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    New England Biolabs nebnext multiplex oligos for illumina
    The newly developed mTSS-Capture method combined with paired-end sequencing maps genome-wide nucleosome distribution in primary patient samples and identifies bona fide nucleosome characteristics, concordant with other human nucleosome mapping studies A . Work-flow of the mTSS-seq method. Following MNase digestion using a titration of MNase, populations of mononucleosomally protected DNA and subnucleosomal fragments are isolated, and prepared as libraries for <t>Illumina</t> sequencing. Solution-based sequence capture is performed using biotinylated <t>oligos,</t> enabling the enrichment of fragments within 2kb of each transcription start site in the human genome. Paired-end 50bp sequencing was then performed on each index. B . Alignment of the mTSS-seq midpoints to the human genome using the UCSC genome browser for LAC patient #4137 Normal tissue is shown for chr11, hg19 ( http://genome.ucsc.edu ). Zooming in twice at 100X allows for further visualization of the sequence capture oligos surrounding the TSS in a 500kb and a 5kb region showing the ATM locus. C . Averaged, normalized reads per million (y-axis) from mTSS-seq plotted as fragments (gray) and midpoints (black), centered on and surrounding 2kb of the TSS for ~22,000 open reading frames in hg19 (x-axis). DNase I-hypersensitivity (GSM736580; green) and RNA polymerase II from ChIP-seq (GSM935299; blue) data from A549 cells are shown. (D) LAC patient 4137 Normal nucleosomal midpoints (blue track) were plotted in the UCSC genome browser against the published human lymphocyte nucleosome distribution maps by Gaffney et. al. (green track) for the ZNF451 and CCDC97 loci. Sequence capture oligos and corresponding RefSeq gene models are shown for each locus. Correlations are shown for ZNF451 and CCDC87, respectively.
    Nebnext Multiplex Oligos For Illumina, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1663 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs nebnext multiplex oligos
    The newly developed mTSS-Capture method combined with paired-end sequencing maps genome-wide nucleosome distribution in primary patient samples and identifies bona fide nucleosome characteristics, concordant with other human nucleosome mapping studies A . Work-flow of the mTSS-seq method. Following MNase digestion using a titration of MNase, populations of mononucleosomally protected DNA and subnucleosomal fragments are isolated, and prepared as libraries for <t>Illumina</t> sequencing. Solution-based sequence capture is performed using biotinylated <t>oligos,</t> enabling the enrichment of fragments within 2kb of each transcription start site in the human genome. Paired-end 50bp sequencing was then performed on each index. B . Alignment of the mTSS-seq midpoints to the human genome using the UCSC genome browser for LAC patient #4137 Normal tissue is shown for chr11, hg19 ( http://genome.ucsc.edu ). Zooming in twice at 100X allows for further visualization of the sequence capture oligos surrounding the TSS in a 500kb and a 5kb region showing the ATM locus. C . Averaged, normalized reads per million (y-axis) from mTSS-seq plotted as fragments (gray) and midpoints (black), centered on and surrounding 2kb of the TSS for ~22,000 open reading frames in hg19 (x-axis). DNase I-hypersensitivity (GSM736580; green) and RNA polymerase II from ChIP-seq (GSM935299; blue) data from A549 cells are shown. (D) LAC patient 4137 Normal nucleosomal midpoints (blue track) were plotted in the UCSC genome browser against the published human lymphocyte nucleosome distribution maps by Gaffney et. al. (green track) for the ZNF451 and CCDC97 loci. Sequence capture oligos and corresponding RefSeq gene models are shown for each locus. Correlations are shown for ZNF451 and CCDC87, respectively.
    Nebnext Multiplex Oligos, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4662 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs nebnext multiplex oligos for illumina index primers set 1
    The newly developed mTSS-Capture method combined with paired-end sequencing maps genome-wide nucleosome distribution in primary patient samples and identifies bona fide nucleosome characteristics, concordant with other human nucleosome mapping studies A . Work-flow of the mTSS-seq method. Following MNase digestion using a titration of MNase, populations of mononucleosomally protected DNA and subnucleosomal fragments are isolated, and prepared as libraries for <t>Illumina</t> sequencing. Solution-based sequence capture is performed using biotinylated <t>oligos,</t> enabling the enrichment of fragments within 2kb of each transcription start site in the human genome. Paired-end 50bp sequencing was then performed on each index. B . Alignment of the mTSS-seq midpoints to the human genome using the UCSC genome browser for LAC patient #4137 Normal tissue is shown for chr11, hg19 ( http://genome.ucsc.edu ). Zooming in twice at 100X allows for further visualization of the sequence capture oligos surrounding the TSS in a 500kb and a 5kb region showing the ATM locus. C . Averaged, normalized reads per million (y-axis) from mTSS-seq plotted as fragments (gray) and midpoints (black), centered on and surrounding 2kb of the TSS for ~22,000 open reading frames in hg19 (x-axis). DNase I-hypersensitivity (GSM736580; green) and RNA polymerase II from ChIP-seq (GSM935299; blue) data from A549 cells are shown. (D) LAC patient 4137 Normal nucleosomal midpoints (blue track) were plotted in the UCSC genome browser against the published human lymphocyte nucleosome distribution maps by Gaffney et. al. (green track) for the ZNF451 and CCDC97 loci. Sequence capture oligos and corresponding RefSeq gene models are shown for each locus. Correlations are shown for ZNF451 and CCDC87, respectively.
    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 908 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 2
    The newly developed mTSS-Capture method combined with paired-end sequencing maps genome-wide nucleosome distribution in primary patient samples and identifies bona fide nucleosome characteristics, concordant with other human nucleosome mapping studies A . Work-flow of the mTSS-seq method. Following MNase digestion using a titration of MNase, populations of mononucleosomally protected DNA and subnucleosomal fragments are isolated, and prepared as libraries for <t>Illumina</t> sequencing. Solution-based sequence capture is performed using biotinylated <t>oligos,</t> enabling the enrichment of fragments within 2kb of each transcription start site in the human genome. Paired-end 50bp sequencing was then performed on each index. B . Alignment of the mTSS-seq midpoints to the human genome using the UCSC genome browser for LAC patient #4137 Normal tissue is shown for chr11, hg19 ( http://genome.ucsc.edu ). Zooming in twice at 100X allows for further visualization of the sequence capture oligos surrounding the TSS in a 500kb and a 5kb region showing the ATM locus. C . Averaged, normalized reads per million (y-axis) from mTSS-seq plotted as fragments (gray) and midpoints (black), centered on and surrounding 2kb of the TSS for ~22,000 open reading frames in hg19 (x-axis). DNase I-hypersensitivity (GSM736580; green) and RNA polymerase II from ChIP-seq (GSM935299; blue) data from A549 cells are shown. (D) LAC patient 4137 Normal nucleosomal midpoints (blue track) were plotted in the UCSC genome browser against the published human lymphocyte nucleosome distribution maps by Gaffney et. al. (green track) for the ZNF451 and CCDC97 loci. Sequence capture oligos and corresponding RefSeq gene models are shown for each locus. Correlations are shown for ZNF451 and CCDC87, respectively.
