generation amplicon deep sequencing Search Results


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  • 92
    Illumina Inc next generation amplicon deep sequencing
    Results from Sanger sequencing and/or deep <t>amplicon</t> sequencing with NexteraXT library of the balanced chromosomal aberrations (BCAs) breakpoints. The figure for every patient includes: in the upper part, a schematically shown normal chromosome and below a chromosome containing the BCAs. Arrows indicate the orientation of the genes affected by translocation. The length of the arrows approximately corresponds to the length of the disrupted coding sequences. The lower part shows the sequencing results. For every BCA, both breakpoints are shown. In deep amplicon sequencing results, only split reads are shown (reads that present the exact structure of the breakpoint). One part of these reads fully maps to the reference genome, while the other part differs from the reference. In Proband 2 an inframe fusion gene might be created.
    Next Generation Amplicon Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    next generation amplicon deep sequencing - by Bioz Stars, 2020-08
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    86
    Roche generation amplicon deep sequencing
    Results from Sanger sequencing and/or deep <t>amplicon</t> sequencing with NexteraXT library of the balanced chromosomal aberrations (BCAs) breakpoints. The figure for every patient includes: in the upper part, a schematically shown normal chromosome and below a chromosome containing the BCAs. Arrows indicate the orientation of the genes affected by translocation. The length of the arrows approximately corresponds to the length of the disrupted coding sequences. The lower part shows the sequencing results. For every BCA, both breakpoints are shown. In deep amplicon sequencing results, only split reads are shown (reads that present the exact structure of the breakpoint). One part of these reads fully maps to the reference genome, while the other part differs from the reference. In Proband 2 an inframe fusion gene might be created.
    Generation Amplicon Deep Sequencing, supplied by Roche, used in various techniques. Bioz Stars score: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc 16s rrna gene amplicon deep sequencing
    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows <t>16S</t> <t>rRNA</t> gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).
    16s Rrna Gene Amplicon Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc 18s rrna gene amplicon deep sequencing
    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows <t>16S</t> <t>rRNA</t> gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).
    18s Rrna Gene Amplicon Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Roche dna sequencing amplicon deep sequencing
    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows <t>16S</t> <t>rRNA</t> gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).
    Dna Sequencing Amplicon Deep Sequencing, supplied by Roche, used in various techniques. Bioz Stars score: 90/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc 16s rrna gene amplicon illumina miseq deep sequencing
    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows <t>16S</t> <t>rRNA</t> gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).
    16s Rrna Gene Amplicon Illumina Miseq Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher amplicon based deep sequencing ads
    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows <t>16S</t> <t>rRNA</t> gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).
    Amplicon Based Deep Sequencing Ads, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche 16s rrna gene amplicon pyrosequencing
    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows <t>16S</t> <t>rRNA</t> gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).
    16s Rrna Gene Amplicon Pyrosequencing, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc miseq platform deep amplicon sequencing
    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows <t>16S</t> <t>rRNA</t> gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).
    Miseq Platform Deep Amplicon Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Roche deep bisulfite amplicon sequencing
    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows <t>16S</t> <t>rRNA</t> gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).
    Deep Bisulfite Amplicon Sequencing, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Eurofins pyrosequencing
    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows <t>16S</t> <t>rRNA</t> gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).
    Pyrosequencing, supplied by Eurofins, used in various techniques. Bioz Stars score: 92/100, based on 87 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche titanium amplicon pyrosequencing
    Frequency and relative expression of KIR genes in the rhesus macaque cohort . A) Y-axis indicates the percentage of animals within the cohort (n = 69) that express the indicated KIR gene. Genes not listed were not present in any animal within our cohort. Mamu-KIR2DL04 was excluded since it is not amplified by our <t>pyrosequencing</t> <t>amplicon.</t> B) Graph illustrates the percent of total pyrosequencing reads per animal (n = 61) for each KIR gene. Averages and SEM are represented by error bars. Each animal included had at least 100 sequencing reads. Genotyping results representing less than 1% of total reads in an animal were excluded to mitigate the influence of PCR artifacts. Ambiguous reads matching more than one KIR gene and splice variants were also excluded.
