ultra dna library prep kit  (New England Biolabs)


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    Name:
    NEBNext Ultra DNA Library Prep Kit for Illumina
    Description:
    NEBNext Ultra DNA Library Prep Kit for Illumina 96 rxns
    Catalog Number:
    e7370l
    Price:
    2118
    Size:
    96 rxns
    Category:
    DNA Template Preparation for PCR
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    Structured Review

    New England Biolabs ultra 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/ultra dna library prep kit/product/New England Biolabs
    Average 99 stars, based on 215 article reviews
    Price from $9.99 to $1999.99
    ultra dna library prep kit - by Bioz Stars, 2020-03
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    Images

    1) Product Images from "A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA"

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0076096

    Analysis of Illumina sequence reads of a black molly ( Poecilia cf. sphenops ) whole fish DNA library before and after enrichment with MBD-Fc protein A paramagnetic beads. Shown is a concordance plot comparing relative abundances of microbial genera between the enriched and unenriched samples.
    Figure Legend Snippet: Analysis of Illumina sequence reads of a black molly ( Poecilia cf. sphenops ) whole fish DNA library before and after enrichment with MBD-Fc protein A paramagnetic beads. Shown is a concordance plot comparing relative abundances of microbial genera between the enriched and unenriched samples.

    Techniques Used: Sequencing, Fluorescence In Situ Hybridization

    MBD-Fc separates human DNA from human-malarial DNA mixtures. (A) Graph of the percentage of 75 bp Illumina reads mapping to the Plasmodium falciparum reference sequence in the mixture before enrichment (Unenriched), after enrichment (Enriched) and the bound fraction following wash and elution as described above (Bound). (B) Evenness of coverage analysis metrics show enriched malaria reads (Enriched Plasmodium ) in line with pure malaria DNA reads ( Plasmodium Only). Unlike the unenriched input sample (Human + Plasmodium ) showing 60% of the Plasmodium genome uncovered (zero depth), enriched sample (Enriched Plasmodium ) showed even coverage of the genome with no regions lacking coverage. The amount of Plasmodium DNA retained in the pellet (Bound Human) following wash and elution was insignificant. (C) GC-content and bias analysis. No base bias was detected in the enriched sample. Average GC content of the enriched sample (Enriched Plasmodium ) matches the pure malaria sample ( Plasmodium Only) and is very close to the theoretical GC coverage (Theoretical).
    Figure Legend Snippet: MBD-Fc separates human DNA from human-malarial DNA mixtures. (A) Graph of the percentage of 75 bp Illumina reads mapping to the Plasmodium falciparum reference sequence in the mixture before enrichment (Unenriched), after enrichment (Enriched) and the bound fraction following wash and elution as described above (Bound). (B) Evenness of coverage analysis metrics show enriched malaria reads (Enriched Plasmodium ) in line with pure malaria DNA reads ( Plasmodium Only). Unlike the unenriched input sample (Human + Plasmodium ) showing 60% of the Plasmodium genome uncovered (zero depth), enriched sample (Enriched Plasmodium ) showed even coverage of the genome with no regions lacking coverage. The amount of Plasmodium DNA retained in the pellet (Bound Human) following wash and elution was insignificant. (C) GC-content and bias analysis. No base bias was detected in the enriched sample. Average GC content of the enriched sample (Enriched Plasmodium ) matches the pure malaria sample ( Plasmodium Only) and is very close to the theoretical GC coverage (Theoretical).

    Techniques Used: Sequencing

    Related Articles

    Clone Assay:

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: After transfection into bacteria, individual clones were subjected to Sanger sequencing. .. 5’ RACE products were analyzed by HTS after library preparation with the NEBNext Ultra DNA Library prep Kit for Illumina.

    Amplification:

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation
    Article Snippet: Third-party comparator kits included NEBNext Ultra DNA Library Prep Kit (New England BioLabs, cat. no. E7370S), Kapa HyperPrep Kits (Roche, cat. Nos. .. KK8502 [with library amplification], KK8503 [without amplification module]), Kapa HyperPlus Kits (Roche, cat. Nos.

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: After touchdown PCR with gene specific primers, nested PCR was performed by which restriction sites were added at both ends of the amplification products (primers: early/late region rev nested). .. 5’ RACE products were analyzed by HTS after library preparation with the NEBNext Ultra DNA Library prep Kit for Illumina.

