illumina genome analyzer Search Results


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  • 99
    Illumina Inc illumina genome analyzer
    PB calling card-seq. When PB transposase is fused to a DNA-binding protein, it causes PB to integrate into the genome near the binding sites for that transcription factor (TF). After PB transposition, cells that have undergone PB transposition are selected, their genomic DNA is harvested and cleaved with restriction enzymes that cut near the end of the transposon, and the resulting fragments are ligated in dilute solution to favor their circularization. The genomic DNA flanking the end of the transposon is then amplified in an inverse PCR (PCR primers contain the <t>Illumina</t> sequencing primers and adaptors). The identity of the inverse-PCR products is then determined by Illumina sequencing. The Illumina sequences are then aligned to the human genome to identify the location of the PB insertions.
    Illumina Genome Analyzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 8889 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 8889 article reviews
    Price from $9.99 to $1999.99
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    86
    Solexa illumina genome analyzer
    Two PhiX samples run on <t>Illumina</t> Genome Analyzer II: Proportion of reads containing mismatches by starting position. For a few positions, almost 100% of the reads covering them do not match the reference genome, substantially inflating the error rate estimates given by mismatch-counting. The widths of the bars reaching almost 1 (100%) and containing 1 mismatch are 36 bases, which is the read length for the PhiX samples.
    Illumina Genome Analyzer, supplied by Solexa, used in various techniques. Bioz Stars score: 86/100, based on 114 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    ATLAS Biolabs GmbH illumina genome analyzer
    Two PhiX samples run on <t>Illumina</t> Genome Analyzer II: Proportion of reads containing mismatches by starting position. For a few positions, almost 100% of the reads covering them do not match the reference genome, substantially inflating the error rate estimates given by mismatch-counting. The widths of the bars reaching almost 1 (100%) and containing 1 mismatch are 36 bases, which is the read length for the PhiX samples.
    Illumina Genome Analyzer, supplied by ATLAS Biolabs GmbH, used in various techniques. Bioz Stars score: 92/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 92 stars, based on 3 article reviews
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    91
    BGI Shenzhen illumina genome analyzer
    Two PhiX samples run on <t>Illumina</t> Genome Analyzer II: Proportion of reads containing mismatches by starting position. For a few positions, almost 100% of the reads covering them do not match the reference genome, substantially inflating the error rate estimates given by mismatch-counting. The widths of the bars reaching almost 1 (100%) and containing 1 mismatch are 36 bases, which is the read length for the PhiX samples.
    Illumina Genome Analyzer, supplied by BGI Shenzhen, used in various techniques. Bioz Stars score: 91/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Agilent technologies illumina genome analyzer
    The validation of the NGS data. ( A ) Validation by pyrosequencing. Data points for 12 CpG sites (located in genomic intervals chr9:137 249 931–137 249 946, chr19:16 045 054–16 045 121 and chr16:87 875 316–87 875 361) in samples 1, 2, 3 and 4 are shown on a single plot. ( B ) Validation by <t>Illumina</t> 450 K BeadChip assay. Data points for 1880 CpG sites in samples 2, 3 and 4 are shown on a single plot.
    Illumina Genome Analyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 87/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Novogene illumina genome analyzer
    The validation of the NGS data. ( A ) Validation by pyrosequencing. Data points for 12 CpG sites (located in genomic intervals chr9:137 249 931–137 249 946, chr19:16 045 054–16 045 121 and chr16:87 875 316–87 875 361) in samples 1, 2, 3 and 4 are shown on a single plot. ( B ) Validation by <t>Illumina</t> 450 K BeadChip assay. Data points for 1880 CpG sites in samples 2, 3 and 4 are shown on a single plot.
    Illumina Genome Analyzer, supplied by Novogene, used in various techniques. Bioz Stars score: 95/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Kapa Biosystems illumina genome analyzer
    The validation of the NGS data. ( A ) Validation by pyrosequencing. Data points for 12 CpG sites (located in genomic intervals chr9:137 249 931–137 249 946, chr19:16 045 054–16 045 121 and chr16:87 875 316–87 875 361) in samples 1, 2, 3 and 4 are shown on a single plot. ( B ) Validation by <t>Illumina</t> 450 K BeadChip assay. Data points for 1880 CpG sites in samples 2, 3 and 4 are shown on a single plot.
    Illumina Genome Analyzer, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 90/100, based on 36 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Beckman Coulter illumina genome analyzer
    The validation of the NGS data. ( A ) Validation by pyrosequencing. Data points for 12 CpG sites (located in genomic intervals chr9:137 249 931–137 249 946, chr19:16 045 054–16 045 121 and chr16:87 875 316–87 875 361) in samples 1, 2, 3 and 4 are shown on a single plot. ( B ) Validation by <t>Illumina</t> 450 K BeadChip assay. Data points for 1880 CpG sites in samples 2, 3 and 4 are shown on a single plot.
    Illumina Genome Analyzer, supplied by Beckman Coulter, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Fasteris Life illumina genome analyzer
    The validation of the NGS data. ( A ) Validation by pyrosequencing. Data points for 12 CpG sites (located in genomic intervals chr9:137 249 931–137 249 946, chr19:16 045 054–16 045 121 and chr16:87 875 316–87 875 361) in samples 1, 2, 3 and 4 are shown on a single plot. ( B ) Validation by <t>Illumina</t> 450 K BeadChip assay. Data points for 1880 CpG sites in samples 2, 3 and 4 are shown on a single plot.
    Illumina Genome Analyzer, supplied by Fasteris Life, used in various techniques. Bioz Stars score: 86/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    illumina genome analyzer - by Bioz Stars, 2020-04
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    87
    Illumina Inc illummina genome analyzer
    The validation of the NGS data. ( A ) Validation by pyrosequencing. Data points for 12 CpG sites (located in genomic intervals chr9:137 249 931–137 249 946, chr19:16 045 054–16 045 121 and chr16:87 875 316–87 875 361) in samples 1, 2, 3 and 4 are shown on a single plot. ( B ) Validation by <t>Illumina</t> 450 K BeadChip assay. Data points for 1880 CpG sites in samples 2, 3 and 4 are shown on a single plot.
    Illummina Genome Analyzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 87/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 87 stars, based on 11 article reviews
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    91
    Illumina Inc illumina genome analyser
    Data interpretation pipeline. Example of DNA-seq Bioinformatics Pipeline for <t>Illumina</t> ® . 1 This steps removes duplicate sequences using the Picard program; 2 GATK: Genome Analysis ToolKit.
    Illumina Genome Analyser, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 463 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Fasteris Life illumina genome analyser
    Data interpretation pipeline. Example of DNA-seq Bioinformatics Pipeline for <t>Illumina</t> ® . 1 This steps removes duplicate sequences using the Picard program; 2 GATK: Genome Analysis ToolKit.