    Titanium Amplicon Pyrosequencing, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche 454 gs flx titanium amplicon pyrosequencing
    Frequency and relative expression of KIR genes in the rhesus macaque cohort . A) Y-axis indicates the percentage of animals within the cohort (n = 69) that express the indicated KIR gene. Genes not listed were not present in any animal within our cohort. Mamu-KIR2DL04 was excluded since it is not amplified by our <t>pyrosequencing</t> <t>amplicon.</t> B) Graph illustrates the percent of total pyrosequencing reads per animal (n = 61) for each KIR gene. Averages and SEM are represented by error bars. Each animal included had at least 100 sequencing reads. Genotyping results representing less than 1% of total reads in an animal were excluded to mitigate the influence of PCR artifacts. Ambiguous reads matching more than one KIR gene and splice variants were also excluded.
    454 Gs Flx Titanium Amplicon Pyrosequencing, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc 16s rrna gene amplicons
    Frequency and relative expression of KIR genes in the rhesus macaque cohort . A) Y-axis indicates the percentage of animals within the cohort (n = 69) that express the indicated KIR gene. Genes not listed were not present in any animal within our cohort. Mamu-KIR2DL04 was excluded since it is not amplified by our <t>pyrosequencing</t> <t>amplicon.</t> B) Graph illustrates the percent of total pyrosequencing reads per animal (n = 61) for each KIR gene. Averages and SEM are represented by error bars. Each animal included had at least 100 sequencing reads. Genotyping results representing less than 1% of total reads in an animal were excluded to mitigate the influence of PCR artifacts. Ambiguous reads matching more than one KIR gene and splice variants were also excluded.
    16s Rrna Gene Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 667 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche 16s rrna amplicon gene library
    Frequency and relative expression of KIR genes in the rhesus macaque cohort . A) Y-axis indicates the percentage of animals within the cohort (n = 69) that express the indicated KIR gene. Genes not listed were not present in any animal within our cohort. Mamu-KIR2DL04 was excluded since it is not amplified by our <t>pyrosequencing</t> <t>amplicon.</t> B) Graph illustrates the percent of total pyrosequencing reads per animal (n = 61) for each KIR gene. Averages and SEM are represented by error bars. Each animal included had at least 100 sequencing reads. Genotyping results representing less than 1% of total reads in an animal were excluded to mitigate the influence of PCR artifacts. Ambiguous reads matching more than one KIR gene and splice variants were also excluded.
    16s Rrna Amplicon Gene Library, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc 16s rrna gene v3 amplicons
    Simplified <t>16S</t> small subunit ribosomal RNA secondary structure. Secondary structure of Escherichia coli (J01695) 16S <t>rRNA</t> (main panel). Amplicon targets (primer inclusive) for the third (V3, 341F/529R) and fourth (V4, 515F/806R) variable regions are highlighted in pink and blue, respectively. Overlapping V3/V4 target sequences are highlighted in purple. Although widely used in ecological studies, the V4 region is impractical for aDNA research because of its long length (approx. 292 bp, primer inclusive). The V3 region is considerably shorter, but comparative sequence analysis ( a–d ) reveals that the V3 region exhibits extensive length polymorphisms (arrows) in archaeal (e.g., Methanobrevibacter oralis ) and bacterial (e.g., Corynebacterium diphtheria , Streptococcus pyogenes ) taxa, with predicted V3 amplicon lengths ranging from 150–194 bp when queried against the SILVA SSU 111 16S rRNA database ( d ). By contrast, the V4 region is relatively length invariant ( e–h ), ranging from 290–295 bp ( h ). 16S rRNA secondary structure has been adapted from Comparative RNA Web Site and Project 78 .
    16s Rrna Gene V3 Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche 454 gs flx titanium system pyrosequencer
    Simplified <t>16S</t> small subunit ribosomal RNA secondary structure. Secondary structure of Escherichia coli (J01695) 16S <t>rRNA</t> (main panel). Amplicon targets (primer inclusive) for the third (V3, 341F/529R) and fourth (V4, 515F/806R) variable regions are highlighted in pink and blue, respectively. Overlapping V3/V4 target sequences are highlighted in purple. Although widely used in ecological studies, the V4 region is impractical for aDNA research because of its long length (approx. 292 bp, primer inclusive). The V3 region is considerably shorter, but comparative sequence analysis ( a–d ) reveals that the V3 region exhibits extensive length polymorphisms (arrows) in archaeal (e.g., Methanobrevibacter oralis ) and bacterial (e.g., Corynebacterium diphtheria , Streptococcus pyogenes ) taxa, with predicted V3 amplicon lengths ranging from 150–194 bp when queried against the SILVA SSU 111 16S rRNA database ( d ). By contrast, the V4 region is relatively length invariant ( e–h ), ranging from 290–295 bp ( h ). 16S rRNA secondary structure has been adapted from Comparative RNA Web Site and Project 78 .
    454 Gs Flx Titanium System Pyrosequencer, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche gs amplicon variant analyzer pipeline
