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  • 99
    New England Biolabs illumina adapters
    Profiling many beneficial mutations in the first selective sweep by deep sequencing. (A) Schematic of the deep sequencing approach. Genomic DNA is directly isolated from the E. coli populations and prepared for <t>Illumina</t> sequencing with unique molecular indexes (colored ends attached to red/green double stranded DNA). DNA fragments matching the targeted genome regions (green centers) are captured by probes (blue) bound to magnetic beads and other sequences are washed away (red centers). Reads with the same unique molecular index, which were amplified from the same original genomic DNA fragment, are used to construct a consensus read to eliminate sequencing errors. Consensus reads are mapped to the reference genome to call sequence variants. (B) Enrichment of reads mapping to eight genes known to be early targets of selection in this environment from the long-term evolution experiment. The final coverage depth of consensus reads in and around these genes is shown for a typical sample (population A7 at 500 generations). (C) Frequency trajectories for mutations in the eight targeted genes as well as the sum total frequency in population A1 over the complete time course of the evolution experiment. When a mutation was not detected at a time point, its trajectory is shown as passing through a frequency of 0.0001% (outside of the graphed region). (D) Mutation frequency trajectories for population A1 during the window from 133 to 213 generations when mutations were first reaching detectable frequencies as they outcompeted the ancestral genotype. At time points when a mutation was not detected, its frequency is shown as 0.001% (at the bottom of the plot). (E) Estimate of average population fitness between the time points in the window when mutations were first detected. The frequency trajectories of the beneficial mutations in the initial sweep shown in D were used to jointly estimate population fitness and the individual selection coefficients of each mutation. Error bars are 95% confidence intervals on fitness estimations.
    Illumina Adapters, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 151 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc illumina multiplexing adapters
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Illumina Multiplexing Adapters, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 198 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs nebnext multiplex oligos for illumina 96 index primers
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Nebnext Multiplex Oligos For Illumina 96 Index Primers, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Illumina Inc illumina multiplex adapters
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Illumina Multiplex Adapters, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 135 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc multiplex barcode adapters
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Multiplex Barcode Adapters, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 106 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs nebnext multiplex oligos for illumina 96 unique dual index primer pairs set 2
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Nebnext Multiplex Oligos For Illumina 96 Unique Dual Index Primer Pairs Set 2, supplied by New England Biolabs, 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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    New England Biolabs nebnext multiplex oligos for illumina index primers set 1
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Nebnext Multiplex Oligos For Illumina Index Primers Set 1, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 869 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs adapters
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Adapters, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 345 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs nebnext multiplex oligos for illumina dual index primers set 1
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Nebnext Multiplex Oligos For Illumina Dual Index Primers Set 1, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 206 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc multiplexing adapter sequence
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Multiplexing Adapter Sequence, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc multiplexing adapter ligation
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Multiplexing Adapter Ligation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Bioo Scientific bioo scientific multiplexed adapters
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Bioo Scientific Multiplexed Adapters, supplied by Bioo Scientific, used in various techniques. Bioz Stars score: 90/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc dna multiplex barcoded oligonucleotide adapters
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    Dna Multiplex Barcoded Oligonucleotide Adapters, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs e7645l nebnext multiplex adapters
    NEXTFlex DNA sample preparation guide. <t>Illumina-compatible</t> libraries were prepared using the above procedure
    E7645l Nebnext Multiplex Adapters, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs illumina adapter
    Library preparation and data normalization for ET-Seq. a , ET-Seq requires low-coverage metagenomic sequencing and customized insertion sequencing. Insertion sequencing relies on custom splinkerette adaptors, which minimize non-specific amplification, a digestion step for degradation of delivery vector containing fragments, and nested PCR to enrich for fragments containing insertions with high specificity. The second round of nested PCR adds unique dual index adaptors for <t>Illumina</t> sequencing. b , This insertion sequencing data is first normalized by the reads to internal standard DNA which is added equally to all samples and serves to correct for variation in reads produced per sample. Secondly, it is normalized by the relative metagenomic abundances of the community members.
    Illumina Adapter, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina adapter/product/New England Biolabs
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    84
    Bioo Scientific illumina compatible bioo scientific multiplexed adapters
    Library preparation and data normalization for ET-Seq. a , ET-Seq requires low-coverage metagenomic sequencing and customized insertion sequencing. Insertion sequencing relies on custom splinkerette adaptors, which minimize non-specific amplification, a digestion step for degradation of delivery vector containing fragments, and nested PCR to enrich for fragments containing insertions with high specificity. The second round of nested PCR adds unique dual index adaptors for <t>Illumina</t> sequencing. b , This insertion sequencing data is first normalized by the reads to internal standard DNA which is added equally to all samples and serves to correct for variation in reads produced per sample. Secondly, it is normalized by the relative metagenomic abundances of the community members.