    Illumina Genome Analyser, supplied by Fasteris Life, 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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    92
    Solexa illumina genome analyser
    Data interpretation pipeline. Example of DNA-seq Bioinformatics Pipeline for <t>Illumina</t> ® . 1 This steps removes duplicate sequences using the Picard program; 2 GATK: Genome Analysis ToolKit.
    Illumina Genome Analyser, supplied by Solexa, used in various techniques. Bioz Stars score: 92/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Solexa illumina genome analyzer solexa
    Data interpretation pipeline. Example of DNA-seq Bioinformatics Pipeline for <t>Illumina</t> ® . 1 This steps removes duplicate sequences using the Picard program; 2 GATK: Genome Analysis ToolKit.
    Illumina Genome Analyzer Solexa, supplied by Solexa, used in various techniques. Bioz Stars score: 86/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc illumina solexa genome analyzer
    The differentially expressed genes upon V.parahaemolyticus infection. By using <t>Solexa/Illumina's</t> DGE platform, 1213 differentially expressed genes were detected in comparative analysis of the expression profiles between V.parahaemolyticus -infected crabs and control crabs, including 538 up-regulated genes and 675 down-regulated genes ( P
    Illumina Solexa Genome Analyzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher illumina solexa genome analyzer
    The differentially expressed genes upon V.parahaemolyticus infection. By using <t>Solexa/Illumina's</t> DGE platform, 1213 differentially expressed genes were detected in comparative analysis of the expression profiles between V.parahaemolyticus -infected crabs and control crabs, including 538 up-regulated genes and 675 down-regulated genes ( P
    Illumina Solexa Genome Analyzer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    LC Sciences solexa illumina genome analyzer
    The differentially expressed genes upon V.parahaemolyticus infection. By using <t>Solexa/Illumina's</t> DGE platform, 1213 differentially expressed genes were detected in comparative analysis of the expression profiles between V.parahaemolyticus -infected crabs and control crabs, including 538 up-regulated genes and 675 down-regulated genes ( P
    Solexa Illumina Genome Analyzer, supplied by LC Sciences, used in various techniques. Bioz Stars score: 86/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Roche illumina s genome analyzer
    The differentially expressed genes upon V.parahaemolyticus infection. By using <t>Solexa/Illumina's</t> DGE platform, 1213 differentially expressed genes were detected in comparative analysis of the expression profiles between V.parahaemolyticus -infected crabs and control crabs, including 538 up-regulated genes and 675 down-regulated genes ( P
    Illumina S Genome Analyzer, supplied by Roche, used in various techniques. Bioz Stars score: 87/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    LC Sciences solaxa illumina genome analyzer
    The differentially expressed genes upon V.parahaemolyticus infection. By using <t>Solexa/Illumina's</t> DGE platform, 1213 differentially expressed genes were detected in comparative analysis of the expression profiles between V.parahaemolyticus -infected crabs and control crabs, including 538 up-regulated genes and 675 down-regulated genes ( P
    Solaxa Illumina Genome Analyzer, supplied by LC Sciences, used in various techniques. Bioz Stars score: 87/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Illumina Inc illumina s genome analyzer
    Observed distribution of coverage of <t>Illumina's</t> Genome Analyzer-2 with a mean coverage over a 4-Mbp region of C. elegans . The distribution best fits a Gamma distribution Γ(α,β) with shape parameters α = 6.3 and . A Poisson
    Illumina S Genome Analyzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 122 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    GeneWorks illumina genome analyzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Illumina Genome Analyzer, supplied by GeneWorks, used in various techniques. Bioz Stars score: 86/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Beijing Genomics Institute Shenzhen illumina genome analyzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Illumina Genome Analyzer, supplied by Beijing Genomics Institute Shenzhen, used in various techniques. Bioz Stars score: 87/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Adaptive Biotechnologies Corp illumina genome analyzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Illumina Genome Analyzer, supplied by Adaptive Biotechnologies Corp, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Thermo Fisher illumina genome analyzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Illumina Genome Analyzer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Sangon Biotech illumina genome analyzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Illumina Genome Analyzer, supplied by Sangon Biotech, 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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    91
    CapitalBio Corporation illumina genome analyzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Illumina Genome Analyzer, supplied by CapitalBio Corporation, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Illumina Inc illumina genome analayzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Illumina Genome Analayzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Illumina Inc genome analyzer gaii technology illumina
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Genome Analyzer Gaii Technology Illumina, supplied by Illumina Inc, 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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    93
    Solexa illumina solexa genome analyzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Illumina Solexa Genome Analyzer, supplied by Solexa, used in various techniques. Bioz Stars score: 93/100, based on 309 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc genome analyzer illumina platform
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Genome Analyzer Illumina Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc 1g illumina genome analyzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    1g Illumina Genome Analyzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 53 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Illumina Inc single illumina genome analyzer
    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an <t>Illumina</t> GA data set and (b) an Illumina HiSeq data set.
    Single Illumina Genome Analyzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    PB calling card-seq. When PB transposase is fused to a DNA-binding protein, it causes PB to integrate into the genome near the binding sites for that transcription factor (TF). After PB transposition, cells that have undergone PB transposition are selected, their genomic DNA is harvested and cleaved with restriction enzymes that cut near the end of the transposon, and the resulting fragments are ligated in dilute solution to favor their circularization. The genomic DNA flanking the end of the transposon is then amplified in an inverse PCR (PCR primers contain the Illumina sequencing primers and adaptors). The identity of the inverse-PCR products is then determined by Illumina sequencing. The Illumina sequences are then aligned to the human genome to identify the location of the PB insertions.

