tru q 7 mutation panel  (New England Biolabs)


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    Name:
    NEBNext dsDNA Fragmentase
    Description:
    NEBNext dsDNA Fragmentase 250 rxns
    Catalog Number:
    m0348l
    Price:
    400
    Size:
    250 rxns
    Category:
    Other Endonucleases
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    Structured Review

    New England Biolabs tru q 7 mutation panel
    NEBNext dsDNA Fragmentase
    NEBNext dsDNA Fragmentase 250 rxns
    https://www.bioz.com/result/tru q 7 mutation panel/product/New England Biolabs
    Average 91 stars, based on 24 article reviews
    Price from $9.99 to $1999.99
    tru q 7 mutation panel - by Bioz Stars, 2020-05
    91/100 stars

    Images

    1) Product Images from "MAGERI: Computational pipeline for molecular-barcoded targeted resequencing"

    Article Title: MAGERI: Computational pipeline for molecular-barcoded targeted resequencing

    Journal: PLoS Computational Biology

    doi: 10.1371/journal.pcbi.1005480

    MAGERI software benchmark using Tru-Q 7 reference standard and control donor DNA. a  Number of detected variant for each variant frequency tier across two independent experiments with the reference standard. Shaded areas show the 95% confidence intervals for expected fraction of recovered variants, i.e. binomial proportion confidence intervals built using known variant frequency and template coverage.  b  Frequency distribution of known Tru-Q 7 variants coming from each frequency tier and errors in the control donor DNA.  c  MAGERI Q score and the empirical P-values of erroneous variants detected in control donor DNA.  d  Comparison of Q score distribution of erroneous variants and variants of each frequency tier. Dotted and dashed lines show P
    Figure Legend Snippet: MAGERI software benchmark using Tru-Q 7 reference standard and control donor DNA. a Number of detected variant for each variant frequency tier across two independent experiments with the reference standard. Shaded areas show the 95% confidence intervals for expected fraction of recovered variants, i.e. binomial proportion confidence intervals built using known variant frequency and template coverage. b Frequency distribution of known Tru-Q 7 variants coming from each frequency tier and errors in the control donor DNA. c MAGERI Q score and the empirical P-values of erroneous variants detected in control donor DNA. d Comparison of Q score distribution of erroneous variants and variants of each frequency tier. Dotted and dashed lines show P

    Techniques Used: Software, Variant Assay

    MAGERI performance on different types of UMI-tagged data. a.  Analysis of single-strand consensuses from duplex sequencing data. Q scores of detected variants are plotted against empirical P-values, a smoothed fitting is shown with red line, ABL variant known to be present in the sample at ~1% frequency is shown with black dot.  b . Analysis of UMI-tagged HIV cDNA sequencing data. MAGERI Q scores are plotted against empirical P-values for a control unmutated HIV cDNA from 8E5 cell line (red) and HIV+ donor plasma sample (blue).  c . Indel variants detected in Tru-Q 7 reference standard and PBMC DNA of a healthy donor. Indel frequency is plotted against its size (number of added/deleted nucleotides). The figure shows known EGFR deletion (ΔE746 − A750) in two independent experiments with a known frequency of 1% (original Tru-Q 7 reference standard) and 0.1% (Tru-Q 7 reference standard diluted in 1:9 ratio with healthy donor DNA), erroneous variants present in healthy donor DNA are shown with empty circles.
    Figure Legend Snippet: MAGERI performance on different types of UMI-tagged data. a. Analysis of single-strand consensuses from duplex sequencing data. Q scores of detected variants are plotted against empirical P-values, a smoothed fitting is shown with red line, ABL variant known to be present in the sample at ~1% frequency is shown with black dot. b . Analysis of UMI-tagged HIV cDNA sequencing data. MAGERI Q scores are plotted against empirical P-values for a control unmutated HIV cDNA from 8E5 cell line (red) and HIV+ donor plasma sample (blue). c . Indel variants detected in Tru-Q 7 reference standard and PBMC DNA of a healthy donor. Indel frequency is plotted against its size (number of added/deleted nucleotides). The figure shows known EGFR deletion (ΔE746 − A750) in two independent experiments with a known frequency of 1% (original Tru-Q 7 reference standard) and 0.1% (Tru-Q 7 reference standard diluted in 1:9 ratio with healthy donor DNA), erroneous variants present in healthy donor DNA are shown with empty circles.

