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bridge amplification  (Illumina Inc)


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    Structured Review

    Illumina Inc bridge amplification
    Bridge Amplification, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 96/100, based on 471 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/bridge+amplification/HiSeq+3000%2F4000+PE+Cluster+Kit/pm41661278-28-12-19
    Average 96 stars, based on 471 article reviews
    bridge amplification - by Bioz Stars, 2026-10
    96/100 stars

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    Related Articles

    other:

    Article Title: Correcting PCR amplification errors in unique molecular identifiers to generate accurate numbers of sequencing molecules
    Article Snippet: We hypothesized that the lower accuracy of Illumina and PacBio, when compared to ONT sequencing, may be due to the use of polymerases that are integral to the sequencing process (for example, bridge amplification and circular consensus sequencing with Illumina and PacBio, respectively).

    Next-Generation Sequencing:

    Article Title: Whole pool amplification and in-sequencer random-access of data encoded by polynucleotides
    Article Snippet: .. For example, random access/retrieval of data can be accomplished in a single method by next generation sequencing (next generation sequencing (NGS); massively parallel sequencing in an automated process; Illumina®) with, for example, bridge amplification of the whole pool or part of the polynucleotides in the container 330. ..

    Sequencing:

    Article Title: Whole pool amplification and in-sequencer random-access of data encoded by polynucleotides
    Article Snippet: .. For example, random access/retrieval of data can be accomplished in a single method by next generation sequencing (next generation sequencing (NGS); massively parallel sequencing in an automated process; Illumina®) with, for example, bridge amplification of the whole pool or part of the polynucleotides in the container 330. ..

    Article Title: A metagenomic study of the gut microbiome in patients with type 2 diabetes mellitus and myocardial infarction.
    Article Snippet: Genomic DNA was fragmented to ~ 300 bp using a Covaris M220 system, and paired-end libraries were prepared with the TruSeqTM DNA Sample Prep Kit. .. Cluster generation was performed using the HiSeq 3000/4000 PE Cluster Kit through bridge amplification, followed by sequencing on the Illumina HiSeq 3000/4000 platform with the SBS Kit, which utilizes fluorescently labeled nucleotides and laser-based detection for base incorporation. ..

    Article Title: Narrative Review: Update on the Molecular Diagnosis of Fragile X Syndrome
    Article Snippet: .. The most popular example of sequencing by synthesis is Illumina, which uses “bridge amplification”. ..

    Amplification:

    Article Title: Whole pool amplification and in-sequencer random-access of data encoded by polynucleotides
    Article Snippet: .. For example, random access/retrieval of data can be accomplished in a single method by next generation sequencing (next generation sequencing (NGS); massively parallel sequencing in an automated process; Illumina®) with, for example, bridge amplification of the whole pool or part of the polynucleotides in the container 330. ..

    Article Title: A metagenomic study of the gut microbiome in patients with type 2 diabetes mellitus and myocardial infarction.
    Article Snippet: Genomic DNA was fragmented to ~ 300 bp using a Covaris M220 system, and paired-end libraries were prepared with the TruSeqTM DNA Sample Prep Kit. .. Cluster generation was performed using the HiSeq 3000/4000 PE Cluster Kit through bridge amplification, followed by sequencing on the Illumina HiSeq 3000/4000 platform with the SBS Kit, which utilizes fluorescently labeled nucleotides and laser-based detection for base incorporation. ..

    Article Title: Linked target capture
    Article Snippet: Methods of the present invention improve amplification on a solid support, such as in the Illumina platform (Illumina, Inc. San Diego, CA) or the Ion Torrent platform (Thermo Fisher Scientific Inc., Waltham, MA). .. In the Illumina technique, using bridge amplification, clusters of amplicons are formed. ..

    Article Title: Comparison of the fecal microbiota of adult healthy dogs fed a plant-based (vegan) or an animal-based diet.
    Article Snippet: All finalized PCR products were evaluated using gel electrophoresis and DNA was measured using spectrophotometry to ensure the concentration of DNA was greater than 15 ng/μl before Illumina sequencing. .. Bridge amplification was completed on an Illumina MISeq system (Illumina, San Diego, CA, USA) at the University of Guelph Agri-Food Labs using terminator nucleotides that were incorporated into the amplified PCR products with the removal of the terminator group (Tal et al., 2020; Chui et al., 2023). ..