    Journal: Genetics

    Article Title: "Calling Cards" for DNA-Binding Proteins in Mammalian Cells

    doi: 10.1534/genetics.111.137315

    Figure Lengend Snippet: PB calling card-seq. When PB transposase is fused to a DNA-binding protein, it causes PB to integrate into the genome near the binding sites for that transcription factor (TF). After PB transposition, cells that have undergone PB transposition are selected, their genomic DNA is harvested and cleaved with restriction enzymes that cut near the end of the transposon, and the resulting fragments are ligated in dilute solution to favor their circularization. The genomic DNA flanking the end of the transposon is then amplified in an inverse PCR (PCR primers contain the Illumina sequencing primers and adaptors). The identity of the inverse-PCR products is then determined by Illumina sequencing. The Illumina sequences are then aligned to the human genome to identify the location of the PB insertions.

    Article Snippet: We are especially grateful to Stefan Moisyadi (Hawaii University) for generously providing reagents and advice and to Jessica Hoisington-Lopez, Laura Langton, Brian Koebbe, and Jim Dover (Washington University) and the Washington University Genome Technology Access Center for their expert assistance with the use of Illumina Genome Analyzer.

    Techniques: Binding Assay, Amplification, Inverse PCR, Polymerase Chain Reaction, Sequencing

    (A) Illumina sequencing chemistry. A sequencing primer (red) is annealed to the template molecules linked to the flow cell surface. Next, DNA polymerase and a mixture of fluorescently labeled nucleotides are added to the flow cell. The nucleotides are modified with a cleavable terminator moiety such that only one nucleotide can be incorporated during each sequencing cycle. After nucleotide incorporation, the array is imaged and the fluorescent signals are recorded for each cluster. The terminator moiety and fluorescent label are cleaved off and removed, and fresh nucleotides and polymerase are added to begin the next sequencing cycle. ( B) Helicos sequencing chemistry. Template molecules modified by the addition of adenosines to the 3’ end are hybridized to poly-T oligonucleotides covalently linked to the surface of the flow cell. The template molecules are fluorescently labeled at the terminal 3’ adenosine so that the instrument can record the position of each template on the flow cell prior to the sequencing reaction. After the first image is acquired, the fluorescent label is removed and washed away. Next, DNA polymerase and one of four fluorescently labeled nucleotides (A, T, C or G) are introduced to the flow cell. Similar to the Illumina approach, the nucleotides are modified with terminator moieties to prevent multiple nucleotide additions during a single sequencing cycle. After nucleotide incorporation, the array is imaged and the fluorescent signals recorded. The fluorescent label and terminator moiety are removed, and the next cycle of sequencing commences with the next fluorescently labeled nucleotide.