    Illumina Compatible Bioo Scientific Multiplexed Adapters, supplied by Bioo Scientific, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Thermo Fisher multiplex adapters
    Library preparation and data normalization for ET-Seq. a , ET-Seq requires low-coverage metagenomic sequencing and customized insertion sequencing. Insertion sequencing relies on custom splinkerette adaptors, which minimize non-specific amplification, a digestion step for degradation of delivery vector containing fragments, and nested PCR to enrich for fragments containing insertions with high specificity. The second round of nested PCR adds unique dual index adaptors for <t>Illumina</t> sequencing. b , This insertion sequencing data is first normalized by the reads to internal standard DNA which is added equally to all samples and serves to correct for variation in reads produced per sample. Secondly, it is normalized by the relative metagenomic abundances of the community members.
    Multiplex Adapters, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/multiplex adapters/product/Thermo Fisher
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    85
    Illumina Inc multiplex sequencing adapters
    Library preparation and data normalization for ET-Seq. a , ET-Seq requires low-coverage metagenomic sequencing and customized insertion sequencing. Insertion sequencing relies on custom splinkerette adaptors, which minimize non-specific amplification, a digestion step for degradation of delivery vector containing fragments, and nested PCR to enrich for fragments containing insertions with high specificity. The second round of nested PCR adds unique dual index adaptors for <t>Illumina</t> sequencing. b , This insertion sequencing data is first normalized by the reads to internal standard DNA which is added equally to all samples and serves to correct for variation in reads produced per sample. Secondly, it is normalized by the relative metagenomic abundances of the community members.
    Multiplex Sequencing Adapters, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/multiplex sequencing adapters/product/Illumina Inc
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    92
    Bioo Scientific multiplex nextflex adapters
    Library preparation and data normalization for ET-Seq. a , ET-Seq requires low-coverage metagenomic sequencing and customized insertion sequencing. Insertion sequencing relies on custom splinkerette adaptors, which minimize non-specific amplification, a digestion step for degradation of delivery vector containing fragments, and nested PCR to enrich for fragments containing insertions with high specificity. The second round of nested PCR adds unique dual index adaptors for <t>Illumina</t> sequencing. b , This insertion sequencing data is first normalized by the reads to internal standard DNA which is added equally to all samples and serves to correct for variation in reads produced per sample. Secondly, it is normalized by the relative metagenomic abundances of the community members.
    Multiplex Nextflex Adapters, supplied by Bioo Scientific, 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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    99
    New England Biolabs nebnext quick ligation module
    Library preparation and data normalization for ET-Seq. a , ET-Seq requires low-coverage metagenomic sequencing and customized insertion sequencing. Insertion sequencing relies on custom splinkerette adaptors, which minimize non-specific amplification, a digestion step for degradation of delivery vector containing fragments, and nested PCR to enrich for fragments containing insertions with high specificity. The second round of nested PCR adds unique dual index adaptors for <t>Illumina</t> sequencing. b , This insertion sequencing data is first normalized by the reads to internal standard DNA which is added equally to all samples and serves to correct for variation in reads produced per sample. Secondly, it is normalized by the relative metagenomic abundances of the community members.
    Nebnext Quick Ligation Module, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 484 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc paired end sequencing multiplex adapters
    Library preparation and data normalization for ET-Seq. a , ET-Seq requires low-coverage metagenomic sequencing and customized insertion sequencing. Insertion sequencing relies on custom splinkerette adaptors, which minimize non-specific amplification, a digestion step for degradation of delivery vector containing fragments, and nested PCR to enrich for fragments containing insertions with high specificity. The second round of nested PCR adds unique dual index adaptors for <t>Illumina</t> sequencing. b , This insertion sequencing data is first normalized by the reads to internal standard DNA which is added equally to all samples and serves to correct for variation in reads produced per sample. Secondly, it is normalized by the relative metagenomic abundances of the community members.
    Paired End Sequencing Multiplex Adapters, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 55 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Profiling many beneficial mutations in the first selective sweep by deep sequencing. (A) Schematic of the deep sequencing approach. Genomic DNA is directly isolated from the E. coli populations and prepared for Illumina sequencing with unique molecular indexes (colored ends attached to red/green double stranded DNA). DNA fragments matching the targeted genome regions (green centers) are captured by probes (blue) bound to magnetic beads and other sequences are washed away (red centers). Reads with the same unique molecular index, which were amplified from the same original genomic DNA fragment, are used to construct a consensus read to eliminate sequencing errors. Consensus reads are mapped to the reference genome to call sequence variants. (B) Enrichment of reads mapping to eight genes known to be early targets of selection in this environment from the long-term evolution experiment. The final coverage depth of consensus reads in and around these genes is shown for a typical sample (population A7 at 500 generations). (C) Frequency trajectories for mutations in the eight targeted genes as well as the sum total frequency in population A1 over the complete time course of the evolution experiment. When a mutation was not detected at a time point, its trajectory is shown as passing through a frequency of 0.0001% (outside of the graphed region). (D) Mutation frequency trajectories for population A1 during the window from 133 to 213 generations when mutations were first reaching detectable frequencies as they outcompeted the ancestral genotype. At time points when a mutation was not detected, its frequency is shown as 0.001% (at the bottom of the plot). (E) Estimate of average population fitness between the time points in the window when mutations were first detected. The frequency trajectories of the beneficial mutations in the initial sweep shown in D were used to jointly estimate population fitness and the individual selection coefficients of each mutation. Error bars are 95% confidence intervals on fitness estimations.