    Techniques Used: Sequencing, Variant Assay

    2) Product Images from "MAGERI: Computational pipeline for molecular-barcoded targeted resequencing"

    Article Title: MAGERI: Computational pipeline for molecular-barcoded targeted resequencing

    Journal: PLoS Computational Biology

    doi: 10.1371/journal.pcbi.1005480

    MAGERI software benchmark using Tru-Q 7 reference standard and control donor DNA. a Number of detected variant for each variant frequency tier across two independent experiments with the reference standard. Shaded areas show the 95% confidence intervals for expected fraction of recovered variants, i.e. binomial proportion confidence intervals built using known variant frequency and template coverage. b Frequency distribution of known Tru-Q 7 variants coming from each frequency tier and errors in the control donor DNA. c MAGERI Q score and the empirical P-values of erroneous variants detected in control donor DNA. d Comparison of Q score distribution of erroneous variants and variants of each frequency tier. Dotted and dashed lines show P
    Figure Legend Snippet: MAGERI software benchmark using Tru-Q 7 reference standard and control donor DNA. a Number of detected variant for each variant frequency tier across two independent experiments with the reference standard. Shaded areas show the 95% confidence intervals for expected fraction of recovered variants, i.e. binomial proportion confidence intervals built using known variant frequency and template coverage. b Frequency distribution of known Tru-Q 7 variants coming from each frequency tier and errors in the control donor DNA. c MAGERI Q score and the empirical P-values of erroneous variants detected in control donor DNA. d Comparison of Q score distribution of erroneous variants and variants of each frequency tier. Dotted and dashed lines show P

    Techniques Used: Software, Variant Assay

    MAGERI performance on different types of UMI-tagged data. a. Analysis of single-strand consensuses from duplex sequencing data. Q scores of detected variants are plotted against empirical P-values, a smoothed fitting is shown with red line, ABL variant known to be present in the sample at ~1% frequency is shown with black dot. b . Analysis of UMI-tagged HIV cDNA sequencing data. MAGERI Q scores are plotted against empirical P-values for a control unmutated HIV cDNA from 8E5 cell line (red) and HIV+ donor plasma sample (blue). c . Indel variants detected in Tru-Q 7 reference standard and PBMC DNA of a healthy donor. Indel frequency is plotted against its size (number of added/deleted nucleotides). The figure shows known EGFR deletion (ΔE746 − A750) in two independent experiments with a known frequency of 1% (original Tru-Q 7 reference standard) and 0.1% (Tru-Q 7 reference standard diluted in 1:9 ratio with healthy donor DNA), erroneous variants present in healthy donor DNA are shown with empty circles.
    Figure Legend Snippet: MAGERI performance on different types of UMI-tagged data. a. Analysis of single-strand consensuses from duplex sequencing data. Q scores of detected variants are plotted against empirical P-values, a smoothed fitting is shown with red line, ABL variant known to be present in the sample at ~1% frequency is shown with black dot. b . Analysis of UMI-tagged HIV cDNA sequencing data. MAGERI Q scores are plotted against empirical P-values for a control unmutated HIV cDNA from 8E5 cell line (red) and HIV+ donor plasma sample (blue). c . Indel variants detected in Tru-Q 7 reference standard and PBMC DNA of a healthy donor. Indel frequency is plotted against its size (number of added/deleted nucleotides). The figure shows known EGFR deletion (ΔE746 − A750) in two independent experiments with a known frequency of 1% (original Tru-Q 7 reference standard) and 0.1% (Tru-Q 7 reference standard diluted in 1:9 ratio with healthy donor DNA), erroneous variants present in healthy donor DNA are shown with empty circles.

    Techniques Used: Sequencing, Variant Assay

    Related Articles

    Sample Prep:

    Article Title: A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing, the Case of the Mitochondrial Genome
    Article Snippet: .. P: Ion Torrent PGM sequencing; T: TruSeq DNA PCR-Free Sample Preparation protocol; NXT: Nextera XT method; S: sample; Ion: Ion shear enzymes; C: Covaris; N: NEBNext dsDNA Fragmentase; TS4.2: analyzed with the Torrent Suite 4.2 software; GATK: analyzed with our in-house pipeline based on GATK. (XLSX) Click here for additional data file. ..