    Journal: Genes

    Article Title: Next Generation DNA Sequencing and the Future of Genomic Medicine

    doi: 10.3390/genes1010038

    Figure Lengend Snippet: (A) Illumina sequencing chemistry. A sequencing primer (red) is annealed to the template molecules linked to the flow cell surface. Next, DNA polymerase and a mixture of fluorescently labeled nucleotides are added to the flow cell. The nucleotides are modified with a cleavable terminator moiety such that only one nucleotide can be incorporated during each sequencing cycle. After nucleotide incorporation, the array is imaged and the fluorescent signals are recorded for each cluster. The terminator moiety and fluorescent label are cleaved off and removed, and fresh nucleotides and polymerase are added to begin the next sequencing cycle. ( B) Helicos sequencing chemistry. Template molecules modified by the addition of adenosines to the 3’ end are hybridized to poly-T oligonucleotides covalently linked to the surface of the flow cell. The template molecules are fluorescently labeled at the terminal 3’ adenosine so that the instrument can record the position of each template on the flow cell prior to the sequencing reaction. After the first image is acquired, the fluorescent label is removed and washed away. Next, DNA polymerase and one of four fluorescently labeled nucleotides (A, T, C or G) are introduced to the flow cell. Similar to the Illumina approach, the nucleotides are modified with terminator moieties to prevent multiple nucleotide additions during a single sequencing cycle. After nucleotide incorporation, the array is imaged and the fluorescent signals recorded. The fluorescent label and terminator moiety are removed, and the next cycle of sequencing commences with the next fluorescently labeled nucleotide.

    Article Snippet: Illumina Genome Analyzer The Illumina Genome Analyzer differs from both the 454 and SOLiD systems in that the clonal amplification step takes place in situ on the surface of the flow cell itself rather than in a separate emulsion PCR reaction.

    Techniques: Sequencing, Flow Cytometry, Labeling, Modification

    Determination of genome-scale methylation states with MethylSeq/MetMap. Genomic DNA is digested with the methylation-sensitive restriction enzyme HpaII. Unmethylated HpaII sites (open circles) are digested and thus found at the ends of restriction fragments, while methylated HpaII sites (black circles) are not digested. Restriction fragments are size-selected according to the Illumina protocol; fragments that are either too long or too short are removed. Fragments that pass the size-selection are used to construct sequencing libraries. After sequencing, the raw reads are aligned against the reference genome and processed with MetMap to derive maps of genome-scale methylation.

    Journal: PLoS Computational Biology

    Article Title: MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations

    doi: 10.1371/journal.pcbi.1000888

    Figure Lengend Snippet: Determination of genome-scale methylation states with MethylSeq/MetMap. Genomic DNA is digested with the methylation-sensitive restriction enzyme HpaII. Unmethylated HpaII sites (open circles) are digested and thus found at the ends of restriction fragments, while methylated HpaII sites (black circles) are not digested. Restriction fragments are size-selected according to the Illumina protocol; fragments that are either too long or too short are removed. Fragments that pass the size-selection are used to construct sequencing libraries. After sequencing, the raw reads are aligned against the reference genome and processed with MetMap to derive maps of genome-scale methylation.

    Article Snippet: Libraries were sequenced on a first-generation Illumina Genome Analyzer and 32 base reads were generated.

    Techniques: Methylation, Methylation Sequencing, Selection, Construct, Sequencing

    Alignment of Illumina sequence reads for Igf2 transcript. The top panel is the summary window or all 1,253 cDNA reads that mapped to the 4,038 bp Igf2 transcript (NM_010514). The blue arrows represent the sense reads and the red arrows represent antisense reads. From the figure, most of the reads were aligned to the 1 kb region near the 3′-end of the transcript. The bottom left panel gives the Illumina read names, and the bottom right gives the sequence alignment. Sense reads are printed in black font and the antisense reads are in red font. There are many overlapping 32-bp reads aligned uniquely to the transcript, with a quality score for each nucleotide. There is a SNP (A/G) located in the middle. By directly counting the number of reference and alternative nucleotides at the SNP, we were able to quantify the relative expression level of the two parental alleles.

    Journal: PLoS ONE

    Article Title: Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

    doi: 10.1371/journal.pone.0003839

    Figure Lengend Snippet: Alignment of Illumina sequence reads for Igf2 transcript. The top panel is the summary window or all 1,253 cDNA reads that mapped to the 4,038 bp Igf2 transcript (NM_010514). The blue arrows represent the sense reads and the red arrows represent antisense reads. From the figure, most of the reads were aligned to the 1 kb region near the 3′-end of the transcript. The bottom left panel gives the Illumina read names, and the bottom right gives the sequence alignment. Sense reads are printed in black font and the antisense reads are in red font. There are many overlapping 32-bp reads aligned uniquely to the transcript, with a quality score for each nucleotide. There is a SNP (A/G) located in the middle. By directly counting the number of reference and alternative nucleotides at the SNP, we were able to quantify the relative expression level of the two parental alleles.