    Nebnext Multiplex Oligos For Illumina Index Primers Set 2, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 525 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
    The newly developed mTSS-Capture method combined with paired-end sequencing maps genome-wide nucleosome distribution in primary patient samples and identifies bona fide nucleosome characteristics, concordant with other human nucleosome mapping studies A . Work-flow of the mTSS-seq method. Following MNase digestion using a titration of MNase, populations of mononucleosomally protected DNA and subnucleosomal fragments are isolated, and prepared as libraries for <t>Illumina</t> sequencing. Solution-based sequence capture is performed using biotinylated <t>oligos,</t> enabling the enrichment of fragments within 2kb of each transcription start site in the human genome. Paired-end 50bp sequencing was then performed on each index. B . Alignment of the mTSS-seq midpoints to the human genome using the UCSC genome browser for LAC patient #4137 Normal tissue is shown for chr11, hg19 ( http://genome.ucsc.edu ). Zooming in twice at 100X allows for further visualization of the sequence capture oligos surrounding the TSS in a 500kb and a 5kb region showing the ATM locus. C . Averaged, normalized reads per million (y-axis) from mTSS-seq plotted as fragments (gray) and midpoints (black), centered on and surrounding 2kb of the TSS for ~22,000 open reading frames in hg19 (x-axis). DNase I-hypersensitivity (GSM736580; green) and RNA polymerase II from ChIP-seq (GSM935299; blue) data from A549 cells are shown. (D) LAC patient 4137 Normal nucleosomal midpoints (blue track) were plotted in the UCSC genome browser against the published human lymphocyte nucleosome distribution maps by Gaffney et. al. (green track) for the ZNF451 and CCDC97 loci. Sequence capture oligos and corresponding RefSeq gene models are shown for each locus. Correlations are shown for ZNF451 and CCDC87, respectively.
    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 66 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
    The newly developed mTSS-Capture method combined with paired-end sequencing maps genome-wide nucleosome distribution in primary patient samples and identifies bona fide nucleosome characteristics, concordant with other human nucleosome mapping studies A . Work-flow of the mTSS-seq method. Following MNase digestion using a titration of MNase, populations of mononucleosomally protected DNA and subnucleosomal fragments are isolated, and prepared as libraries for <t>Illumina</t> sequencing. Solution-based sequence capture is performed using biotinylated <t>oligos,</t> enabling the enrichment of fragments within 2kb of each transcription start site in the human genome. Paired-end 50bp sequencing was then performed on each index. B . Alignment of the mTSS-seq midpoints to the human genome using the UCSC genome browser for LAC patient #4137 Normal tissue is shown for chr11, hg19 ( http://genome.ucsc.edu ). Zooming in twice at 100X allows for further visualization of the sequence capture oligos surrounding the TSS in a 500kb and a 5kb region showing the ATM locus. C . Averaged, normalized reads per million (y-axis) from mTSS-seq plotted as fragments (gray) and midpoints (black), centered on and surrounding 2kb of the TSS for ~22,000 open reading frames in hg19 (x-axis). DNase I-hypersensitivity (GSM736580; green) and RNA polymerase II from ChIP-seq (GSM935299; blue) data from A549 cells are shown. (D) LAC patient 4137 Normal nucleosomal midpoints (blue track) were plotted in the UCSC genome browser against the published human lymphocyte nucleosome distribution maps by Gaffney et. al. (green track) for the ZNF451 and CCDC97 loci. Sequence capture oligos and corresponding RefSeq gene models are shown for each locus. Correlations are shown for ZNF451 and CCDC87, respectively.
    Nebnext Multiplex Oligos For Illumina 96 Index Primers, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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 159 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs oligonucleotide primers
    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.
    Oligonucleotide Primers, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 331 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs dual index nebnext multiplex oligos
    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.
    Dual Index Nebnext Multiplex Oligos, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 77 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    The newly developed mTSS-Capture method combined with paired-end sequencing maps genome-wide nucleosome distribution in primary patient samples and identifies bona fide nucleosome characteristics, concordant with other human nucleosome mapping studies A . Work-flow of the mTSS-seq method. Following MNase digestion using a titration of MNase, populations of mononucleosomally protected DNA and subnucleosomal fragments are isolated, and prepared as libraries for Illumina sequencing. Solution-based sequence capture is performed using biotinylated oligos, enabling the enrichment of fragments within 2kb of each transcription start site in the human genome. Paired-end 50bp sequencing was then performed on each index. B . Alignment of the mTSS-seq midpoints to the human genome using the UCSC genome browser for LAC patient #4137 Normal tissue is shown for chr11, hg19 ( http://genome.ucsc.edu ). Zooming in twice at 100X allows for further visualization of the sequence capture oligos surrounding the TSS in a 500kb and a 5kb region showing the ATM locus. C . Averaged, normalized reads per million (y-axis) from mTSS-seq plotted as fragments (gray) and midpoints (black), centered on and surrounding 2kb of the TSS for ~22,000 open reading frames in hg19 (x-axis). DNase I-hypersensitivity (GSM736580; green) and RNA polymerase II from ChIP-seq (GSM935299; blue) data from A549 cells are shown. (D) LAC patient 4137 Normal nucleosomal midpoints (blue track) were plotted in the UCSC genome browser against the published human lymphocyte nucleosome distribution maps by Gaffney et. al. (green track) for the ZNF451 and CCDC97 loci. Sequence capture oligos and corresponding RefSeq gene models are shown for each locus. Correlations are shown for ZNF451 and CCDC87, respectively.

    Journal: Oncotarget

    Article Title: Comprehensive nucleosome mapping of the human genome in cancer progression

    doi: 10.18632/oncotarget.6811

    Figure Lengend Snippet: The newly developed mTSS-Capture method combined with paired-end sequencing maps genome-wide nucleosome distribution in primary patient samples and identifies bona fide nucleosome characteristics, concordant with other human nucleosome mapping studies A . Work-flow of the mTSS-seq method. Following MNase digestion using a titration of MNase, populations of mononucleosomally protected DNA and subnucleosomal fragments are isolated, and prepared as libraries for Illumina sequencing. Solution-based sequence capture is performed using biotinylated oligos, enabling the enrichment of fragments within 2kb of each transcription start site in the human genome. Paired-end 50bp sequencing was then performed on each index. B . Alignment of the mTSS-seq midpoints to the human genome using the UCSC genome browser for LAC patient #4137 Normal tissue is shown for chr11, hg19 ( http://genome.ucsc.edu ). Zooming in twice at 100X allows for further visualization of the sequence capture oligos surrounding the TSS in a 500kb and a 5kb region showing the ATM locus. C . Averaged, normalized reads per million (y-axis) from mTSS-seq plotted as fragments (gray) and midpoints (black), centered on and surrounding 2kb of the TSS for ~22,000 open reading frames in hg19 (x-axis). DNase I-hypersensitivity (GSM736580; green) and RNA polymerase II from ChIP-seq (GSM935299; blue) data from A549 cells are shown. (D) LAC patient 4137 Normal nucleosomal midpoints (blue track) were plotted in the UCSC genome browser against the published human lymphocyte nucleosome distribution maps by Gaffney et. al. (green track) for the ZNF451 and CCDC97 loci. Sequence capture oligos and corresponding RefSeq gene models are shown for each locus. Correlations are shown for ZNF451 and CCDC87, respectively.

    Article Snippet: Universal and indexed sequences were added through 8 cycles of PCR, using NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, NEB #E7335S/L).

    Techniques: Sequencing, Genome Wide, Titration, Isolation, Chromatin Immunoprecipitation

    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