    Journal: bioRxiv

    Article Title: Profiling the initial burst of beneficial genetic diversity to anticipate evolution of a cell population

    doi: 10.1101/2020.07.10.196832

    Figure Lengend Snippet: Profiling many beneficial mutations in the first selective sweep by deep sequencing. (A) Schematic of the deep sequencing approach. Genomic DNA is directly isolated from the E. coli populations and prepared for Illumina sequencing with unique molecular indexes (colored ends attached to red/green double stranded DNA). DNA fragments matching the targeted genome regions (green centers) are captured by probes (blue) bound to magnetic beads and other sequences are washed away (red centers). Reads with the same unique molecular index, which were amplified from the same original genomic DNA fragment, are used to construct a consensus read to eliminate sequencing errors. Consensus reads are mapped to the reference genome to call sequence variants. (B) Enrichment of reads mapping to eight genes known to be early targets of selection in this environment from the long-term evolution experiment. The final coverage depth of consensus reads in and around these genes is shown for a typical sample (population A7 at 500 generations). (C) Frequency trajectories for mutations in the eight targeted genes as well as the sum total frequency in population A1 over the complete time course of the evolution experiment. When a mutation was not detected at a time point, its trajectory is shown as passing through a frequency of 0.0001% (outside of the graphed region). (D) Mutation frequency trajectories for population A1 during the window from 133 to 213 generations when mutations were first reaching detectable frequencies as they outcompeted the ancestral genotype. At time points when a mutation was not detected, its frequency is shown as 0.001% (at the bottom of the plot). (E) Estimate of average population fitness between the time points in the window when mutations were first detected. The frequency trajectories of the beneficial mutations in the initial sweep shown in D were used to jointly estimate population fitness and the individual selection coefficients of each mutation. Error bars are 95% confidence intervals on fitness estimations.

    Article Snippet: Illumina adapters containing 12-base molecular indexes were ligated to the T-tailed fragments as previously described [ ], except full-length adapter sequences containing unique external sample barcodes were directly ligated to the T-tailed dsDNA inserts to reduce the risk of cross-contamination between samples.

    Techniques: Sequencing, Isolation, Magnetic Beads, Amplification, Construct, Selection, Mutagenesis

    NEXTFlex DNA sample preparation guide. Illumina-compatible libraries were prepared using the above procedure

    Journal: AMB Express

    Article Title: Meta-barcoding in combination with palynological inference is a potent diagnostic marker for honey floral composition

    doi: 10.1186/s13568-017-0429-7

    Figure Lengend Snippet: NEXTFlex DNA sample preparation guide. Illumina-compatible libraries were prepared using the above procedure

    Article Snippet: Next, the fragmented DNA was cleaned up using HighPrep beads (MagBio Genomics, Inc, Gaithersburg, Maryland) followed by end-repair, A-tailing, and ligation of the Illumina multiplexing adapters.

    Techniques: Sample Prep

    Library preparation and data normalization for ET-Seq. a , ET-Seq requires low-coverage metagenomic sequencing and customized insertion sequencing. Insertion sequencing relies on custom splinkerette adaptors, which minimize non-specific amplification, a digestion step for degradation of delivery vector containing fragments, and nested PCR to enrich for fragments containing insertions with high specificity. The second round of nested PCR adds unique dual index adaptors for Illumina sequencing. b , This insertion sequencing data is first normalized by the reads to internal standard DNA which is added equally to all samples and serves to correct for variation in reads produced per sample. Secondly, it is normalized by the relative metagenomic abundances of the community members.

    Journal: bioRxiv

    Article Title: Targeted Genome Editing of Bacteria Within Microbial Communities

    doi: 10.1101/2020.07.17.209189

    Figure Lengend Snippet: Library preparation and data normalization for ET-Seq. a , ET-Seq requires low-coverage metagenomic sequencing and customized insertion sequencing. Insertion sequencing relies on custom splinkerette adaptors, which minimize non-specific amplification, a digestion step for degradation of delivery vector containing fragments, and nested PCR to enrich for fragments containing insertions with high specificity. The second round of nested PCR adds unique dual index adaptors for Illumina sequencing. b , This insertion sequencing data is first normalized by the reads to internal standard DNA which is added equally to all samples and serves to correct for variation in reads produced per sample. Secondly, it is normalized by the relative metagenomic abundances of the community members.

    Article Snippet: Raw sequencing reads were processed to remove Illumina adapter and phiX sequence using BBduk with default parameters, and quality trimmed at 3’ ends with Sickle using default parameters ( https://github.com/najoshi/sickle ).

    Techniques: Sequencing, Amplification, Plasmid Preparation, Nested PCR, Produced