    Article Snippet: One Illumina Genome Analyzer run of each reciprocal F1 sample was run on the Illumina Genome Analyzer.

    Techniques: Sequencing, Expressing

    Verification for known imprinted gene Nnat (also known as Peg5 ). (A) Allele counts for Perlegen SNP NES08901860, NES08901861, NES08901863 and NES08901864. The blue bars (from left to right) represent the Illumina read counts from the paternal allele in PWD x AKR and AKR x PWD F1s respectively (maternal genotype listed first). The red bars represent the maternal allele Illumina read counts. (B) Sanger sequencing verification for Perlegen SNP NES08901861. We discovered an adjacent SNP position before NES08901861. The target sequence is GCCCT(AC/GA)ATCT. (C), Pyrosequencing verification for Perlegen SNP NES08901861. The target sequence is GCCCT(AC/GA)ATCT.

    Journal: PLoS ONE

    Article Title: Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

    doi: 10.1371/journal.pone.0003839

    Figure Lengend Snippet: Verification for known imprinted gene Nnat (also known as Peg5 ). (A) Allele counts for Perlegen SNP NES08901860, NES08901861, NES08901863 and NES08901864. The blue bars (from left to right) represent the Illumina read counts from the paternal allele in PWD x AKR and AKR x PWD F1s respectively (maternal genotype listed first). The red bars represent the maternal allele Illumina read counts. (B) Sanger sequencing verification for Perlegen SNP NES08901861. We discovered an adjacent SNP position before NES08901861. The target sequence is GCCCT(AC/GA)ATCT. (C), Pyrosequencing verification for Perlegen SNP NES08901861. The target sequence is GCCCT(AC/GA)ATCT.

    Article Snippet: One Illumina Genome Analyzer run of each reciprocal F1 sample was run on the Illumina Genome Analyzer.

    Techniques: Sequencing

    Sense-antisense gene pairs covered by the Illumina sequence data. Gene structures of the three gene pairs showing nested structures. The blue shading represents the paternal allele and the pink shading indicates for the maternal allele. Boxes with dashed lines indicate no expression. The arrows represent the direction of transcription. The sum of the heights of the two parental exons for each gene is in proportion to the expression level, which is quantified by the total counts of the perfect-match Illumina reads. The relative heights of the exons for the paternal and maternal allele within the same gene represent the relative expression level of the two parental alleles. The short vertical lines under the exons indicate the SNP positions, and the total counts of the two reciprocal crosses for the maternal and paternal allele are labeled.

    Journal: PLoS ONE

    Article Title: Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

    doi: 10.1371/journal.pone.0003839

    Figure Lengend Snippet: Sense-antisense gene pairs covered by the Illumina sequence data. Gene structures of the three gene pairs showing nested structures. The blue shading represents the paternal allele and the pink shading indicates for the maternal allele. Boxes with dashed lines indicate no expression. The arrows represent the direction of transcription. The sum of the heights of the two parental exons for each gene is in proportion to the expression level, which is quantified by the total counts of the perfect-match Illumina reads. The relative heights of the exons for the paternal and maternal allele within the same gene represent the relative expression level of the two parental alleles. The short vertical lines under the exons indicate the SNP positions, and the total counts of the two reciprocal crosses for the maternal and paternal allele are labeled.

    Article Snippet: One Illumina Genome Analyzer run of each reciprocal F1 sample was run on the Illumina Genome Analyzer.

    Techniques: Sequencing, Expressing, Labeling

    Chromosomal scans of imprinting status. (A) Imprinting status for chromosome 2. (B) Imprinting status for chromosome 7. Each plot contains unique Entrez genes covered by SNP-containing Illumina reads with counts no less than 4 in both reciprocal crosses. The height of each bar is the difference of the AKR percentage in the two reciprocal crosses (p1-p2), representing the intensity of imprinting. The color stands for the direction of imprinting, blue for paternal expression and red for maternal expression. The intensity of the color represents the significance, grey for not significant ( q -value ≥0.10), lighter blue and pink for marginally significant (0.05≤ q -value

    Journal: PLoS ONE

    Article Title: Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

    doi: 10.1371/journal.pone.0003839

    Figure Lengend Snippet: Chromosomal scans of imprinting status. (A) Imprinting status for chromosome 2. (B) Imprinting status for chromosome 7. Each plot contains unique Entrez genes covered by SNP-containing Illumina reads with counts no less than 4 in both reciprocal crosses. The height of each bar is the difference of the AKR percentage in the two reciprocal crosses (p1-p2), representing the intensity of imprinting. The color stands for the direction of imprinting, blue for paternal expression and red for maternal expression. The intensity of the color represents the significance, grey for not significant ( q -value ≥0.10), lighter blue and pink for marginally significant (0.05≤ q -value

    Article Snippet: One Illumina Genome Analyzer run of each reciprocal F1 sample was run on the Illumina Genome Analyzer.