    Article Title: From the Cover: Germline-restricted chromosome (GRC) is widespread among songbirds
    Article Snippet: Paragraph title: Preparation of Amplified DNA and Library Construction. ... DNA library for NGS sequencing was prepared using the microdissected GRC DNA libraries using the NEBNext Ultra DNA Library Prep kit (New England Biolabs).

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: Preparation of Next-generation Sequencing Libraries DNA extracted from saliva and leukocytes were used to generate SOLiD 4 libraries using NEBNext® Fast DNA Library Prep Set for Ion Torrent (NEB #E6270) with SOLiD 4 adaptors and primers; mixtures of DNA extracted form E. coli K-12 MG1655 and IMR-90 cells were used to generate Ion Torrent libraries using NEBNext Fast DNA Library Prep Set for Ion Torrent (NEB #E6270); DNA extracted from black molly was used to generate Illumina paired end sequencing libraries using NEBNext Ultra DNA Library Prep Kit and Multiplex Oligos for Illumina (NEB #E7370 and #E7335). .. Sheared DNA was end repaired, dA-tailed (Illumina libraries only), ligated to platform specific adaptors, size selected to an average size of ∼300–350 bp by Agencourt AMPure XP beads (Beckman Coulter #A63880), and amplified by 6 to 12 cycles of PCR.

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA. .. Fragmented DNA was immunoprecipitated with antibody against 5mC as described above, and the amplified library was prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) following the manufacturer’s instructions.

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: Paragraph title: Rolling circle amplification (RCA) ... Libraries of RCA products for HTS analysis were generated with the NEBNext Ultra DNA Library Prep Kit for Illumina and sequenced on an Illumina HiSeq2500 instrument.

    Whole Genome Amplification:

    Article Title: From the Cover: Germline-restricted chromosome (GRC) is widespread among songbirds
    Article Snippet: DNA amplification of microdissected GRC chromosomal material was performed with the GenomePlex Single Cell Whole Genome Amplification kit (WGA4) (Sigma-Aldrich) according to the manufacturer’s protocol. .. DNA library for NGS sequencing was prepared using the microdissected GRC DNA libraries using the NEBNext Ultra DNA Library Prep kit (New England Biolabs).

    Synthesized:

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: Briefly, 5 μg of total RNA were dephosphorylated, decapped and then ligated to a 5’ RACE RNA adapter. cDNA was synthesized with gene specific primers (early/late region rev, ) using Superscript III according to the manufacturer’s instructions. .. 5’ RACE products were analyzed by HTS after library preparation with the NEBNext Ultra DNA Library prep Kit for Illumina.

    Methylated DNA Immunoprecipitation Sequencing:

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: .. For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA. .. Fragmented DNA was immunoprecipitated with antibody against 5mC as described above, and the amplified library was prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) following the manufacturer’s instructions.

    Real-time Polymerase Chain Reaction:

    Article Title: An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)
    Article Snippet: DNAs were manually size-selected into 300-500 bp fragments using gel electrophoresis, and libraries were prepared according to the methodology originally described in the NEBNext Ultra DNA Library Prep Kit from Illumina. .. Three libraries were quantified by realtime fluorescence quantitative PCR, and run in three lanes on Illumina HiSeq 2000 using 150 base PE reads (v3 chemistry kit, Illumina, USA).

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: The immunocomplexes were recovered using 8 μL Dynabeads (M-280; Thermofisher, Waltham, MA, USA), and the pull-down products were detected by quantitative-PCR. .. For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA.

    Article Title: Reference Materials for Calibration of Analytical Biases in Quantification of DNA Methylation
    Article Snippet: NGS analysis NGS libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions starting with 100 ng to 1 μg of purified amplicons. .. To quantify the library DNA, qPCR was performed using the 2× KAPA SYBR Fast Universal qPCR Kit (KAPA Biosystems).

    Article Title: Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery
    Article Snippet: .. After immunoprecipitation, purification, and decross-linking, DNA was extracted and used for qPCR measurements and/or library preparation for sequencing (NEBNext Ultra DNA library preparation kit, Illumina). ..

    Incubation:

    Article Title: Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery
    Article Snippet: For the RNA Pol II ChIP, we incubated 75% of the chromatin with α-Rbp3 and 25% with α-H3K9me3. .. After immunoprecipitation, purification, and decross-linking, DNA was extracted and used for qPCR measurements and/or library preparation for sequencing (NEBNext Ultra DNA library preparation kit, Illumina).

    In Silico:

    Article Title: Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile
    Article Snippet: SFV1 genome library was prepared with the NEBNext Ultra DNA library Prep Kit for Illumina (New England Biolabs), and samples were sequenced by Illumina Miseq with paried-end 150-bp read lengths (Genomics Platform, Institut Pasteur, France). .. Homologs of the in silico- translated protein sequences were searched using BLASTP with an upper threshold E value of 1e-3, against the non-redundant protein database at the National Center for Biotechnology Information.

    Genome Wide:

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA. .. The mapped reads were filtered for duplicates and used to compute genome-wide reads-per-million (RPM) normalized signal tracks.

    Touchdown PCR:

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: After touchdown PCR with gene specific primers, nested PCR was performed by which restriction sites were added at both ends of the amplification products (primers: early/late region rev nested). .. 5’ RACE products were analyzed by HTS after library preparation with the NEBNext Ultra DNA Library prep Kit for Illumina.

    Flow Cytometry:

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation
    Article Snippet: Third-party comparator kits included NEBNext Ultra DNA Library Prep Kit (New England BioLabs, cat. no. E7370S), Kapa HyperPrep Kits (Roche, cat. Nos. .. Libraries were prepared from 100 ng NA12878 following the manufacturers’ instructions for each kit, and sequenced on a HiSeq X with six samples per flow cell.

    RAST Test:

    Article Title: Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile
    Article Snippet: SFV1 genome library was prepared with the NEBNext Ultra DNA library Prep Kit for Illumina (New England Biolabs), and samples were sequenced by Illumina Miseq with paried-end 150-bp read lengths (Genomics Platform, Institut Pasteur, France). .. ORFs were predicted by using RAST v2.0 .

    Ligation:

    Article Title: A high throughput screen for active human transposable elements
    Article Snippet: .. Library construction consisting of end repair, adapter ligation and PCR extension was performed using NEBNext Ultra DNA Library Kit for Illumina (New England Biolabs, Ipswich, Massachusetts; cat. E7370) to generate libraries with full-length adapters including index 1 (i7) for Illumina paired-end sequencing. .. TE-target amplification TE-containing fragments were exponentially amplified from genomic library using the two TE-targeting primers in conjunction with the Illumina Universal PCR primer (P5) in a multiplex reaction (Additional file : Table S2).

    Generated:

    Article Title: Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme
    Article Snippet: .. Illumina libraries were generated for each purified PCR product using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs Inc., USA) following manufacturer’s instructions and sequenced on an Illumina MiSeq. ..

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: .. Libraries of RCA products for HTS analysis were generated with the NEBNext Ultra DNA Library Prep Kit for Illumina and sequenced on an Illumina HiSeq2500 instrument. ..

    DNA Sequencing:

    Article Title: An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)
    Article Snippet: Paragraph title: DNA sequencing ... DNAs were manually size-selected into 300-500 bp fragments using gel electrophoresis, and libraries were prepared according to the methodology originally described in the NEBNext Ultra DNA Library Prep Kit from Illumina.

    Polymerase Chain Reaction:

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation
    Article Snippet: FC-121-4001, FC-121-4002, FC-121-4003), and TruSeq DNA PCR-free (Illumina, cat. Nos. .. Third-party comparator kits included NEBNext Ultra DNA Library Prep Kit (New England BioLabs, cat. no. E7370S), Kapa HyperPrep Kits (Roche, cat. Nos.

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: All RACE PCR amplifications were performed with Pfu Ultra II (Agilent technologies) according to the manufacturer’s protocol. .. 5’ RACE products were analyzed by HTS after library preparation with the NEBNext Ultra DNA Library prep Kit for Illumina.

    Article Title: Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme
    Article Snippet: .. Illumina libraries were generated for each purified PCR product using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs Inc., USA) following manufacturer’s instructions and sequenced on an Illumina MiSeq. ..

    Article Title: A high throughput screen for active human transposable elements
    Article Snippet: .. Library construction consisting of end repair, adapter ligation and PCR extension was performed using NEBNext Ultra DNA Library Kit for Illumina (New England Biolabs, Ipswich, Massachusetts; cat. E7370) to generate libraries with full-length adapters including index 1 (i7) for Illumina paired-end sequencing. .. TE-target amplification TE-containing fragments were exponentially amplified from genomic library using the two TE-targeting primers in conjunction with the Illumina Universal PCR primer (P5) in a multiplex reaction (Additional file : Table S2).

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: Preparation of Next-generation Sequencing Libraries DNA extracted from saliva and leukocytes were used to generate SOLiD 4 libraries using NEBNext® Fast DNA Library Prep Set for Ion Torrent (NEB #E6270) with SOLiD 4 adaptors and primers; mixtures of DNA extracted form E. coli K-12 MG1655 and IMR-90 cells were used to generate Ion Torrent libraries using NEBNext Fast DNA Library Prep Set for Ion Torrent (NEB #E6270); DNA extracted from black molly was used to generate Illumina paired end sequencing libraries using NEBNext Ultra DNA Library Prep Kit and Multiplex Oligos for Illumina (NEB #E7370 and #E7335). .. Sheared DNA was end repaired, dA-tailed (Illumina libraries only), ligated to platform specific adaptors, size selected to an average size of ∼300–350 bp by Agencourt AMPure XP beads (Beckman Coulter #A63880), and amplified by 6 to 12 cycles of PCR.

    Sonication:

    Article Title: An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)
    Article Snippet: Each DNA sample was separately sonicated using a Fisher Scientific Model 500 Ultrasonic Dismembrator. .. DNAs were manually size-selected into 300-500 bp fragments using gel electrophoresis, and libraries were prepared according to the methodology originally described in the NEBNext Ultra DNA Library Prep Kit from Illumina.

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: Sonicated DNA was denatured and then immunoprecipitated using an antibody against 5mC (Eurogentec; #BI-MECY-1000) or mouse IgG antibody, as previously described [ ]. .. For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA.

    Article Title: Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery
    Article Snippet: Twenty million cells depleted for studied proteins were fixed with 1% PFA followed by chromatin extraction and sonication. .. After immunoprecipitation, purification, and decross-linking, DNA was extracted and used for qPCR measurements and/or library preparation for sequencing (NEBNext Ultra DNA library preparation kit, Illumina).

    ChIP-sequencing:

    Article Title: Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration
    Article Snippet: .. ChIP-seq ChIP libraries of GFP, H3K27me3, and H3K4me3 were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) with biological duplicates. .. The libraries were sequenced on Illumina HiSeq 1500 sequencers.

    Article Title: Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration
    Article Snippet: Paragraph title: ChIP-seq ... ChIP libraries of GFP, H3K27me3, and H3K4me3 were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) with biological duplicates.

    Nucleic Acid Electrophoresis:

    Article Title: An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)
    Article Snippet: .. DNAs were manually size-selected into 300-500 bp fragments using gel electrophoresis, and libraries were prepared according to the methodology originally described in the NEBNext Ultra DNA Library Prep Kit from Illumina. .. Three libraries were quantified by realtime fluorescence quantitative PCR, and run in three lanes on Illumina HiSeq 2000 using 150 base PE reads (v3 chemistry kit, Illumina, USA).

    Fluorescence:

    Article Title: An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)
    Article Snippet: DNAs were manually size-selected into 300-500 bp fragments using gel electrophoresis, and libraries were prepared according to the methodology originally described in the NEBNext Ultra DNA Library Prep Kit from Illumina. .. Three libraries were quantified by realtime fluorescence quantitative PCR, and run in three lanes on Illumina HiSeq 2000 using 150 base PE reads (v3 chemistry kit, Illumina, USA).

    Methylation:

    Article Title: Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme
    Article Snippet: Paragraph title: L1 promoter methylation ... Illumina libraries were generated for each purified PCR product using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs Inc., USA) following manufacturer’s instructions and sequenced on an Illumina MiSeq.

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: DNA Methylation The DNA methylation analyses were performed by the methylated DNA immunoprecipitation assay coupled with quantitative-PCR (MeDIP-qPCR) or high-throughput sequencing (MeDIP-seq). .. For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA.

    Isolation:

    Article Title: Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile
    Article Snippet: Extraction and analysis of viral DNA Nucleic acid was isolated from the purified virions with phenol/chloroform/isoamyl alcohol (25:24:1 vol/vol). .. SFV1 genome library was prepared with the NEBNext Ultra DNA library Prep Kit for Illumina (New England Biolabs), and samples were sequenced by Illumina Miseq with paried-end 150-bp read lengths (Genomics Platform, Institut Pasteur, France).

    Transfection:

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: 5’ RACE analysis of MCVSyn transfected PFSK-1 cells was performed with the GeneRacer Kit protocol (Invitrogen) according to the manufacturer’s instructions. .. 5’ RACE products were analyzed by HTS after library preparation with the NEBNext Ultra DNA Library prep Kit for Illumina.

    Purification:

    Article Title: Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme
    Article Snippet: .. Illumina libraries were generated for each purified PCR product using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs Inc., USA) following manufacturer’s instructions and sequenced on an Illumina MiSeq. ..

    Article Title: Reference Materials for Calibration of Analytical Biases in Quantification of DNA Methylation
    Article Snippet: .. NGS analysis NGS libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions starting with 100 ng to 1 μg of purified amplicons. .. Since the sequences of amplicons for P14 , P16 , and MLH1 were different and could be easily discriminated in the sequencing results, three amplicons were mixed together and processed as a set.

    Article Title: Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile
    Article Snippet: Extraction and analysis of viral DNA Nucleic acid was isolated from the purified virions with phenol/chloroform/isoamyl alcohol (25:24:1 vol/vol). .. SFV1 genome library was prepared with the NEBNext Ultra DNA library Prep Kit for Illumina (New England Biolabs), and samples were sequenced by Illumina Miseq with paried-end 150-bp read lengths (Genomics Platform, Institut Pasteur, France).

    Article Title: Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery
    Article Snippet: .. After immunoprecipitation, purification, and decross-linking, DNA was extracted and used for qPCR measurements and/or library preparation for sequencing (NEBNext Ultra DNA library preparation kit, Illumina). ..

    Sequencing:

    Article Title: Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random
    Article Snippet: .. Sequencing of Genomic and DsGTA-DNA Paired end cDNA libraries were prepared using the NEBNext Ultra DNA Library Preparation Kit for Illumina (NEB, Ipswich, MA). .. Sequencing was done on the MiSeq 2000 (Illumina) using MiSeq Reagent Kits v2 (Illumina) for 250 cycles resulting in 2×250 bp paired end reads.

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: After transfection into bacteria, individual clones were subjected to Sanger sequencing. .. 5’ RACE products were analyzed by HTS after library preparation with the NEBNext Ultra DNA Library prep Kit for Illumina.

    Article Title: From the Cover: Germline-restricted chromosome (GRC) is widespread among songbirds
    Article Snippet: .. DNA library for NGS sequencing was prepared using the microdissected GRC DNA libraries using the NEBNext Ultra DNA Library Prep kit (New England Biolabs). .. NEBNext Ultra library was sequenced on an Illumina NextSeq 550 system with single-end reads at the “Genomics” core facility of the ICG SB RAS (Novosibirsk, Russia).

    Article Title: An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus)
    Article Snippet: DNA sequencing The DNAs of M1, F1 and F’-Mix, three samples were built into libraries and used for sequencing. .. DNAs were manually size-selected into 300-500 bp fragments using gel electrophoresis, and libraries were prepared according to the methodology originally described in the NEBNext Ultra DNA Library Prep Kit from Illumina.

    Article Title: A high throughput screen for active human transposable elements
    Article Snippet: .. Library construction consisting of end repair, adapter ligation and PCR extension was performed using NEBNext Ultra DNA Library Kit for Illumina (New England Biolabs, Ipswich, Massachusetts; cat. E7370) to generate libraries with full-length adapters including index 1 (i7) for Illumina paired-end sequencing. .. TE-target amplification TE-containing fragments were exponentially amplified from genomic library using the two TE-targeting primers in conjunction with the Illumina Universal PCR primer (P5) in a multiplex reaction (Additional file : Table S2).

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: .. Preparation of Next-generation Sequencing Libraries DNA extracted from saliva and leukocytes were used to generate SOLiD 4 libraries using NEBNext® Fast DNA Library Prep Set for Ion Torrent (NEB #E6270) with SOLiD 4 adaptors and primers; mixtures of DNA extracted form E. coli K-12 MG1655 and IMR-90 cells were used to generate Ion Torrent libraries using NEBNext Fast DNA Library Prep Set for Ion Torrent (NEB #E6270); DNA extracted from black molly was used to generate Illumina paired end sequencing libraries using NEBNext Ultra DNA Library Prep Kit and Multiplex Oligos for Illumina (NEB #E7370 and #E7335). .. Briefly, genomic DNA was sheared using a Covaris S2 device to obtain an average fragment size of ∼200 bp.

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: DNA Methylation The DNA methylation analyses were performed by the methylated DNA immunoprecipitation assay coupled with quantitative-PCR (MeDIP-qPCR) or high-throughput sequencing (MeDIP-seq). .. For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA.

    Article Title: Reference Materials for Calibration of Analytical Biases in Quantification of DNA Methylation
    Article Snippet: NGS analysis NGS libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions starting with 100 ng to 1 μg of purified amplicons. .. Since the sequences of amplicons for P14 , P16 , and MLH1 were different and could be easily discriminated in the sequencing results, three amplicons were mixed together and processed as a set.

    Article Title: Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile
    Article Snippet: SFV1 genome library was prepared with the NEBNext Ultra DNA library Prep Kit for Illumina (New England Biolabs), and samples were sequenced by Illumina Miseq with paried-end 150-bp read lengths (Genomics Platform, Institut Pasteur, France). .. The genome sequence was assembled using the CLC Genomics Workbench software package.

    Article Title: Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery
    Article Snippet: .. After immunoprecipitation, purification, and decross-linking, DNA was extracted and used for qPCR measurements and/or library preparation for sequencing (NEBNext Ultra DNA library preparation kit, Illumina). ..

    Gel Extraction:

    Article Title: Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme
    Article Snippet: The ~350 bp PCR product was gel purified using QIAquick gel extraction kit (QIAGEN, NLD). .. Illumina libraries were generated for each purified PCR product using the NEBNext Ultra DNA Library Prep Kit (New England Biolabs Inc., USA) following manufacturer’s instructions and sequenced on an Illumina MiSeq.

    Nested PCR:

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: After touchdown PCR with gene specific primers, nested PCR was performed by which restriction sites were added at both ends of the amplification products (primers: early/late region rev nested). .. 5’ RACE products were analyzed by HTS after library preparation with the NEBNext Ultra DNA Library prep Kit for Illumina.

    Chromatin Immunoprecipitation:

    Article Title: Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration
    Article Snippet: .. ChIP-seq ChIP libraries of GFP, H3K27me3, and H3K4me3 were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) with biological duplicates. .. The libraries were sequenced on Illumina HiSeq 1500 sequencers.

    Article Title: Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration
    Article Snippet: .. ChIP libraries of GFP, H3K27me3, and H3K4me3 were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) with biological duplicates. .. The libraries were sequenced on Illumina HiSeq 1500 sequencers.

    Article Title: Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery
    Article Snippet: Paragraph title: ChIP ... After immunoprecipitation, purification, and decross-linking, DNA was extracted and used for qPCR measurements and/or library preparation for sequencing (NEBNext Ultra DNA library preparation kit, Illumina).

    Software:

    Article Title: Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile
    Article Snippet: SFV1 genome library was prepared with the NEBNext Ultra DNA library Prep Kit for Illumina (New England Biolabs), and samples were sequenced by Illumina Miseq with paried-end 150-bp read lengths (Genomics Platform, Institut Pasteur, France). .. The genome sequence was assembled using the CLC Genomics Workbench software package.

    Multiplex Assay:

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: .. Preparation of Next-generation Sequencing Libraries DNA extracted from saliva and leukocytes were used to generate SOLiD 4 libraries using NEBNext® Fast DNA Library Prep Set for Ion Torrent (NEB #E6270) with SOLiD 4 adaptors and primers; mixtures of DNA extracted form E. coli K-12 MG1655 and IMR-90 cells were used to generate Ion Torrent libraries using NEBNext Fast DNA Library Prep Set for Ion Torrent (NEB #E6270); DNA extracted from black molly was used to generate Illumina paired end sequencing libraries using NEBNext Ultra DNA Library Prep Kit and Multiplex Oligos for Illumina (NEB #E7370 and #E7335). .. Briefly, genomic DNA was sheared using a Covaris S2 device to obtain an average fragment size of ∼200 bp.

    Selection:

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation
    Article Snippet: Comparison of different library preparation kits The performance of library preparation for large genomes was compared between Nextera DNA Flex and a selection of other commercially available library preparation kits. .. Third-party comparator kits included NEBNext Ultra DNA Library Prep Kit (New England BioLabs, cat. no. E7370S), Kapa HyperPrep Kits (Roche, cat. Nos.

    Agarose Gel Electrophoresis:

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: RCA products were digested with restriction enzymes, separated on a 0.8% agarose gel and analyzed by ethidium bromide staining. .. Libraries of RCA products for HTS analysis were generated with the NEBNext Ultra DNA Library Prep Kit for Illumina and sequenced on an Illumina HiSeq2500 instrument.

    Next-Generation Sequencing:

    Article Title: From the Cover: Germline-restricted chromosome (GRC) is widespread among songbirds
    Article Snippet: .. DNA library for NGS sequencing was prepared using the microdissected GRC DNA libraries using the NEBNext Ultra DNA Library Prep kit (New England Biolabs). .. NEBNext Ultra library was sequenced on an Illumina NextSeq 550 system with single-end reads at the “Genomics” core facility of the ICG SB RAS (Novosibirsk, Russia).

    Article Title: A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA
    Article Snippet: .. Preparation of Next-generation Sequencing Libraries DNA extracted from saliva and leukocytes were used to generate SOLiD 4 libraries using NEBNext® Fast DNA Library Prep Set for Ion Torrent (NEB #E6270) with SOLiD 4 adaptors and primers; mixtures of DNA extracted form E. coli K-12 MG1655 and IMR-90 cells were used to generate Ion Torrent libraries using NEBNext Fast DNA Library Prep Set for Ion Torrent (NEB #E6270); DNA extracted from black molly was used to generate Illumina paired end sequencing libraries using NEBNext Ultra DNA Library Prep Kit and Multiplex Oligos for Illumina (NEB #E7370 and #E7335). .. Briefly, genomic DNA was sheared using a Covaris S2 device to obtain an average fragment size of ∼200 bp.

    Article Title: Reference Materials for Calibration of Analytical Biases in Quantification of DNA Methylation
    Article Snippet: .. NGS analysis NGS libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions starting with 100 ng to 1 μg of purified amplicons. .. Since the sequences of amplicons for P14 , P16 , and MLH1 were different and could be easily discriminated in the sequencing results, three amplicons were mixed together and processed as a set.

    DNA Methylation Assay:

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: Paragraph title: 4.6. DNA Methylation ... For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA.

    Immunoprecipitation:

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: Sonicated DNA was denatured and then immunoprecipitated using an antibody against 5mC (Eurogentec; #BI-MECY-1000) or mouse IgG antibody, as previously described [ ]. .. For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA.

    Article Title: Silencio/CG9754 connects the Piwi–piRNA complex to the cellular heterochromatin machinery
    Article Snippet: .. After immunoprecipitation, purification, and decross-linking, DNA was extracted and used for qPCR measurements and/or library preparation for sequencing (NEBNext Ultra DNA library preparation kit, Illumina). ..

    Methylated DNA Immunoprecipitation:

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: For MeDIP-qPCR, genomic DNA was randomly sheared by sonication to generate fragments between 300 and 700 bp. .. For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA.

    High Throughput Screening Assay:

    Article Title: Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
    Article Snippet: DNA Methylation The DNA methylation analyses were performed by the methylated DNA immunoprecipitation assay coupled with quantitative-PCR (MeDIP-qPCR) or high-throughput sequencing (MeDIP-seq). .. For MeDIP-seq, adaptors from the NEBNext Ultra DNA Library Prep Kit from Illumina were added to the fragmented DNA.

    Staining:

    Article Title: A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
    Article Snippet: RCA products were digested with restriction enzymes, separated on a 0.8% agarose gel and analyzed by ethidium bromide staining. .. Libraries of RCA products for HTS analysis were generated with the NEBNext Ultra DNA Library Prep Kit for Illumina and sequenced on an Illumina HiSeq2500 instrument.

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    New England Biolabs nebnext fast dna library prep set for ion torrent
    Nebnext Fast Dna Library Prep Set For Ion Torrent, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 3 article reviews
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