    Generated:

    Article Title: A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing, the Case of the Mitochondrial Genome
    Article Snippet: .. The average read depth for the different datasets generated with the MiSeq were 3723, 4701 and 19418 for the TruSeq Covaris, TruSeq NEBNext dsDNA Fragmentase and the Nextera XT methods, respectively. .. The reads generated by MiSeq (paired end reads), had a 150 bp fixed length, while reads generated by Ion Torrent PGM showed a variable single-end read length with an average of 145 bp.

    Polymerase Chain Reaction:

    Article Title: From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes
    Article Snippet: .. If samples of different length are pooled for library construction then the mass of DNA used for each sample should be adjusted accordingly to ensure coverage levels are the same across all samples (see ‘Fragmentation of PCR products using NEBNext dsDNA fragmentase’ above). ..

    Article Title: From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes
    Article Snippet: .. Fragmentation of PCR products using NEBNext dsDNA fragmentase For each individual, the two LR-PCR products (HumLR_1 and _2) were pooled in equimolar ratios (493.5 ng and 506.5 ng respectively) to yield a total of 1 μg DNA for fragmentation. .. Next, the pooled DNA was fragmented using the NEBNext dsDNA Fragmentase according to the manufacturer’s instructions and Additional file .

    Article Title: A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing, the Case of the Mitochondrial Genome
    Article Snippet: .. P: Ion Torrent PGM sequencing; T: TruSeq DNA PCR-Free Sample Preparation protocol; NXT: Nextera XT method; S: sample; Ion: Ion shear enzymes; C: Covaris; N: NEBNext dsDNA Fragmentase; TS4.2: analyzed with the Torrent Suite 4.2 software; GATK: analyzed with our in-house pipeline based on GATK. (XLSX) Click here for additional data file. ..

    Incubation:

    Article Title: A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing, the Case of the Mitochondrial Genome
    Article Snippet: .. The protocol described, before concerning the NEBNext dsDNA Fragmentase, was the same except for the incubation time that was adapted to 15 min to obtain 350 bp fragments. .. Next, samples were further processed using the TruSeq DNA PCR-Free Sample Preparation protocol as instructed by the supplier (Illumina, Eindhoven, The Netherlands).

    Sequencing:

    Article Title: A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing, the Case of the Mitochondrial Genome
    Article Snippet: .. P: Ion Torrent PGM sequencing; T: TruSeq DNA PCR-Free Sample Preparation protocol; NXT: Nextera XT method; S: sample; Ion: Ion shear enzymes; C: Covaris; N: NEBNext dsDNA Fragmentase; TS4.2: analyzed with the Torrent Suite 4.2 software; GATK: analyzed with our in-house pipeline based on GATK. (XLSX) Click here for additional data file. ..

    Article Title: Generation of a transgenic ORFeome library in Drosophila
    Article Snippet: .. For sequencing library preparation, a time course with the dsDNA fragmentase is useful for optimal digestion ( ). ..

    Plasmid Preparation:

    Article Title: A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing, the Case of the Mitochondrial Genome
    Article Snippet: .. One µg of pUC19 plasmid DNA (Thermo Fisher, Erembodegem-Aalst, Belgium) was sheared by the Covaris or NEBNext dsDNA Fragmentase. .. Subsequently, samples were processed using the TruSeq DNA PCR-Free Sample Preparation protocol, and sequenced on the MiSeq.

    Software:

    Article Title: A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing, the Case of the Mitochondrial Genome
    Article Snippet: .. P: Ion Torrent PGM sequencing; T: TruSeq DNA PCR-Free Sample Preparation protocol; NXT: Nextera XT method; S: sample; Ion: Ion shear enzymes; C: Covaris; N: NEBNext dsDNA Fragmentase; TS4.2: analyzed with the Torrent Suite 4.2 software; GATK: analyzed with our in-house pipeline based on GATK. (XLSX) Click here for additional data file. ..

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  • 93
    New England Biolabs dsdna fragmentase buffer
    Dsdna Fragmentase Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dsdna fragmentase buffer/product/New England Biolabs
    Average 93 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    dsdna fragmentase buffer - by Bioz Stars, 2020-05
    93/100 stars
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