    Techniques: Expressing

    Atad2 is involved in ES cell differentiation. ( A ) Both control ES cells (WT, expressing an inactive shRNA) and cells with reduced amounts of Atad2 (KD, stably expressing an active anti- Atad2 shRNA) were seeded in LIF-depleted media for 6 days. Extracts were prepared and the indicated proteins were visualized. ( B ) WT and KD ES cells were seeded, and cell growth was monitored as a function of time. ( C ) WT and KD ES cells were cultured in the differentiation medium, and the diameter of EBs was measured after 6 days of differentiation and presented as box plots. Forty-eight EBs were measured for each condition, and the P -value (Mann–Whitney) corresponding to size differences between the two cell populations is indicated. The corresponding values are presented in Supplementary Table S3 . Six representative EBs for each condition are shown. ( D ) Control ES cells and cells with reduced amounts of Atad2 were placed in the differentiation medium for 3 days. RNA was prepared and the transcriptome was revealed following hybridization on Illumina chip. The heatmaps show genes differentially expressed between control cells (ct) and cells with Atad2 knockdown (Sh Atad2). Illustrations of GSEA categories of genes whose expression is regulated by Atad2 knockdown are shown. ( E ) WT and KD ES cells were placed in LIF-depleted media for 7 days. Cells were harvested every day and RNA were prepared. The expression of the indicated genes, specific representatives of differentiation into the three germ layers, was monitored by RT-qPCR and normalized with respect to the expression of actin . The data shown are representative of two independent experiments. Standard deviations are shown.

    Journal: Journal of Molecular Cell Biology

    Article Title: Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells

    doi: 10.1093/jmcb/mjv060

    Figure Lengend Snippet: Atad2 is involved in ES cell differentiation. ( A ) Both control ES cells (WT, expressing an inactive shRNA) and cells with reduced amounts of Atad2 (KD, stably expressing an active anti- Atad2 shRNA) were seeded in LIF-depleted media for 6 days. Extracts were prepared and the indicated proteins were visualized. ( B ) WT and KD ES cells were seeded, and cell growth was monitored as a function of time. ( C ) WT and KD ES cells were cultured in the differentiation medium, and the diameter of EBs was measured after 6 days of differentiation and presented as box plots. Forty-eight EBs were measured for each condition, and the P -value (Mann–Whitney) corresponding to size differences between the two cell populations is indicated. The corresponding values are presented in Supplementary Table S3 . Six representative EBs for each condition are shown. ( D ) Control ES cells and cells with reduced amounts of Atad2 were placed in the differentiation medium for 3 days. RNA was prepared and the transcriptome was revealed following hybridization on Illumina chip. The heatmaps show genes differentially expressed between control cells (ct) and cells with Atad2 knockdown (Sh Atad2). Illustrations of GSEA categories of genes whose expression is regulated by Atad2 knockdown are shown. ( E ) WT and KD ES cells were placed in LIF-depleted media for 7 days. Cells were harvested every day and RNA were prepared. The expression of the indicated genes, specific representatives of differentiation into the three germ layers, was monitored by RT-qPCR and normalized with respect to the expression of actin . The data shown are representative of two independent experiments. Standard deviations are shown.

    Article Snippet: The purified DNA was size-selected at 150 base pairs and processed for sequencing onto a single Illumina genome analyzer channel using the procedures recommended by the manufacturer.

    Techniques: Cell Differentiation, Expressing, shRNA, Stable Transfection, Cell Culture, MANN-WHITNEY, Hybridization, Chromatin Immunoprecipitation, Quantitative RT-PCR

    Percentage of total and unique clean tags that are mapped to the reference Verticillium dahliae genome VDLs 17 in the non-germinated (A) and germinated (B) microsclerotium libraries in relation to the total number of tags. New unique tag (y axis) of VDMG-b and VDM libraries decreased as the Illumina sequencing increased (x axis).

    Journal: PLoS ONE

    Article Title: Whole Genome Wide Expression Profiles on Germination of Verticillium dahliae Microsclerotia

    doi: 10.1371/journal.pone.0100046

    Figure Lengend Snippet: Percentage of total and unique clean tags that are mapped to the reference Verticillium dahliae genome VDLs 17 in the non-germinated (A) and germinated (B) microsclerotium libraries in relation to the total number of tags. New unique tag (y axis) of VDMG-b and VDM libraries decreased as the Illumina sequencing increased (x axis).

    Article Snippet: Illumina sequencing Illumina Genome Analyzer platform (GA II) was used to perform a Serial Analysis of Gene Expression (SAGE)-derived Digital Gene Expression (DGE) analysis for the transcriptome of germinated and non-germinated V. dahliae microsclerotia (BGI, China).

    Techniques: Sequencing

    Correctly-mapped versus incorrectly-mapped simulated reads. Total correctly mapped versus incorrectly mapped reads, plotted for decreasing MAPQ, for 1 million simulated 100 nt paired-end Illumina reads (2 million total reads). Results for unpaired reads and for 250 nt reads are similar ( Supplementary Figures S1 – S8 ).