    Simplified <t>16S</t> small subunit ribosomal RNA secondary structure. Secondary structure of Escherichia coli (J01695) 16S <t>rRNA</t> (main panel). Amplicon targets (primer inclusive) for the third (V3, 341F/529R) and fourth (V4, 515F/806R) variable regions are highlighted in pink and blue, respectively. Overlapping V3/V4 target sequences are highlighted in purple. Although widely used in ecological studies, the V4 region is impractical for aDNA research because of its long length (approx. 292 bp, primer inclusive). The V3 region is considerably shorter, but comparative sequence analysis ( a–d ) reveals that the V3 region exhibits extensive length polymorphisms (arrows) in archaeal (e.g., Methanobrevibacter oralis ) and bacterial (e.g., Corynebacterium diphtheria , Streptococcus pyogenes ) taxa, with predicted V3 amplicon lengths ranging from 150–194 bp when queried against the SILVA SSU 111 16S rRNA database ( d ). By contrast, the V4 region is relatively length invariant ( e–h ), ranging from 290–295 bp ( h ). 16S rRNA secondary structure has been adapted from Comparative RNA Web Site and Project 78 .
    Gs Amplicon Variant Analyzer Pipeline, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseqcustom amplicon
    Simplified <t>16S</t> small subunit ribosomal RNA secondary structure. Secondary structure of Escherichia coli (J01695) 16S <t>rRNA</t> (main panel). Amplicon targets (primer inclusive) for the third (V3, 341F/529R) and fourth (V4, 515F/806R) variable regions are highlighted in pink and blue, respectively. Overlapping V3/V4 target sequences are highlighted in purple. Although widely used in ecological studies, the V4 region is impractical for aDNA research because of its long length (approx. 292 bp, primer inclusive). The V3 region is considerably shorter, but comparative sequence analysis ( a–d ) reveals that the V3 region exhibits extensive length polymorphisms (arrows) in archaeal (e.g., Methanobrevibacter oralis ) and bacterial (e.g., Corynebacterium diphtheria , Streptococcus pyogenes ) taxa, with predicted V3 amplicon lengths ranging from 150–194 bp when queried against the SILVA SSU 111 16S rRNA database ( d ). By contrast, the V4 region is relatively length invariant ( e–h ), ranging from 290–295 bp ( h ). 16S rRNA secondary structure has been adapted from Comparative RNA Web Site and Project 78 .
    Truseqcustom Amplicon, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc 16s rrna gene
    Simplified <t>16S</t> small subunit ribosomal RNA secondary structure. Secondary structure of Escherichia coli (J01695) 16S <t>rRNA</t> (main panel). Amplicon targets (primer inclusive) for the third (V3, 341F/529R) and fourth (V4, 515F/806R) variable regions are highlighted in pink and blue, respectively. Overlapping V3/V4 target sequences are highlighted in purple. Although widely used in ecological studies, the V4 region is impractical for aDNA research because of its long length (approx. 292 bp, primer inclusive). The V3 region is considerably shorter, but comparative sequence analysis ( a–d ) reveals that the V3 region exhibits extensive length polymorphisms (arrows) in archaeal (e.g., Methanobrevibacter oralis ) and bacterial (e.g., Corynebacterium diphtheria , Streptococcus pyogenes ) taxa, with predicted V3 amplicon lengths ranging from 150–194 bp when queried against the SILVA SSU 111 16S rRNA database ( d ). By contrast, the V4 region is relatively length invariant ( e–h ), ranging from 290–295 bp ( h ). 16S rRNA secondary structure has been adapted from Comparative RNA Web Site and Project 78 .
    16s Rrna Gene, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 7249 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche 454 genome sequencers gs flx
    Simplified <t>16S</t> small subunit ribosomal RNA secondary structure. Secondary structure of Escherichia coli (J01695) 16S <t>rRNA</t> (main panel). Amplicon targets (primer inclusive) for the third (V3, 341F/529R) and fourth (V4, 515F/806R) variable regions are highlighted in pink and blue, respectively. Overlapping V3/V4 target sequences are highlighted in purple. Although widely used in ecological studies, the V4 region is impractical for aDNA research because of its long length (approx. 292 bp, primer inclusive). The V3 region is considerably shorter, but comparative sequence analysis ( a–d ) reveals that the V3 region exhibits extensive length polymorphisms (arrows) in archaeal (e.g., Methanobrevibacter oralis ) and bacterial (e.g., Corynebacterium diphtheria , Streptococcus pyogenes ) taxa, with predicted V3 amplicon lengths ranging from 150–194 bp when queried against the SILVA SSU 111 16S rRNA database ( d ). By contrast, the V4 region is relatively length invariant ( e–h ), ranging from 290–295 bp ( h ). 16S rRNA secondary structure has been adapted from Comparative RNA Web Site and Project 78 .
    454 Genome Sequencers Gs Flx, supplied by Roche, used in various techniques. Bioz Stars score: 89/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Results from Sanger sequencing and/or deep amplicon sequencing with NexteraXT library of the balanced chromosomal aberrations (BCAs) breakpoints. The figure for every patient includes: in the upper part, a schematically shown normal chromosome and below a chromosome containing the BCAs. Arrows indicate the orientation of the genes affected by translocation. The length of the arrows approximately corresponds to the length of the disrupted coding sequences. The lower part shows the sequencing results. For every BCA, both breakpoints are shown. In deep amplicon sequencing results, only split reads are shown (reads that present the exact structure of the breakpoint). One part of these reads fully maps to the reference genome, while the other part differs from the reference. In Proband 2 an inframe fusion gene might be created.

    Journal: Journal of Clinical Medicine

    Article Title: Breakpoint Mapping of Symptomatic Balanced Translocations Links the EPHA6, KLF13 and UBR3 Genes to Novel Disease Phenotype

    doi: 10.3390/jcm9051245

    Figure Lengend Snippet: Results from Sanger sequencing and/or deep amplicon sequencing with NexteraXT library of the balanced chromosomal aberrations (BCAs) breakpoints. The figure for every patient includes: in the upper part, a schematically shown normal chromosome and below a chromosome containing the BCAs. Arrows indicate the orientation of the genes affected by translocation. The length of the arrows approximately corresponds to the length of the disrupted coding sequences. The lower part shows the sequencing results. For every BCA, both breakpoints are shown. In deep amplicon sequencing results, only split reads are shown (reads that present the exact structure of the breakpoint). One part of these reads fully maps to the reference genome, while the other part differs from the reference. In Proband 2 an inframe fusion gene might be created.

    Article Snippet: The exact structure of the BCTs was verified by Sanger sequencing or deep amplicon sequencing (Nextera XT DNA Preparation Kit (Illumina), sequenced on Illumina Hiseq 1500 (2 × 100 bp).

    Techniques: Sequencing, Amplification, Translocation Assay

    Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows 16S rRNA gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).

    Journal: PLoS ONE

    Article Title: Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes

    doi: 10.1371/journal.pone.0134848

    Figure Lengend Snippet: Quantitative evaluations. of controlled cleanroom (CCR) and uncontrolled adjoining facility (UAF) per square meter floor surface. Upper panel shows ATP counts for total (grey bars) and intracellular ATP (black bars) in CCR and UAF (total and intracellular ATP was determined in duplicate). Lower panel shows 16S rRNA gene copies in CCR and UAF with (black bars)–and without (grey bars) PMA (propidium monoazide) treatment in triplicate (error bars represent positive and negative standard deviations).

    Article Snippet: Consequently, this study has been focused on the potential viable microbiome and its origin by a combination of the DNA masking agent PMA assay [ , ] with Illumina 16S rRNA gene amplicon deep sequencing and qPCR analysis.

    Techniques:

    Frequency and relative expression of KIR genes in the rhesus macaque cohort . A) Y-axis indicates the percentage of animals within the cohort (n = 69) that express the indicated KIR gene. Genes not listed were not present in any animal within our cohort. Mamu-KIR2DL04 was excluded since it is not amplified by our pyrosequencing amplicon. B) Graph illustrates the percent of total pyrosequencing reads per animal (n = 61) for each KIR gene. Averages and SEM are represented by error bars. Each animal included had at least 100 sequencing reads. Genotyping results representing less than 1% of total reads in an animal were excluded to mitigate the influence of PCR artifacts. Ambiguous reads matching more than one KIR gene and splice variants were also excluded.

    Journal: BMC Genomics

    Article Title: Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques

    doi: 10.1186/1471-2164-12-295

    Figure Lengend Snippet: Frequency and relative expression of KIR genes in the rhesus macaque cohort . A) Y-axis indicates the percentage of animals within the cohort (n = 69) that express the indicated KIR gene. Genes not listed were not present in any animal within our cohort. Mamu-KIR2DL04 was excluded since it is not amplified by our pyrosequencing amplicon. B) Graph illustrates the percent of total pyrosequencing reads per animal (n = 61) for each KIR gene. Averages and SEM are represented by error bars. Each animal included had at least 100 sequencing reads. Genotyping results representing less than 1% of total reads in an animal were excluded to mitigate the influence of PCR artifacts. Ambiguous reads matching more than one KIR gene and splice variants were also excluded.

    Article Snippet: Emulsion PCR, Roche/454 Titanium amplicon pyrosequencing, image processing, and base calling were performed according to the manufacturer's instructions (Roche/454 Life Sciences, Branford, CT) at the University of Illinois at Urbana-Champaign High-Throughput Sequencing Center.

    Techniques: Expressing, Amplification, Sequencing, Polymerase Chain Reaction

    Novel rhesus macaque KIR haplotypes . KIR genes are indicated along the top axis. The identity of the allele is indicated within the schematic boxes if it was determined. Because data were generated from cDNA expression, only expressed KIRs are shown, and the physical map of gene order is arbitrary. Brackets indicate gene duplication. Since Mamu-KIR2DL04 cannot be amplified by our pyrosequencing amplicon, dotted boxes indicate haplotypes in which a false negative typing for this locus is possible.

    Journal: BMC Genomics

    Article Title: Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques

    doi: 10.1186/1471-2164-12-295

    Figure Lengend Snippet: Novel rhesus macaque KIR haplotypes . KIR genes are indicated along the top axis. The identity of the allele is indicated within the schematic boxes if it was determined. Because data were generated from cDNA expression, only expressed KIRs are shown, and the physical map of gene order is arbitrary. Brackets indicate gene duplication. Since Mamu-KIR2DL04 cannot be amplified by our pyrosequencing amplicon, dotted boxes indicate haplotypes in which a false negative typing for this locus is possible.

    Article Snippet: Emulsion PCR, Roche/454 Titanium amplicon pyrosequencing, image processing, and base calling were performed according to the manufacturer's instructions (Roche/454 Life Sciences, Branford, CT) at the University of Illinois at Urbana-Champaign High-Throughput Sequencing Center.

    Techniques: Generated, Expressing, Amplification

    Simplified 16S small subunit ribosomal RNA secondary structure. Secondary structure of Escherichia coli (J01695) 16S rRNA (main panel). Amplicon targets (primer inclusive) for the third (V3, 341F/529R) and fourth (V4, 515F/806R) variable regions are highlighted in pink and blue, respectively. Overlapping V3/V4 target sequences are highlighted in purple. Although widely used in ecological studies, the V4 region is impractical for aDNA research because of its long length (approx. 292 bp, primer inclusive). The V3 region is considerably shorter, but comparative sequence analysis ( a–d ) reveals that the V3 region exhibits extensive length polymorphisms (arrows) in archaeal (e.g., Methanobrevibacter oralis ) and bacterial (e.g., Corynebacterium diphtheria , Streptococcus pyogenes ) taxa, with predicted V3 amplicon lengths ranging from 150–194 bp when queried against the SILVA SSU 111 16S rRNA database ( d ). By contrast, the V4 region is relatively length invariant ( e–h ), ranging from 290–295 bp ( h ). 16S rRNA secondary structure has been adapted from Comparative RNA Web Site and Project 78 .

    Journal: Scientific Reports

    Article Title: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

    doi: 10.1038/srep16498

    Figure Lengend Snippet: Simplified 16S small subunit ribosomal RNA secondary structure. Secondary structure of Escherichia coli (J01695) 16S rRNA (main panel). Amplicon targets (primer inclusive) for the third (V3, 341F/529R) and fourth (V4, 515F/806R) variable regions are highlighted in pink and blue, respectively. Overlapping V3/V4 target sequences are highlighted in purple. Although widely used in ecological studies, the V4 region is impractical for aDNA research because of its long length (approx. 292 bp, primer inclusive). The V3 region is considerably shorter, but comparative sequence analysis ( a–d ) reveals that the V3 region exhibits extensive length polymorphisms (arrows) in archaeal (e.g., Methanobrevibacter oralis ) and bacterial (e.g., Corynebacterium diphtheria , Streptococcus pyogenes ) taxa, with predicted V3 amplicon lengths ranging from 150–194 bp when queried against the SILVA SSU 111 16S rRNA database ( d ). By contrast, the V4 region is relatively length invariant ( e–h ), ranging from 290–295 bp ( h ). 16S rRNA secondary structure has been adapted from Comparative RNA Web Site and Project 78 .

    Article Snippet: Following deep sequencing of 16S rRNA gene V3 amplicons on an Illumina MiSeq platform, we assigned sequences to Operational Taxonomic Units (OTUs) at 97% similarity using the closed-reference OTU protocol implemented in QIIME , and the Greengenes 13.8 database as a reference (see Methods).

    Techniques: Amplification, Sequencing

    Length distribution box plots of aDNA extracted from archaeological dental calculus and calculated V3 and V4 16S rRNA amplicon lengths for microbes in the SILVA SSU 111 database. As expected for aDNA, the genetic material within dental calculus is highly fragmented to median lengths

    Journal: Scientific Reports

    Article Title: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

    doi: 10.1038/srep16498

    Figure Lengend Snippet: Length distribution box plots of aDNA extracted from archaeological dental calculus and calculated V3 and V4 16S rRNA amplicon lengths for microbes in the SILVA SSU 111 database. As expected for aDNA, the genetic material within dental calculus is highly fragmented to median lengths

    Article Snippet: Following deep sequencing of 16S rRNA gene V3 amplicons on an Illumina MiSeq platform, we assigned sequences to Operational Taxonomic Units (OTUs) at 97% similarity using the closed-reference OTU protocol implemented in QIIME , and the Greengenes 13.8 database as a reference (see Methods).

    Techniques: Amplification

    Fold changes in taxon frequency between 16S rRNA V3 U341F/534R amplicon and shotgun metagenome data. Genera with relatively short median amplicon lengths ( Methanobrevibacter , Anaerolineae G-1 , TM7) are overrepresented in the 16S rRNA V3 U341F/534R amplicon dataset, while genera with relatively long median amplicon lengths ( Treponema , Neisseria ) are strongly underrepresented.

    Journal: Scientific Reports

    Article Title: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

    doi: 10.1038/srep16498

    Figure Lengend Snippet: Fold changes in taxon frequency between 16S rRNA V3 U341F/534R amplicon and shotgun metagenome data. Genera with relatively short median amplicon lengths ( Methanobrevibacter , Anaerolineae G-1 , TM7) are overrepresented in the 16S rRNA V3 U341F/534R amplicon dataset, while genera with relatively long median amplicon lengths ( Treponema , Neisseria ) are strongly underrepresented.

    Article Snippet: Following deep sequencing of 16S rRNA gene V3 amplicons on an Illumina MiSeq platform, we assigned sequences to Operational Taxonomic Units (OTUs) at 97% similarity using the closed-reference OTU protocol implemented in QIIME , and the Greengenes 13.8 database as a reference (see Methods).

    Techniques: Amplification

    Heatmap of 16S rRNA V3 amplicon lengths reveals high variability but broad taxonomic patterns. ( a ) 16S rRNA V3 sequence data was analyzed in silico for 36,634 OTUs belonging to 31 representative oral microbiome genera from 9 major microbial phyla: Euryarchaeota (yellow), TM7 (orange), Chlorflexi (red), Actinobacteria (green), Fi rmicutes (blue), Fusobacteria (purple), Bacteroidetes (gray), Proteobacteria (pink), Spirochaetes (brown). ( b ) Log fold changes in genus frequency within archaeological dental calculus when comparing data generated by targeted V3 U341F/534R amplicon sequencing to non-targeted shotgun metagenomics data. Methanobrevibacter , Anaerolinea , and TM7, which have very short predicted V3 U341F/534R amplicon lengths, strongly overamplify compared to frequency data obtained from non-targeted shotgun metagenomic sequencing. Most other taxa underamplify, especially genera with very long predicted V3 U341F/534R amplicon lengths, such as Treponema and members of Proteobacteria, and Bacteroidetes.

    Journal: Scientific Reports

    Article Title: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

    doi: 10.1038/srep16498

    Figure Lengend Snippet: Heatmap of 16S rRNA V3 amplicon lengths reveals high variability but broad taxonomic patterns. ( a ) 16S rRNA V3 sequence data was analyzed in silico for 36,634 OTUs belonging to 31 representative oral microbiome genera from 9 major microbial phyla: Euryarchaeota (yellow), TM7 (orange), Chlorflexi (red), Actinobacteria (green), Fi rmicutes (blue), Fusobacteria (purple), Bacteroidetes (gray), Proteobacteria (pink), Spirochaetes (brown). ( b ) Log fold changes in genus frequency within archaeological dental calculus when comparing data generated by targeted V3 U341F/534R amplicon sequencing to non-targeted shotgun metagenomics data. Methanobrevibacter , Anaerolinea , and TM7, which have very short predicted V3 U341F/534R amplicon lengths, strongly overamplify compared to frequency data obtained from non-targeted shotgun metagenomic sequencing. Most other taxa underamplify, especially genera with very long predicted V3 U341F/534R amplicon lengths, such as Treponema and members of Proteobacteria, and Bacteroidetes.

    Article Snippet: Following deep sequencing of 16S rRNA gene V3 amplicons on an Illumina MiSeq platform, we assigned sequences to Operational Taxonomic Units (OTUs) at 97% similarity using the closed-reference OTU protocol implemented in QIIME , and the Greengenes 13.8 database as a reference (see Methods).

    Techniques: Amplification, Sequencing, In Silico, Generated

    Unusual microbiome profiles observed in 16S rRNA gene V3 amplicon data from archaeological dental calculus. Relative abundance charts summarizing: ( a ) Frequency of oral-associated genera in dental calculus and control samples. The Dutch, UK, Nepalese, and Spanish calculus samples show a greater proportion of oral-associated genera compared to the St. Helena and pre-Columbian Caribbean samples. ( b ) Contribution of oral, gut, and environmental sources to microbiome composition estimated by Bayesian source tracking. The oral microbiome (saliva, supragingival plaque, subgingival plaque) is a major source ( > 50%) in only a small proportion of archaeological dental calculus samples (10%), and an oral source is not indicated for more than a quarter of samples (26%). Laboratory controls (osteologist hands and osteology lab bench surfaces) and extraction blanks are largely consistent with a skin microbiome source and unassigned contaminants. ( c ) Frequency of microbial phyla inferred from V3 amplicon sequencing. The taxonomic profile reveals an unusual and non-biological pattern of exceptionally high Euryarchaeota levels in the Dutch, UK, and some Caribbean dental calculus samples. All Euryarchaeota OTUs are assigned to the genus Methanobrevibacter , the only prevalent genus of Archaea in the oral cavity. Methanobrevibacter is typically found at low frequencies (

    Journal: Scientific Reports

    Article Title: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

    doi: 10.1038/srep16498

    Figure Lengend Snippet: Unusual microbiome profiles observed in 16S rRNA gene V3 amplicon data from archaeological dental calculus. Relative abundance charts summarizing: ( a ) Frequency of oral-associated genera in dental calculus and control samples. The Dutch, UK, Nepalese, and Spanish calculus samples show a greater proportion of oral-associated genera compared to the St. Helena and pre-Columbian Caribbean samples. ( b ) Contribution of oral, gut, and environmental sources to microbiome composition estimated by Bayesian source tracking. The oral microbiome (saliva, supragingival plaque, subgingival plaque) is a major source ( > 50%) in only a small proportion of archaeological dental calculus samples (10%), and an oral source is not indicated for more than a quarter of samples (26%). Laboratory controls (osteologist hands and osteology lab bench surfaces) and extraction blanks are largely consistent with a skin microbiome source and unassigned contaminants. ( c ) Frequency of microbial phyla inferred from V3 amplicon sequencing. The taxonomic profile reveals an unusual and non-biological pattern of exceptionally high Euryarchaeota levels in the Dutch, UK, and some Caribbean dental calculus samples. All Euryarchaeota OTUs are assigned to the genus Methanobrevibacter , the only prevalent genus of Archaea in the oral cavity. Methanobrevibacter is typically found at low frequencies (

    Article Snippet: Following deep sequencing of 16S rRNA gene V3 amplicons on an Illumina MiSeq platform, we assigned sequences to Operational Taxonomic Units (OTUs) at 97% similarity using the closed-reference OTU protocol implemented in QIIME , and the Greengenes 13.8 database as a reference (see Methods).

    Techniques: Amplification, Sequencing