Isolation:

    Article Title: Genome Sequence of Mycobacterium Phage LilHazelnut
    Article Snippet: Genomic DNA was isolated from LilHazelnut lysates with a Wizard DNA extraction kit (Promega). .. A NEBNext Ultra II FS kit with dual-indexed barcoding was used to prepare a sequencing library from genomic DNA.

    Article Title: Genome Sequences of Six Cluster N Mycobacteriophages, Kevin1, Nenae, Parmesanjohn, ShrimpFriedEgg, Smurph, and SpongeBob, Isolated on Mycobacterium smegmatis mc2155
    Article Snippet: .. Briefly, sequencing libraries were prepared from genomic DNA (isolated by phenol-chloroform extraction) using an Ultra II FS kit (NEB) with dual-indexed barcoding and pooled with others for 48 total libraries run on an Illumina MiSeq instrument, yielding at least 482,600 single-end 150-base reads and at least 201-fold coverage for each genome. ..

    Article Title: Complete Genome Sequence of GD1108, a Moderate-Virulence Strain of Human-Associated ST398 Methicillin-Susceptible Staphylococcus aureus
    Article Snippet: Strain GD1108 was isolated from a school child from a prevalence survey in 2011 in Guangzhou, People’s Republic of China. .. The library was prepared using the NEBNext Ultra II FS DNA fragment library kit, and then 600 cycle MiSeq v3 sequencing was done.

    Article Title: Complete Genome Sequence of Bartonella bacilliformis Strain KC584 (ATCC 35686)
    Article Snippet: B. bacilliformis strain KC584 was originally isolated in 1959 and characterized in greater detail in 1991 ( , ). .. A short-read sequencing library was generated utilizing a NEBNext Ultra II FS DNA library prep kit (NEB, Ipswich, MA, USA).

    Article Title: Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica
    Article Snippet: Here, we present the draft genome sequence of Geobacillus sp. strain LEMMJ02, isolated from Antarctic volcano sediment collected near a fumarole (500 g of sediment from 0 to 5 cm deep; environmental temperature, 100°C) in Fumarole Bay, Deception Island (62°58′2.7″S; 60°42′36.4″W). .. A NEBNext Ultra II FS DNA library kit (New England Biolabs, Ipswich, USA) was used to prepare a paired-end 300-bp library, which was sequenced on an Illumina MiSeq system.

    Microscopy:

    Article Title: Complete Genome Sequences of Mycobacteriophages Candle, Schatzie, Sumter, and Waleliano
    Article Snippet: Imaging with a transmission electron microscope showed that all four phages belong to the family Siphoviridae, given the noncontractile tails, which ranged from 142.0 to 335.29 nm long, and with isometric heads ranging from 42.0 to 83.3 nm. .. The NEBNext Ultra II FS kit (New England BioLabs, Ipswich, MA) with dual-indexed barcoding was used to build DNA libraries, which were then pooled for sequencing.

    Purification:

    Article Title: Genome Sequence of Mycobacterium Phage LilHazelnut
    Article Snippet: Here, we describe a new mycobacteriophage, LilHazelnut, isolated as part of the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program ( ) from a single plaque in an enrichment of a 0.22-μm filtered 7H9 liquid medium-washed soil sample from North Georgia (coordinates 24.527904, 83.987719) using the host Mycobacterium smegmatis mc2 155 and purified using three consecutive serial dilutions. .. A NEBNext Ultra II FS kit with dual-indexed barcoding was used to prepare a sequencing library from genomic DNA.

    Article Title: Genome Sequences of Six Cluster N Mycobacteriophages, Kevin1, Nenae, Parmesanjohn, ShrimpFriedEgg, Smurph, and SpongeBob, Isolated on Mycobacterium smegmatis mc2155
    Article Snippet: After purification and amplification of the phages, electron microscopy determined a Siphoviridae morphology for each of them. .. Briefly, sequencing libraries were prepared from genomic DNA (isolated by phenol-chloroform extraction) using an Ultra II FS kit (NEB) with dual-indexed barcoding and pooled with others for 48 total libraries run on an Illumina MiSeq instrument, yielding at least 482,600 single-end 150-base reads and at least 201-fold coverage for each genome.

    Article Title: Complete Genome Sequences of Mycobacteriophages Candle, Schatzie, Sumter, and Waleliano
    Article Snippet: Purified high-titer lysates (HTLs) were collected from plaques, and the phage life cycles are given in . .. The NEBNext Ultra II FS kit (New England BioLabs, Ipswich, MA) with dual-indexed barcoding was used to build DNA libraries, which were then pooled for sequencing.

    Article Title: Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development
    Article Snippet: Whole genome sequencing, SNP profile analysis, and TIDAL analysis Genomic DNA libraries were prepared using NEB Ultra II FS kit E7805. .. Library PCR amplification was also carried out as per manual instructions for six cycles and purified using one round of AmpureXP beads addition at 0.9X volume.

    Polymerase Chain Reaction:

    Article Title: In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi
    Article Snippet: The Illumina libraries were constructed for M . perstans and M . ozzardi using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs Inc., USA) as described by the manufacturer. .. A library was prepared from each time point then PCR amplified with a different index primer to enable multiplexing.

    Article Title: SMURF-seq: efficient copy number profiling on long-read sequencers
    Article Snippet: DNA from SK-BR-3 cells was used to construct WGS library with the NEBNext UltraII FS DNA Library Prep Kit (NEB, Cat. no. E7805) following the manufacturer’s instructions. .. The reads were mapped with BWA-MEM using the default parameters, PCR duplicates were removed, and CNV profiles were generated using exactly the same method as used for SMURF-seq reads.

    Article Title: PCR-free whole exome sequencing: Cost-effective and efficient in detecting rare mutations
    Article Snippet: .. PCR-free library preparation of DNA sheared enzymatically, followed by adaptor ligation using NEBNext Ultra II FS DNA Library Prep Kit (PCRfree-Frag) Using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (NEB, MA, USA), 2 μg DNA was fragmented by DNA Fragmentase at 37°C for 15 min, followed by end repair, A-tailing, and adaptor ligation according to the manufacturer’s instructions, except that the ligation condition used was 4°C for 4 h to maximize the efficiency of adaptor ligation ( ). .. Target enrichment with SureSelect XT Human All Exon V5 kit Input DNA amount for hybridization with the V5 kit was changed from 500 ng to 3000 ng for each library preparation method ( ).

    Article Title: Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development
    Article Snippet: Whole genome sequencing, SNP profile analysis, and TIDAL analysis Genomic DNA libraries were prepared using NEB Ultra II FS kit E7805. .. Library PCR amplification was also carried out as per manual instructions for six cycles and purified using one round of AmpureXP beads addition at 0.9X volume.

    Chromatin Immunoprecipitation:

    Article Title: In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi
    Article Snippet: The Illumina libraries were constructed for M . perstans and M . ozzardi using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs Inc., USA) as described by the manufacturer. .. The quality and concentration of each library was determined using a 2100 Bioanalyzer with a high sensitivity DNA chip (Agilent Technologies, USA).

    Plasmid Preparation:

    Article Title: A Fosmid-Based System for the Generation of Recombinant Cercopithecine Alphaherpesvirus 2 Encoding Reporter Genes
    Article Snippet: Next-Generation Sequencing and Assembly Library preparation of fosmid-DNA was performed using the NEBnext Ultra II FS DNA Library Prep Kit (New England BioLabs, Ipswich, MA, USA) following the manufacturer’s protocol for < 100 ng DNA input (30–46 ng input amount). .. Sequence annotations were transferred from the reference vector constructs using Geneious Prime (Biomatters, Auckland, New Zealand).

    Selection:

    Article Title: Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development
    Article Snippet: Whole genome sequencing, SNP profile analysis, and TIDAL analysis Genomic DNA libraries were prepared using NEB Ultra II FS kit E7805. .. Size selection was performed with two rounds of AmpureXP beads addition to select for insert size 150–250 bp as per kit manual.

    Next-Generation Sequencing:

    Article Title: A Fosmid-Based System for the Generation of Recombinant Cercopithecine Alphaherpesvirus 2 Encoding Reporter Genes
    Article Snippet: .. Next-Generation Sequencing and Assembly Library preparation of fosmid-DNA was performed using the NEBnext Ultra II FS DNA Library Prep Kit (New England BioLabs, Ipswich, MA, USA) following the manufacturer’s protocol for < 100 ng DNA input (30–46 ng input amount). .. The quality was controlled using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and the libraries were subsequently sequenced on an Illumina MiSeq (Illumina, San Diego, CA, USA) with a 600v3 sequencing kit (2 × 300 bp paired-end reads).

    dsDNA Assay:

    Article Title: SMURF-seq: efficient copy number profiling on long-read sequencers
    Article Snippet: DNA from SK-BR-3 cells was used to construct WGS library with the NEBNext UltraII FS DNA Library Prep Kit (NEB, Cat. no. E7805) following the manufacturer’s instructions. .. After library quality and quantity assessment with Qubit 3.0 HS dsDNA assay and BioAnalyzer HS dsDNA assay (Agilent), libraries were sequenced on HiSeq 2500 (Illumina) with single-end 130 cycles mode.

    Produced:

    Article Title: SMURF-seq: efficient copy number profiling on long-read sequencers
    Article Snippet: DNA from SK-BR-3 cells was used to construct WGS library with the NEBNext UltraII FS DNA Library Prep Kit (NEB, Cat. no. E7805) following the manufacturer’s instructions. .. The scatter plots and Pearson correlations comparing the CNV profiles were produced using R.