    Journal: PeerJ

    Article Title: Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

    doi: 10.7717/peerj.808

    Figure Lengend Snippet: Correctly-mapped versus incorrectly-mapped simulated reads. Total correctly mapped versus incorrectly mapped reads, plotted for decreasing MAPQ, for 1 million simulated 100 nt paired-end Illumina reads (2 million total reads). Results for unpaired reads and for 250 nt reads are similar ( Supplementary Figures S1 – S8 ).

    Article Snippet: For experiments with Illumina data, we used 100 nt paired-end Illumina Genome Analyzer data from the YanHuang genome ( ).

    Techniques:

    Two PhiX samples run on Illumina Genome Analyzer II: Proportion of reads containing mismatches by starting position. For a few positions, almost 100% of the reads covering them do not match the reference genome, substantially inflating the error rate estimates given by mismatch-counting. The widths of the bars reaching almost 1 (100%) and containing 1 mismatch are 36 bases, which is the read length for the PhiX samples.

    Journal: BMC Bioinformatics

    Article Title: Estimation of sequencing error rates in short reads

    doi: 10.1186/1471-2105-13-185

    Figure Lengend Snippet: Two PhiX samples run on Illumina Genome Analyzer II: Proportion of reads containing mismatches by starting position. For a few positions, almost 100% of the reads covering them do not match the reference genome, substantially inflating the error rate estimates given by mismatch-counting. The widths of the bars reaching almost 1 (100%) and containing 1 mismatch are 36 bases, which is the read length for the PhiX samples.

    Article Snippet: In the case of Illumina Genome Analyzer (Solexa), a sample corresponds to a lane in a flow-cell.

    Techniques:

    Two PhiX samples run on Illumina Genome Analyzer II: scatter plots of read count and shadow count. The solid lines are robust regression lines fit to the data.

    Journal: BMC Bioinformatics

    Article Title: Estimation of sequencing error rates in short reads

    doi: 10.1186/1471-2105-13-185

    Figure Lengend Snippet: Two PhiX samples run on Illumina Genome Analyzer II: scatter plots of read count and shadow count. The solid lines are robust regression lines fit to the data.

    Article Snippet: In the case of Illumina Genome Analyzer (Solexa), a sample corresponds to a lane in a flow-cell.

    Techniques:

    The validation of the NGS data. ( A ) Validation by pyrosequencing. Data points for 12 CpG sites (located in genomic intervals chr9:137 249 931–137 249 946, chr19:16 045 054–16 045 121 and chr16:87 875 316–87 875 361) in samples 1, 2, 3 and 4 are shown on a single plot. ( B ) Validation by Illumina 450 K BeadChip assay. Data points for 1880 CpG sites in samples 2, 3 and 4 are shown on a single plot.

    Journal: Nucleic Acids Research

    Article Title: In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes

    doi: 10.1093/nar/gks1467

    Figure Lengend Snippet: The validation of the NGS data. ( A ) Validation by pyrosequencing. Data points for 12 CpG sites (located in genomic intervals chr9:137 249 931–137 249 946, chr19:16 045 054–16 045 121 and chr16:87 875 316–87 875 361) in samples 1, 2, 3 and 4 are shown on a single plot. ( B ) Validation by Illumina 450 K BeadChip assay. Data points for 1880 CpG sites in samples 2, 3 and 4 are shown on a single plot.

    Article Snippet: Purified post-capture PCR products, which successfully passed the quality check on the Agilent 2100 Bioanalyzer, High Sensitivity DNA assay were precisely quantified with Agilent QPCR NGS Library Quantification Kit for Illumina Genome Analyzer (Agilent Technologies Cat. #G4880A).

    Techniques: Next-Generation Sequencing

    Data interpretation pipeline. Example of DNA-seq Bioinformatics Pipeline for Illumina ® . 1 This steps removes duplicate sequences using the Picard program; 2 GATK: Genome Analysis ToolKit.

    Journal: International Journal of Molecular Sciences

    Article Title: Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification

    doi: 10.3390/ijms18020308

    Figure Lengend Snippet: Data interpretation pipeline. Example of DNA-seq Bioinformatics Pipeline for Illumina ® . 1 This steps removes duplicate sequences using the Picard program; 2 GATK: Genome Analysis ToolKit.

    Article Snippet: One of the first reports demonstrating the potential of NGS to detect somatic alterations explored the mutation landscape in two lung cancer cell lines using the Illumina® Genome Analyser and proved that NGS technology was able to overcome the shortcomings of other technologies available at that time, which were either insensitive, inaccurate or labour intensive [ ].