    Article Title: Integrative analysis of single-nucleus RNA-seq and bulk RNA-seq reveals germline cells development dynamics and niches in the Pacific oyster gonad
    Article Snippet: Then, the cDNA was amplified with 11 PCR cycles and purified with SPRlselect (Beckman Coulter B23318). .. Illumina bridge amplification was carried out using the final libraries that contained the P5 and P7 primers after primers had been added. ..

    Article Title: Narrative Review: Update on the Molecular Diagnosis of Fragile X Syndrome
    Article Snippet: .. The most popular example of sequencing by synthesis is Illumina, which uses “bridge amplification”. ..

    Article Title: Metagenomic approaches and opportunities in arid soil research.
    Article Snippet: • Soil metagenomics reveals diverse microbes adapted to harsh deserts, thriving under extreme heat, radiation, and

    Labeling:

    Article Title: A metagenomic study of the gut microbiome in patients with type 2 diabetes mellitus and myocardial infarction.
    Article Snippet: Genomic DNA was fragmented to ~ 300 bp using a Covaris M220 system, and paired-end libraries were prepared with the TruSeqTM DNA Sample Prep Kit. .. Cluster generation was performed using the HiSeq 3000/4000 PE Cluster Kit through bridge amplification, followed by sequencing on the Illumina HiSeq 3000/4000 platform with the SBS Kit, which utilizes fluorescently labeled nucleotides and laser-based detection for base incorporation. ..

    Polymerase Chain Reaction:

    Article Title: Comparison of the fecal microbiota of adult healthy dogs fed a plant-based (vegan) or an animal-based diet.
    Article Snippet: All finalized PCR products were evaluated using gel electrophoresis and DNA was measured using spectrophotometry to ensure the concentration of DNA was greater than 15 ng/μl before Illumina sequencing. .. Bridge amplification was completed on an Illumina MISeq system (Illumina, San Diego, CA, USA) at the University of Guelph Agri-Food Labs using terminator nucleotides that were incorporated into the amplified PCR products with the removal of the terminator group (Tal et al., 2020; Chui et al., 2023). ..



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    Prophage distribution in P. <t>aeruginosa</t> genomes. Illustration of the correlation coefficients between the total number of intact, incomplete, and questionable prophages (A) , and total number of prophages in P. aeruginosa genomes, categorized as intact, incomplete, and questionable (B) . Prophages were detected and classified using the PHASTER with default arguments and its scoring system. (A) Correlation and scatter plot of prophage genome types and their distribution. The analysis reveals a significant correlation between the total category and all three subcategories, as the strongest relationship is with Incomplete, followed by Intact, while the weakest is with Questionable, all with p-values <0.05; these correlations are statistically significant. (B) There were differences in the distribution of prophages of varying completeness on the chromosomes of P. aeruginosa . The integration of intact prophages in the bacterial genome indicates a recent infection with a temperate phage ( <xref ref-type=Costa et al., 2018 ). There is a significantly high prevalence of defective phages ( Figure 1 , Supplementary Table 2 ). " width="250" height="auto" />
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    Prophage distribution in P. <t>aeruginosa</t> genomes. Illustration of the correlation coefficients between the total number of intact, incomplete, and questionable prophages (A) , and total number of prophages in P. aeruginosa genomes, categorized as intact, incomplete, and questionable (B) . Prophages were detected and classified using the PHASTER with default arguments and its scoring system. (A) Correlation and scatter plot of prophage genome types and their distribution. The analysis reveals a significant correlation between the total category and all three subcategories, as the strongest relationship is with Incomplete, followed by Intact, while the weakest is with Questionable, all with p-values <0.05; these correlations are statistically significant. (B) There were differences in the distribution of prophages of varying completeness on the chromosomes of P. aeruginosa . The integration of intact prophages in the bacterial genome indicates a recent infection with a temperate phage ( <xref ref-type=Costa et al., 2018 ). There is a significantly high prevalence of defective phages ( Figure 1 , Supplementary Table 2 ). " width="250" height="auto" />
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    Prophage distribution in P. <t>aeruginosa</t> genomes. Illustration of the correlation coefficients between the total number of intact, incomplete, and questionable prophages (A) , and total number of prophages in P. aeruginosa genomes, categorized as intact, incomplete, and questionable (B) . Prophages were detected and classified using the PHASTER with default arguments and its scoring system. (A) Correlation and scatter plot of prophage genome types and their distribution. The analysis reveals a significant correlation between the total category and all three subcategories, as the strongest relationship is with Incomplete, followed by Intact, while the weakest is with Questionable, all with p-values <0.05; these correlations are statistically significant. (B) There were differences in the distribution of prophages of varying completeness on the chromosomes of P. aeruginosa . The integration of intact prophages in the bacterial genome indicates a recent infection with a temperate phage ( <xref ref-type=Costa et al., 2018 ). There is a significantly high prevalence of defective phages ( Figure 1 , Supplementary Table 2 ). " width="250" height="auto" />
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    Illumina Inc bridged amplification reaction
    Prophage distribution in P. <t>aeruginosa</t> genomes. Illustration of the correlation coefficients between the total number of intact, incomplete, and questionable prophages (A) , and total number of prophages in P. aeruginosa genomes, categorized as intact, incomplete, and questionable (B) . Prophages were detected and classified using the PHASTER with default arguments and its scoring system. (A) Correlation and scatter plot of prophage genome types and their distribution. The analysis reveals a significant correlation between the total category and all three subcategories, as the strongest relationship is with Incomplete, followed by Intact, while the weakest is with Questionable, all with p-values <0.05; these correlations are statistically significant. (B) There were differences in the distribution of prophages of varying completeness on the chromosomes of P. aeruginosa . The integration of intact prophages in the bacterial genome indicates a recent infection with a temperate phage ( <xref ref-type=Costa et al., 2018 ). There is a significantly high prevalence of defective phages ( Figure 1 , Supplementary Table 2 ). " width="250" height="auto" />
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    Prophage distribution in P. <t>aeruginosa</t> genomes. Illustration of the correlation coefficients between the total number of intact, incomplete, and questionable prophages (A) , and total number of prophages in P. aeruginosa genomes, categorized as intact, incomplete, and questionable (B) . Prophages were detected and classified using the PHASTER with default arguments and its scoring system. (A) Correlation and scatter plot of prophage genome types and their distribution. The analysis reveals a significant correlation between the total category and all three subcategories, as the strongest relationship is with Incomplete, followed by Intact, while the weakest is with Questionable, all with p-values <0.05; these correlations are statistically significant. (B) There were differences in the distribution of prophages of varying completeness on the chromosomes of P. aeruginosa . The integration of intact prophages in the bacterial genome indicates a recent infection with a temperate phage ( <xref ref-type=Costa et al., 2018 ). There is a significantly high prevalence of defective phages ( Figure 1 , Supplementary Table 2 ). " width="250" height="auto" />
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    Illumina Inc bridge amplification method
    Sequencing technologies [Adapted from 37] (A) Illumina sequencing follows sequencing by synthesis method. This involves the denaturation of DNA, adaptor ligation, and bridge <t>amplification</t> which takes place on a flow cell surface. All 4 nucleotides are included which are individually labelled with different fluorophores which are useful for detection. (B) PacBio sequencing works on single-molecule real-time (SMRT) technology. The DNA molecule forms a loop with the help of hairpin adapters and is sequenced in a zero-mode waveguide which allows the detection of individual fluorophores in real-time with continuous light-pulse-based detection. (C) Nanopore sequencing uses a protein nanopore that is fixated on an electrically resistant polymer membrane. Electric current is passed through the membrane. A change in the current is observed when a DNA/RNA is passed through the nanopore and this allows the identification of sequences in real time.
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    Illumina Inc bridge amplification sequencing
    Sequencing technologies [Adapted from 37] (A) Illumina sequencing follows sequencing by synthesis method. This involves the denaturation of DNA, adaptor ligation, and bridge <t>amplification</t> which takes place on a flow cell surface. All 4 nucleotides are included which are individually labelled with different fluorophores which are useful for detection. (B) PacBio sequencing works on single-molecule real-time (SMRT) technology. The DNA molecule forms a loop with the help of hairpin adapters and is sequenced in a zero-mode waveguide which allows the detection of individual fluorophores in real-time with continuous light-pulse-based detection. (C) Nanopore sequencing uses a protein nanopore that is fixated on an electrically resistant polymer membrane. Electric current is passed through the membrane. A change in the current is observed when a DNA/RNA is passed through the nanopore and this allows the identification of sequences in real time.
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    Image Search Results


    Prophage distribution in P. aeruginosa genomes. Illustration of the correlation coefficients between the total number of intact, incomplete, and questionable prophages (A) , and total number of prophages in P. aeruginosa genomes, categorized as intact, incomplete, and questionable (B) . Prophages were detected and classified using the PHASTER with default arguments and its scoring system. (A) Correlation and scatter plot of prophage genome types and their distribution. The analysis reveals a significant correlation between the total category and all three subcategories, as the strongest relationship is with Incomplete, followed by Intact, while the weakest is with Questionable, all with p-values <0.05; these correlations are statistically significant. (B) There were differences in the distribution of prophages of varying completeness on the chromosomes of P. aeruginosa . The integration of intact prophages in the bacterial genome indicates a recent infection with a temperate phage ( <xref ref-type=Costa et al., 2018 ). There is a significantly high prevalence of defective phages ( Figure 1 , Supplementary Table 2 ). " width="100%" height="100%">

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: Genomic analysis of prophages in 44 clinical strains of Pseudomonas aeruginosa isolated in Saudi Arabia

    doi: 10.3389/fcimb.2025.1563781

    Figure Lengend Snippet: Prophage distribution in P. aeruginosa genomes. Illustration of the correlation coefficients between the total number of intact, incomplete, and questionable prophages (A) , and total number of prophages in P. aeruginosa genomes, categorized as intact, incomplete, and questionable (B) . Prophages were detected and classified using the PHASTER with default arguments and its scoring system. (A) Correlation and scatter plot of prophage genome types and their distribution. The analysis reveals a significant correlation between the total category and all three subcategories, as the strongest relationship is with Incomplete, followed by Intact, while the weakest is with Questionable, all with p-values <0.05; these correlations are statistically significant. (B) There were differences in the distribution of prophages of varying completeness on the chromosomes of P. aeruginosa . The integration of intact prophages in the bacterial genome indicates a recent infection with a temperate phage ( Costa et al., 2018 ). There is a significantly high prevalence of defective phages ( Figure 1 , Supplementary Table 2 ).

    Article Snippet: One limitation of our study is that some of the P. aeruginosa isolates were sequenced using short-read bridge amplification technology (Illumina, Oxford Genomics Centre, Oxford, UK), generating 150 bp fragments.

    Techniques: Infection

    Distribution of intact prophages in the 44 P . aeruginosa strains. Among the identified prophages, AA18 was the dominant intact prophage in 13 P . aeruginosa genomes in the study, followed by AA20 in 12 genomes and AA19 in eight genomes. Prophages AA13, AA08, and AA03 were present in six, five, and four genomes, respectively. Four prophages were identified in three genomes each, while six other prophages were found in two genomes each.

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: Genomic analysis of prophages in 44 clinical strains of Pseudomonas aeruginosa isolated in Saudi Arabia

    doi: 10.3389/fcimb.2025.1563781

    Figure Lengend Snippet: Distribution of intact prophages in the 44 P . aeruginosa strains. Among the identified prophages, AA18 was the dominant intact prophage in 13 P . aeruginosa genomes in the study, followed by AA20 in 12 genomes and AA19 in eight genomes. Prophages AA13, AA08, and AA03 were present in six, five, and four genomes, respectively. Four prophages were identified in three genomes each, while six other prophages were found in two genomes each.

    Article Snippet: One limitation of our study is that some of the P. aeruginosa isolates were sequenced using short-read bridge amplification technology (Illumina, Oxford Genomics Centre, Oxford, UK), generating 150 bp fragments.

    Techniques:

    Phylogenetic Tree of P. aeruginosa -associated prophages. The phylogeny tree was constructed using the neighbor-joining method with the MAFFT program based on major capsid protein (MCP) sequences. Only prophage genomes containing MCP sequences were included in the analysis, while prophages without MCPs were excluded. The schematic representation of the tree was visualized using the iTOL v6 software .

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: Genomic analysis of prophages in 44 clinical strains of Pseudomonas aeruginosa isolated in Saudi Arabia

    doi: 10.3389/fcimb.2025.1563781

    Figure Lengend Snippet: Phylogenetic Tree of P. aeruginosa -associated prophages. The phylogeny tree was constructed using the neighbor-joining method with the MAFFT program based on major capsid protein (MCP) sequences. Only prophage genomes containing MCP sequences were included in the analysis, while prophages without MCPs were excluded. The schematic representation of the tree was visualized using the iTOL v6 software .

    Article Snippet: One limitation of our study is that some of the P. aeruginosa isolates were sequenced using short-read bridge amplification technology (Illumina, Oxford Genomics Centre, Oxford, UK), generating 150 bp fragments.

    Techniques: Construct, Software

    Prophage counts in most common sequence types (STs). Prophages were predominantly identified in the 44 P . aeruginosa strains belonging to ST235 (n=19), followed by ST233 (n = 5) and ST357 (n = 4).

    Journal: Frontiers in Cellular and Infection Microbiology

    Article Title: Genomic analysis of prophages in 44 clinical strains of Pseudomonas aeruginosa isolated in Saudi Arabia

    doi: 10.3389/fcimb.2025.1563781

    Figure Lengend Snippet: Prophage counts in most common sequence types (STs). Prophages were predominantly identified in the 44 P . aeruginosa strains belonging to ST235 (n=19), followed by ST233 (n = 5) and ST357 (n = 4).

    Article Snippet: One limitation of our study is that some of the P. aeruginosa isolates were sequenced using short-read bridge amplification technology (Illumina, Oxford Genomics Centre, Oxford, UK), generating 150 bp fragments.

    Techniques: Sequencing

    Sequencing technologies [Adapted from 37] (A) Illumina sequencing follows sequencing by synthesis method. This involves the denaturation of DNA, adaptor ligation, and bridge amplification which takes place on a flow cell surface. All 4 nucleotides are included which are individually labelled with different fluorophores which are useful for detection. (B) PacBio sequencing works on single-molecule real-time (SMRT) technology. The DNA molecule forms a loop with the help of hairpin adapters and is sequenced in a zero-mode waveguide which allows the detection of individual fluorophores in real-time with continuous light-pulse-based detection. (C) Nanopore sequencing uses a protein nanopore that is fixated on an electrically resistant polymer membrane. Electric current is passed through the membrane. A change in the current is observed when a DNA/RNA is passed through the nanopore and this allows the identification of sequences in real time.

    Journal: Heliyon

    Article Title: Precision oncology through next generation sequencing in hepatocellular carcinoma

    doi: 10.1016/j.heliyon.2025.e42054

    Figure Lengend Snippet: Sequencing technologies [Adapted from 37] (A) Illumina sequencing follows sequencing by synthesis method. This involves the denaturation of DNA, adaptor ligation, and bridge amplification which takes place on a flow cell surface. All 4 nucleotides are included which are individually labelled with different fluorophores which are useful for detection. (B) PacBio sequencing works on single-molecule real-time (SMRT) technology. The DNA molecule forms a loop with the help of hairpin adapters and is sequenced in a zero-mode waveguide which allows the detection of individual fluorophores in real-time with continuous light-pulse-based detection. (C) Nanopore sequencing uses a protein nanopore that is fixated on an electrically resistant polymer membrane. Electric current is passed through the membrane. A change in the current is observed when a DNA/RNA is passed through the nanopore and this allows the identification of sequences in real time.

    Article Snippet: Illumina employs the bridge amplification method ( A).

    Techniques: Sequencing, Illumina Sequencing, Ligation, Amplification, PacBio Sequencing, Nanopore Sequencing, Polymer, Membrane