    Concentration Assay:

    Article Title: In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardi
    Article Snippet: The Illumina libraries were constructed for M . perstans and M . ozzardi using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs Inc., USA) as described by the manufacturer. .. The quality and concentration of each library was determined using a 2100 Bioanalyzer with a high sensitivity DNA chip (Agilent Technologies, USA).

    DNA Purification:

    Article Title: Draft Genome Sequence of Geobacillus sp. Strain LEMMJ02, a Thermophile Isolated from Deception Island, an Active Volcano in Antarctica
    Article Snippet: After incubation at 55°C for 48 h, a single colony was used for genomic DNA extraction with a Wizard genomic DNA purification kit (Promega, Madison, USA), and the DNA was then quantified using a Qubit fluorometer (Thermo Fisher Scientific, Waltham, USA). .. A NEBNext Ultra II FS DNA library kit (New England Biolabs, Ipswich, USA) was used to prepare a paired-end 300-bp library, which was sequenced on an Illumina MiSeq system.

    Environmental Sampling:

    Article Title: Genome Sequences of Three Microbacterium Phages Isolated from Flowers
    Article Snippet: ANNOUNCEMENT Numerous bacteriophages infecting actinobacterial hosts have been isolated from environmental samples, such as soil and compost ( ). .. Phage DNA was isolated from phage lysates using the Wizard DNA extraction kit (Promega), and then sequencing libraries were prepared using an NEB Ultra II FS kit and run on an Illumina MiSeq platform, yielding at least 100,000 single-end 150-base reads for each genome.

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    New England Biolabs ultra ii fs dna library prep kit
    Cloning and characterization of CeHV-2 fosmids. ( a ) Scheme of CeHV-2 genome cloning. Viral <t>DNA</t> was isolated from virus particles, sheared, end-repaired and size fractionated on an agarose gel. Fractionated fragments were ligated into <t>fosmid</t> vector pCC1FOS (red) and packaged into phage lambda particles, which were then used to transduce cells of E. coli strain EPI300. Individual colonies were further characterized by colony PCR, end-sequencing, and restriction digest. ( b ) An overview of all fosmid clones that are characterized by colony PCR and end-sequencing. The genome of CeHV-2 is schematically represented on top, with U S regions drawn on both sides of the U L region. The direction of gene order, in the U L and U S regions, is indicated by arrows and inverted repeats are drawn as boxes. The positions of fosmid inserts are drawn as lines. The names of the fosmids and nucleotide positions of the insertions are given above the respective lines.
    Ultra Ii Fs Dna Library Prep Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Cloning and characterization of CeHV-2 fosmids. ( a ) Scheme of CeHV-2 genome cloning. Viral DNA was isolated from virus particles, sheared, end-repaired and size fractionated on an agarose gel. Fractionated fragments were ligated into fosmid vector pCC1FOS (red) and packaged into phage lambda particles, which were then used to transduce cells of E. coli strain EPI300. Individual colonies were further characterized by colony PCR, end-sequencing, and restriction digest. ( b ) An overview of all fosmid clones that are characterized by colony PCR and end-sequencing. The genome of CeHV-2 is schematically represented on top, with U S regions drawn on both sides of the U L region. The direction of gene order, in the U L and U S regions, is indicated by arrows and inverted repeats are drawn as boxes. The positions of fosmid inserts are drawn as lines. The names of the fosmids and nucleotide positions of the insertions are given above the respective lines.

    Journal: Viruses

    Article Title: A Fosmid-Based System for the Generation of Recombinant Cercopithecine Alphaherpesvirus 2 Encoding Reporter Genes

    doi: 10.3390/v11111026

    Figure Lengend Snippet: Cloning and characterization of CeHV-2 fosmids. ( a ) Scheme of CeHV-2 genome cloning. Viral DNA was isolated from virus particles, sheared, end-repaired and size fractionated on an agarose gel. Fractionated fragments were ligated into fosmid vector pCC1FOS (red) and packaged into phage lambda particles, which were then used to transduce cells of E. coli strain EPI300. Individual colonies were further characterized by colony PCR, end-sequencing, and restriction digest. ( b ) An overview of all fosmid clones that are characterized by colony PCR and end-sequencing. The genome of CeHV-2 is schematically represented on top, with U S regions drawn on both sides of the U L region. The direction of gene order, in the U L and U S regions, is indicated by arrows and inverted repeats are drawn as boxes. The positions of fosmid inserts are drawn as lines. The names of the fosmids and nucleotide positions of the insertions are given above the respective lines.

    Article Snippet: Next-Generation Sequencing and Assembly Library preparation of fosmid-DNA was performed using the NEBnext Ultra II FS DNA Library Prep Kit (New England BioLabs, Ipswich, MA, USA) following the manufacturer’s protocol for < 100 ng DNA input (30–46 ng input amount).

    Techniques: Clone Assay, Isolation, Agarose Gel Electrophoresis, Plasmid Preparation, Transduction, Polymerase Chain Reaction, Sequencing