    Techniques: DNA Sequencing

    Pipeline illustrating the four major blocks in next-generation sequencing (NGS) studies. 1 Illumina ® ; 2 Agilent Technology ® ; 3 Nimblegen ® ; 4 MIP: Molecular Inversion Probe. This method is normally in house developed using specific tools (SciTools ® , Integrated DNA Technologies, Coralville, Iowa, U.S.) assisting in probe design; 5 ThermoFisher ® ; 6 Roche ® ; 7 PacBio ® . Because of their recent development, information about the Qiagen GeneReader ® and 10x Genomics ® technology are not included in this figure. $ Users have reported up to 200,000 pb; * To detect low expressed transcripts, > 2000× coverage is needed.

    Journal: International Journal of Molecular Sciences

    Article Title: Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification

    doi: 10.3390/ijms18020308

    Figure Lengend Snippet: Pipeline illustrating the four major blocks in next-generation sequencing (NGS) studies. 1 Illumina ® ; 2 Agilent Technology ® ; 3 Nimblegen ® ; 4 MIP: Molecular Inversion Probe. This method is normally in house developed using specific tools (SciTools ® , Integrated DNA Technologies, Coralville, Iowa, U.S.) assisting in probe design; 5 ThermoFisher ® ; 6 Roche ® ; 7 PacBio ® . Because of their recent development, information about the Qiagen GeneReader ® and 10x Genomics ® technology are not included in this figure. $ Users have reported up to 200,000 pb; * To detect low expressed transcripts, > 2000× coverage is needed.

    Article Snippet: One of the first reports demonstrating the potential of NGS to detect somatic alterations explored the mutation landscape in two lung cancer cell lines using the Illumina® Genome Analyser and proved that NGS technology was able to overcome the shortcomings of other technologies available at that time, which were either insensitive, inaccurate or labour intensive [ ].

    Techniques: Next-Generation Sequencing

    The differentially expressed genes upon V.parahaemolyticus infection. By using Solexa/Illumina's DGE platform, 1213 differentially expressed genes were detected in comparative analysis of the expression profiles between V.parahaemolyticus -infected crabs and control crabs, including 538 up-regulated genes and 675 down-regulated genes ( P

    Journal: PLoS ONE

    Article Title: Transcriptome and Expression Profiling Analysis of the Hemocytes Reveals a Large Number of Immune-Related Genes in Mud Crab Scylla paramamosain during Vibrio parahaemolyticus Infection

    doi: 10.1371/journal.pone.0114500

    Figure Lengend Snippet: The differentially expressed genes upon V.parahaemolyticus infection. By using Solexa/Illumina's DGE platform, 1213 differentially expressed genes were detected in comparative analysis of the expression profiles between V.parahaemolyticus -infected crabs and control crabs, including 538 up-regulated genes and 675 down-regulated genes ( P

    Article Snippet: The next-generation sequencing platforms, such as the Solexa/Illumina Genome Analyzer, ABI/SOLiD Gene Sequencer, and Roche/454 Pyrosequencer, can sequence in parallel massive amounts of DNA molecules derived directly from mRNA and produce millions or even billions of high-quality short reads .

    Techniques: Infection, Expressing

    Observed distribution of coverage of Illumina's Genome Analyzer-2 with a mean coverage over a 4-Mbp region of C. elegans . The distribution best fits a Gamma distribution Γ(α,β) with shape parameters α = 6.3 and . A Poisson

    Journal: Genome Research

    Article Title: Overlapping pools for high-throughput targeted resequencing

    doi: 10.1101/gr.088559.108

    Figure Lengend Snippet: Observed distribution of coverage of Illumina's Genome Analyzer-2 with a mean coverage over a 4-Mbp region of C. elegans . The distribution best fits a Gamma distribution Γ(α,β) with shape parameters α = 6.3 and . A Poisson

    Article Snippet: Illumina's Genome Analyzer , ABI's SOLiD sequencer , 454 Life Sciences' (Roche) Genome Sequencer FLX , to name a few, are the current primary technology providers offering throughputs on the order of giga base pairs in a single run ( ).

    Techniques:

    Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an Illumina GA data set and (b) an Illumina HiSeq data set.

    Journal: BMC Bioinformatics

    Article Title: Sequencing error correction without a reference genome

    doi: 10.1186/1471-2105-14-367

    Figure Lengend Snippet: Example model fit. Data points and fitted model for the probability of an A being misread as a C, for (a) an Illumina GA data set and (b) an Illumina HiSeq data set.

    Article Snippet: The first samples were 36 base reads run on the Illumina Genome Analyzer (GeneWorks Pty.

    Techniques:

    Modelled error rates. Modelled error rates from (a) an Illumina GA data set (lane 2), (b) an Illumina GA data set (lane 4) and (c) an Illumina HiSeq data set (lane 2).

    Journal: BMC Bioinformatics

    Article Title: Sequencing error correction without a reference genome

    doi: 10.1186/1471-2105-14-367

    Figure Lengend Snippet: Modelled error rates. Modelled error rates from (a) an Illumina GA data set (lane 2), (b) an Illumina GA data set (lane 4) and (c) an Illumina HiSeq data set (lane 2).

    Article Snippet: The first samples were 36 base reads run on the Illumina Genome Analyzer (GeneWorks Pty.

    Techniques: