∼ 300-bp Search Results


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  • 98
    Thermo Fisher 300 bp dna fragment
    300 Bp Dna Fragment, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 64 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp dna fragment/product/Thermo Fisher
    Average 98 stars, based on 64 article reviews
    Price from $9.99 to $1999.99
    300 bp dna fragment - by Bioz Stars, 2020-09
    98/100 stars
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    92
    Illumina Inc 300 bp paired end sequencing
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    300 Bp Paired End Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 558 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp paired end sequencing/product/Illumina Inc
    Average 92 stars, based on 558 article reviews
    Price from $9.99 to $1999.99
    300 bp paired end sequencing - by Bioz Stars, 2020-09
    92/100 stars
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    90
    Illumina Inc 300 bp paired end
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    300 Bp Paired End, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 456 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp paired end/product/Illumina Inc
    Average 90 stars, based on 456 article reviews
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    91
    Illumina Inc miseq 300 bp paired end sequencing
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    Miseq 300 Bp Paired End Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 103 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/miseq 300 bp paired end sequencing/product/Illumina Inc
    Average 91 stars, based on 103 article reviews
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    88
    Illumina Inc miseq 300 bp paired end run
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    Miseq 300 Bp Paired End Run, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/miseq 300 bp paired end run/product/Illumina Inc
    Average 88 stars, based on 32 article reviews
    Price from $9.99 to $1999.99
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    91
    Illumina Inc 300 bp illumina miseq
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    300 Bp Illumina Miseq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp illumina miseq/product/Illumina Inc
    Average 91 stars, based on 32 article reviews
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    300 bp illumina miseq - by Bioz Stars, 2020-09
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    89
    Thermo Fisher 300 bp chemistry ion torrent pgm platform
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    300 Bp Chemistry Ion Torrent Pgm Platform, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 52 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp chemistry ion torrent pgm platform/product/Thermo Fisher
    Average 89 stars, based on 52 article reviews
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    300 bp chemistry ion torrent pgm platform - by Bioz Stars, 2020-09
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    90
    Illumina Inc 300 bp dna fragments
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    300 Bp Dna Fragments, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 76 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp dna fragments/product/Illumina Inc
    Average 90 stars, based on 76 article reviews
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    90
    Illumina Inc 300 bp paired end protocol
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    300 Bp Paired End Protocol, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp paired end protocol/product/Illumina Inc
    Average 90 stars, based on 29 article reviews
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    300 bp paired end protocol - by Bioz Stars, 2020-09
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    89
    Illumina Inc 300 bp paired end v3 illumina chemistry
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    300 Bp Paired End V3 Illumina Chemistry, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 50 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp paired end v3 illumina chemistry/product/Illumina Inc
    Average 89 stars, based on 50 article reviews
    Price from $9.99 to $1999.99
    300 bp paired end v3 illumina chemistry - by Bioz Stars, 2020-09
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    90
    Illumina Inc 300 bp fragments
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    300 Bp Fragments, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 70 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp fragments/product/Illumina Inc
    Average 90 stars, based on 70 article reviews
    Price from $9.99 to $1999.99
    300 bp fragments - by Bioz Stars, 2020-09
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    90
    Illumina Inc 300bp
    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of <t>300</t> bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.
    300bp, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300bp/product/Illumina Inc
    Average 90 stars, based on 28 article reviews
    Price from $9.99 to $1999.99
    300bp - by Bioz Stars, 2020-09
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    88
    Illumina Inc 200 300 bp fragments
    Schematic overview of Poly(A)ClickSeq (PAC-seq). ( A ) RT-PCR is launched from a non-anchored Poly(T) primer containing a portion of the Illumina p7 adaptor. RT-PCR is performed in the presence of AzATP, AzGTP and AzCTP, but not AzTTP, thus only allowing chain termination to occur upstream of the poly(A) tail in the 3΄UTR. ( B ) 3΄-Azido-blocked cDNA fragments are ‘click-ligated’ to 5΄-hexynyl–functionalised DNA oligos containing the p5 Illumina adaptor. This yields triazole-linked ssDNA which can be PCR-amplified using primers to the p5 and p7 Illumina adaptors. ( C ) The cDNA library is analysed by gel electrophoresis and should consist of a smear of DNA products centered <t>∼200–300</t> bp. Appropriate cDNA fragment sizes are cut out of the gel and purified to yield a final library. ( D ) The final library consists of DNA fragments containing the Illumina p5 adaptor, a portion of the 3΄UTR, a stretch of As derived from both the RNA template and the poly(T) primer, and finally the p7 Illumina Indexing primer.
    200 300 Bp Fragments, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/200 300 bp fragments/product/Illumina Inc
    Average 88 stars, based on 37 article reviews
    Price from $9.99 to $1999.99
    200 300 bp fragments - by Bioz Stars, 2020-09
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    88
    Diagenode 300 bp dna fragments
    Schematic overview of Poly(A)ClickSeq (PAC-seq). ( A ) RT-PCR is launched from a non-anchored Poly(T) primer containing a portion of the Illumina p7 adaptor. RT-PCR is performed in the presence of AzATP, AzGTP and AzCTP, but not AzTTP, thus only allowing chain termination to occur upstream of the poly(A) tail in the 3΄UTR. ( B ) 3΄-Azido-blocked cDNA fragments are ‘click-ligated’ to 5΄-hexynyl–functionalised DNA oligos containing the p5 Illumina adaptor. This yields triazole-linked ssDNA which can be PCR-amplified using primers to the p5 and p7 Illumina adaptors. ( C ) The cDNA library is analysed by gel electrophoresis and should consist of a smear of DNA products centered <t>∼200–300</t> bp. Appropriate cDNA fragment sizes are cut out of the gel and purified to yield a final library. ( D ) The final library consists of DNA fragments containing the Illumina p5 adaptor, a portion of the 3΄UTR, a stretch of As derived from both the RNA template and the poly(T) primer, and finally the p7 Illumina Indexing primer.
    300 Bp Dna Fragments, supplied by Diagenode, used in various techniques. Bioz Stars score: 88/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp dna fragments/product/Diagenode
    Average 88 stars, based on 20 article reviews
    Price from $9.99 to $1999.99
    300 bp dna fragments - by Bioz Stars, 2020-09
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    91
    Diagenode 300 bp fragments
    Schematic overview of Poly(A)ClickSeq (PAC-seq). ( A ) RT-PCR is launched from a non-anchored Poly(T) primer containing a portion of the Illumina p7 adaptor. RT-PCR is performed in the presence of AzATP, AzGTP and AzCTP, but not AzTTP, thus only allowing chain termination to occur upstream of the poly(A) tail in the 3΄UTR. ( B ) 3΄-Azido-blocked cDNA fragments are ‘click-ligated’ to 5΄-hexynyl–functionalised DNA oligos containing the p5 Illumina adaptor. This yields triazole-linked ssDNA which can be PCR-amplified using primers to the p5 and p7 Illumina adaptors. ( C ) The cDNA library is analysed by gel electrophoresis and should consist of a smear of DNA products centered <t>∼200–300</t> bp. Appropriate cDNA fragment sizes are cut out of the gel and purified to yield a final library. ( D ) The final library consists of DNA fragments containing the Illumina p5 adaptor, a portion of the 3΄UTR, a stretch of As derived from both the RNA template and the poly(T) primer, and finally the p7 Illumina Indexing primer.
    300 Bp Fragments, supplied by Diagenode, used in various techniques. Bioz Stars score: 91/100, based on 77 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp fragments/product/Diagenode
    Average 91 stars, based on 77 article reviews
    Price from $9.99 to $1999.99
    300 bp fragments - by Bioz Stars, 2020-09
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    90
    Illumina Inc 300 bp insert library
    Schematic overview of Poly(A)ClickSeq (PAC-seq). ( A ) RT-PCR is launched from a non-anchored Poly(T) primer containing a portion of the Illumina p7 adaptor. RT-PCR is performed in the presence of AzATP, AzGTP and AzCTP, but not AzTTP, thus only allowing chain termination to occur upstream of the poly(A) tail in the 3΄UTR. ( B ) 3΄-Azido-blocked cDNA fragments are ‘click-ligated’ to 5΄-hexynyl–functionalised DNA oligos containing the p5 Illumina adaptor. This yields triazole-linked ssDNA which can be PCR-amplified using primers to the p5 and p7 Illumina adaptors. ( C ) The cDNA library is analysed by gel electrophoresis and should consist of a smear of DNA products centered <t>∼200–300</t> bp. Appropriate cDNA fragment sizes are cut out of the gel and purified to yield a final library. ( D ) The final library consists of DNA fragments containing the Illumina p5 adaptor, a portion of the 3΄UTR, a stretch of As derived from both the RNA template and the poly(T) primer, and finally the p7 Illumina Indexing primer.
    300 Bp Insert Library, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/300 bp insert library/product/Illumina Inc
    Average 90 stars, based on 37 article reviews
    Price from $9.99 to $1999.99
    300 bp insert library - by Bioz Stars, 2020-09
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    Image Search Results


    —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of 300 bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.

    Journal: Genome Biology and Evolution

    Article Title: Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance

    doi: 10.1093/gbe/evx115

    Figure Lengend Snippet: —Presence of bla NDM-1 -plasmids in the clinical isolates and transconjugants. Complete sequence of bla NDM-1-plasmids circulating among Colombian and Mexican NDM-1-positive isolates and some related bla NDM-1 -positive (pPrY2001 and pNDM-BJ01) and bla NDM -negative (p06-1619-2) plasmids are shown along the x axis. Black shading indicates a match of ≥90% nucleotide identity in a window of 300 bp, calculated by comparing the query sequence ( x axis, reference plasmids) against the consensus from mapped reads for each strain ( y axis). Horizontal orange and light green bars represent the Tra1 and pPrY-like regions, respectively; blue rectangles represent the Tn 125 (or remnants) region in each plasmid. Vertical bars correspond to: gray for Klebsiella pneumoniae from Bogota (Colombia), red for Providencia rettgeri from Bogota (Colombia), blue for P. rettgeri from Bucaramanga (Colombia), green for P. rettgeri from Monterrey (Mexico), purple for Acinetobacter baumannii from Cali (Colombia). Simulated reads for the reference plasmids were included as an internal control.

    Article Snippet: Multiplexed total DNA libraries were prepared using the Nextera XT Library Preparation Kit and 300-bp paired end sequencing was performed on the Illumina MiSeq platform using the MiSeq v3 600-cycle reagent kit.

    Techniques: Sequencing, Plasmid Preparation

    Schematic overview of Poly(A)ClickSeq (PAC-seq). ( A ) RT-PCR is launched from a non-anchored Poly(T) primer containing a portion of the Illumina p7 adaptor. RT-PCR is performed in the presence of AzATP, AzGTP and AzCTP, but not AzTTP, thus only allowing chain termination to occur upstream of the poly(A) tail in the 3΄UTR. ( B ) 3΄-Azido-blocked cDNA fragments are ‘click-ligated’ to 5΄-hexynyl–functionalised DNA oligos containing the p5 Illumina adaptor. This yields triazole-linked ssDNA which can be PCR-amplified using primers to the p5 and p7 Illumina adaptors. ( C ) The cDNA library is analysed by gel electrophoresis and should consist of a smear of DNA products centered ∼200–300 bp. Appropriate cDNA fragment sizes are cut out of the gel and purified to yield a final library. ( D ) The final library consists of DNA fragments containing the Illumina p5 adaptor, a portion of the 3΄UTR, a stretch of As derived from both the RNA template and the poly(T) primer, and finally the p7 Illumina Indexing primer.

    Journal: Nucleic Acids Research

    Article Title: Poly(A)-ClickSeq: click-chemistry for next-generation 3΄-end sequencing without RNA enrichment or fragmentation

    doi: 10.1093/nar/gkx286

    Figure Lengend Snippet: Schematic overview of Poly(A)ClickSeq (PAC-seq). ( A ) RT-PCR is launched from a non-anchored Poly(T) primer containing a portion of the Illumina p7 adaptor. RT-PCR is performed in the presence of AzATP, AzGTP and AzCTP, but not AzTTP, thus only allowing chain termination to occur upstream of the poly(A) tail in the 3΄UTR. ( B ) 3΄-Azido-blocked cDNA fragments are ‘click-ligated’ to 5΄-hexynyl–functionalised DNA oligos containing the p5 Illumina adaptor. This yields triazole-linked ssDNA which can be PCR-amplified using primers to the p5 and p7 Illumina adaptors. ( C ) The cDNA library is analysed by gel electrophoresis and should consist of a smear of DNA products centered ∼200–300 bp. Appropriate cDNA fragment sizes are cut out of the gel and purified to yield a final library. ( D ) The final library consists of DNA fragments containing the Illumina p5 adaptor, a portion of the 3΄UTR, a stretch of As derived from both the RNA template and the poly(T) primer, and finally the p7 Illumina Indexing primer.

    Article Snippet: Optimized thermocycler conditions are as follows: 94° 4 min; 53° 30 s; 68° 10 min; [94° 30 s, 53° 30 s, 68° 2 min] × 20–22; 68° 5 min. Amplified PCR product was then run on a 2% precast agarose e-gel (Invitrogen, E-Gel Electrophoresis System) for 10 min and ∼200–300 bp fragments (for 1 × 150 SE Illumina) or ∼200–400 bp fragments (for 1 × 250 SE Illumina) were excised and cleaned using the Zymo Research Gel DNA Recovery Kit.

    Techniques: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Amplification, cDNA Library Assay, Nucleic Acid Electrophoresis, Purification, Derivative Assay