plasmids puc19 Thermo Fisher Search Results


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  • 78
    Thermo Fisher puc 19 plasmid
    Puc 19 Plasmid, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 78 stars, based on 3 article reviews
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    93
    Thermo Fisher plasmid puc19
    Overview of the microarray strategy . A library of chromosomal DNA fragments of P. syringae pv. phaseolicola NPS3121 (Psp NPS3121) was constructed in the <t>pUC19</t> vector and introduced into the E. coli Top10 strain. 30% (2880 clones) of the genomic library was sequenced, aligned and annotated against the complete genome of P. syringae pv. phaseolicola 1448A. This strategy allowed selection of 1911 clones that provided approximately 1× coverage of the genome. The fragments of 1911 clones were amplified by PCR reaction, and the products were printed on a microarray slide. This microarray was used to identify genes that are differentially expressed when bean leaf or pod extracts and apoplastic fluid were added to the growth medium.
    Plasmid Puc19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 111 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 93 stars, based on 111 article reviews
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    79
    Thermo Fisher supercoiled puc19 plasmid
    Bsu Ku binds circular DNA. ( A ) Left panel , Bsu Ku binding to covalently closed <t>pUC19</t> plasmid. The assay was performed as described in Materials and Methods incubating the indicated amounts of Bsu Ku with 100 ng of <t>supercoiled</t> plasmid pUC19. Products were analysed on 0.7% agarose electrophoresis. One half of each reaction mixture was loaded directly onto the agarose gel (direct loading lanes), while the other half was being treated with Proteinase K. After proteolytic digestion, those samples were loaded in the same agarose gel (Proteinase K treatment lanes). The electrophoretical mobility of the pUC19 plasmid in each case is indicated. In lane c, DNA was incubated with 50 ng of BSA. Right panel , Bsu Ku binding to supercoiled and relaxed plasmid DNA. The assay was performed essentially as described above. ( B ) Bsu Ku AP lyase activity can act on circular substrates. The assay was performed as described in Materials and Methods, incubating either 142 nM of Bsu Ku with 100 ng of plasmid without AP sites (pcDNA3.1) or 18, 36, 72 and 142 nM of Bsu Ku with 100 ng of plasmid containing AP sites (pcDNA3.1-AP) (left panel). The absence and presence of the AP sites in pcDNA3.1 and pcDNA3.1-AP, respectively, was confirmed after digestion with h APE1. As a control of the linear form, plasmids were also digested with EcoRI. NC : nicked circles; SC : supercoiled; L : linear. The assay shown in the right panel was performed by incubating 100 ng of plasmid without (pUC19) or with (pUC19-AP) AP sites with either h APE1 or 142 nM of Bsu Ku, as indicated. Figure 5B , right panel is a composite image made from different parts of the same experiment.
    Supercoiled Puc19 Plasmid, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    70
    Thermo Fisher xbai psti cut puc19 plasmid
    Bsu Ku binds circular DNA. ( A ) Left panel , Bsu Ku binding to covalently closed <t>pUC19</t> plasmid. The assay was performed as described in Materials and Methods incubating the indicated amounts of Bsu Ku with 100 ng of <t>supercoiled</t> plasmid pUC19. Products were analysed on 0.7% agarose electrophoresis. One half of each reaction mixture was loaded directly onto the agarose gel (direct loading lanes), while the other half was being treated with Proteinase K. After proteolytic digestion, those samples were loaded in the same agarose gel (Proteinase K treatment lanes). The electrophoretical mobility of the pUC19 plasmid in each case is indicated. In lane c, DNA was incubated with 50 ng of BSA. Right panel , Bsu Ku binding to supercoiled and relaxed plasmid DNA. The assay was performed essentially as described above. ( B ) Bsu Ku AP lyase activity can act on circular substrates. The assay was performed as described in Materials and Methods, incubating either 142 nM of Bsu Ku with 100 ng of plasmid without AP sites (pcDNA3.1) or 18, 36, 72 and 142 nM of Bsu Ku with 100 ng of plasmid containing AP sites (pcDNA3.1-AP) (left panel). The absence and presence of the AP sites in pcDNA3.1 and pcDNA3.1-AP, respectively, was confirmed after digestion with h APE1. As a control of the linear form, plasmids were also digested with EcoRI. NC : nicked circles; SC : supercoiled; L : linear. The assay shown in the right panel was performed by incubating 100 ng of plasmid without (pUC19) or with (pUC19-AP) AP sites with either h APE1 or 142 nM of Bsu Ku, as indicated. Figure 5B , right panel is a composite image made from different parts of the same experiment.
    Xbai Psti Cut Puc19 Plasmid, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 70/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 70 stars, based on 1 article reviews
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    78
    Thermo Fisher cip treated plasmid puc19
    Bsu Ku binds circular DNA. ( A ) Left panel , Bsu Ku binding to covalently closed <t>pUC19</t> plasmid. The assay was performed as described in Materials and Methods incubating the indicated amounts of Bsu Ku with 100 ng of <t>supercoiled</t> plasmid pUC19. Products were analysed on 0.7% agarose electrophoresis. One half of each reaction mixture was loaded directly onto the agarose gel (direct loading lanes), while the other half was being treated with Proteinase K. After proteolytic digestion, those samples were loaded in the same agarose gel (Proteinase K treatment lanes). The electrophoretical mobility of the pUC19 plasmid in each case is indicated. In lane c, DNA was incubated with 50 ng of BSA. Right panel , Bsu Ku binding to supercoiled and relaxed plasmid DNA. The assay was performed essentially as described above. ( B ) Bsu Ku AP lyase activity can act on circular substrates. The assay was performed as described in Materials and Methods, incubating either 142 nM of Bsu Ku with 100 ng of plasmid without AP sites (pcDNA3.1) or 18, 36, 72 and 142 nM of Bsu Ku with 100 ng of plasmid containing AP sites (pcDNA3.1-AP) (left panel). The absence and presence of the AP sites in pcDNA3.1 and pcDNA3.1-AP, respectively, was confirmed after digestion with h APE1. As a control of the linear form, plasmids were also digested with EcoRI. NC : nicked circles; SC : supercoiled; L : linear. The assay shown in the right panel was performed by incubating 100 ng of plasmid without (pUC19) or with (pUC19-AP) AP sites with either h APE1 or 142 nM of Bsu Ku, as indicated. Figure 5B , right panel is a composite image made from different parts of the same experiment.
    Cip Treated Plasmid Puc19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 78 stars, based on 8 article reviews
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    cip treated plasmid puc19 - by Bioz Stars, 2020-01
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    78
    Thermo Fisher supercoiled puc19 plasmid vector
    Bsu Ku binds circular DNA. ( A ) Left panel , Bsu Ku binding to covalently closed <t>pUC19</t> plasmid. The assay was performed as described in Materials and Methods incubating the indicated amounts of Bsu Ku with 100 ng of <t>supercoiled</t> plasmid pUC19. Products were analysed on 0.7% agarose electrophoresis. One half of each reaction mixture was loaded directly onto the agarose gel (direct loading lanes), while the other half was being treated with Proteinase K. After proteolytic digestion, those samples were loaded in the same agarose gel (Proteinase K treatment lanes). The electrophoretical mobility of the pUC19 plasmid in each case is indicated. In lane c, DNA was incubated with 50 ng of BSA. Right panel , Bsu Ku binding to supercoiled and relaxed plasmid DNA. The assay was performed essentially as described above. ( B ) Bsu Ku AP lyase activity can act on circular substrates. The assay was performed as described in Materials and Methods, incubating either 142 nM of Bsu Ku with 100 ng of plasmid without AP sites (pcDNA3.1) or 18, 36, 72 and 142 nM of Bsu Ku with 100 ng of plasmid containing AP sites (pcDNA3.1-AP) (left panel). The absence and presence of the AP sites in pcDNA3.1 and pcDNA3.1-AP, respectively, was confirmed after digestion with h APE1. As a control of the linear form, plasmids were also digested with EcoRI. NC : nicked circles; SC : supercoiled; L : linear. The assay shown in the right panel was performed by incubating 100 ng of plasmid without (pUC19) or with (pUC19-AP) AP sites with either h APE1 or 142 nM of Bsu Ku, as indicated. Figure 5B , right panel is a composite image made from different parts of the same experiment.
    Supercoiled Puc19 Plasmid Vector, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher puc19 plasmid dna
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Puc19 Plasmid Dna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 102 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher vectors puc19
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Vectors Puc19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 124 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Thermo Fisher bamhi linearized puc19 vectors
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Bamhi Linearized Puc19 Vectors, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    81
    Thermo Fisher cloning vector puc19
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Cloning Vector Puc19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 81/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    Thermo Fisher dephosphorylated puc19 vector
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Dephosphorylated Puc19 Vector, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 77/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Thermo Fisher puc19 smai vector
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Puc19 Smai Vector, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Thermo Fisher puc19 standard puc19
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Puc19 Standard Puc19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Thermo Fisher suicide vector puc19
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Suicide Vector Puc19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Thermo Fisher high copy number puc19
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    High Copy Number Puc19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Thermo Fisher kpni xhoi digested puc19 vector
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Kpni Xhoi Digested Puc19 Vector, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Thermo Fisher non specific puc19 vector
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Non Specific Puc19 Vector, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Thermo Fisher kpni digested puc19 vector
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Kpni Digested Puc19 Vector, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    Thermo Fisher empty vector puc19
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Empty Vector Puc19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 77/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Thermo Fisher puc19 vector carrying lacz sequence
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Puc19 Vector Carrying Lacz Sequence, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Thermo Fisher non supercoiled dna a 2 7 kb
    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the <t>pUC19</t> plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq <t>DNA</t> PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.
    Non Supercoiled Dna A 2 7 Kb, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Thermo Fisher high copy number cloning vector puc19
    In vivo functionality of E. coli CD (CodA, in pQE70 expression vector) and the DNA fragments that were selected from four metagenomic libraries: KANOS, URA4, URA3, and Vcz (in <t>pUC19</t> vector). Empty pQE70 vector was used as a negative control. Minimal medium (M9) was supplemented 100 mg/L ampicillin, 15 mg/L kanamycin, 0.1 mM IPTG, and either with 20 mg/L cytosine (M9 + C), isocytosine (M9 + isoC) or uracil (M9 + U, positive control).
    High Copy Number Cloning Vector Puc19, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher max efficiency dh5α
    In vivo DNA assembly and cloning in E . coli <t>DH5α.</t> ( A ) E . coli DH5α-mediated DNA assembly involves only two basic steps: 1) preparation of fragments with homologous ends and 2) introduction of the fragments into competent cells. This approach minimizes the time and reagents required for DNA assembly in comparison to other common methods, which contain a separate assembly step before the introduction of the constructed plasmid into a recombination-impaired cloning strain such as DH5α ( B-D ). Assembly is typically carried out either with added enzymes in vitro ( B ), or in vivo , using as a host S . cerevisiae ( C ) or specialized E . coli strains expressing the λ Red or RecET phage-based systems ( D ).
    Max Efficiency Dh5α, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 89 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Overview of the microarray strategy . A library of chromosomal DNA fragments of P. syringae pv. phaseolicola NPS3121 (Psp NPS3121) was constructed in the pUC19 vector and introduced into the E. coli Top10 strain. 30% (2880 clones) of the genomic library was sequenced, aligned and annotated against the complete genome of P. syringae pv. phaseolicola 1448A. This strategy allowed selection of 1911 clones that provided approximately 1× coverage of the genome. The fragments of 1911 clones were amplified by PCR reaction, and the products were printed on a microarray slide. This microarray was used to identify genes that are differentially expressed when bean leaf or pod extracts and apoplastic fluid were added to the growth medium.

    Journal: BMC Microbiology

    Article Title: Transcriptional profile of Pseudomonas syringae pv. phaseolicola NPS3121 in response to tissue extracts from a susceptible Phaseolus vulgaris L. cultivar

    doi: 10.1186/1471-2180-9-257

    Figure Lengend Snippet: Overview of the microarray strategy . A library of chromosomal DNA fragments of P. syringae pv. phaseolicola NPS3121 (Psp NPS3121) was constructed in the pUC19 vector and introduced into the E. coli Top10 strain. 30% (2880 clones) of the genomic library was sequenced, aligned and annotated against the complete genome of P. syringae pv. phaseolicola 1448A. This strategy allowed selection of 1911 clones that provided approximately 1× coverage of the genome. The fragments of 1911 clones were amplified by PCR reaction, and the products were printed on a microarray slide. This microarray was used to identify genes that are differentially expressed when bean leaf or pod extracts and apoplastic fluid were added to the growth medium.

    Article Snippet: The genomic fragments were ligated into the plasmid vector pUC19 (Invitrogen, California, USA) previously digested with BamHI, and the ligation mixture was used to transform Escherichia coli TOP10 cells (Invitrogen, California, USA).

    Techniques: Microarray, Construct, Plasmid Preparation, Selection, Clone Assay, Amplification, Polymerase Chain Reaction

    Non-sequence-specific endonucleolytic activity of the integrases. Supercoiled (CC) pUC19 DNA (200 ng) was incubated as described in Materials and Methods with the different INs (5 pmol) for 2 h at 37°C. The products were separated on 1%

    Journal: Nucleic Acids Research

    Article Title: Biochemical and random mutagenesis analysis of the region carrying the catalytic E152 amino acid of HIV-1 integrase

    doi: 10.1093/nar/gkh298

    Figure Lengend Snippet: Non-sequence-specific endonucleolytic activity of the integrases. Supercoiled (CC) pUC19 DNA (200 ng) was incubated as described in Materials and Methods with the different INs (5 pmol) for 2 h at 37°C. The products were separated on 1%

    Article Snippet: The pUC19 vector substrate of the endonucleolytic IN activity was purchased (Gibco) and maintained in E.coli DH5α bacterial strain.

    Techniques: Sequencing, Activity Assay, Incubation

    Bsu Ku binds circular DNA. ( A ) Left panel , Bsu Ku binding to covalently closed pUC19 plasmid. The assay was performed as described in Materials and Methods incubating the indicated amounts of Bsu Ku with 100 ng of supercoiled plasmid pUC19. Products were analysed on 0.7% agarose electrophoresis. One half of each reaction mixture was loaded directly onto the agarose gel (direct loading lanes), while the other half was being treated with Proteinase K. After proteolytic digestion, those samples were loaded in the same agarose gel (Proteinase K treatment lanes). The electrophoretical mobility of the pUC19 plasmid in each case is indicated. In lane c, DNA was incubated with 50 ng of BSA. Right panel , Bsu Ku binding to supercoiled and relaxed plasmid DNA. The assay was performed essentially as described above. ( B ) Bsu Ku AP lyase activity can act on circular substrates. The assay was performed as described in Materials and Methods, incubating either 142 nM of Bsu Ku with 100 ng of plasmid without AP sites (pcDNA3.1) or 18, 36, 72 and 142 nM of Bsu Ku with 100 ng of plasmid containing AP sites (pcDNA3.1-AP) (left panel). The absence and presence of the AP sites in pcDNA3.1 and pcDNA3.1-AP, respectively, was confirmed after digestion with h APE1. As a control of the linear form, plasmids were also digested with EcoRI. NC : nicked circles; SC : supercoiled; L : linear. The assay shown in the right panel was performed by incubating 100 ng of plasmid without (pUC19) or with (pUC19-AP) AP sites with either h APE1 or 142 nM of Bsu Ku, as indicated. Figure 5B , right panel is a composite image made from different parts of the same experiment.

    Journal: Nucleic Acids Research

    Article Title: Efficient processing of abasic sites by bacterial nonhomologous end-joining Ku proteins

    doi: 10.1093/nar/gku1029

    Figure Lengend Snippet: Bsu Ku binds circular DNA. ( A ) Left panel , Bsu Ku binding to covalently closed pUC19 plasmid. The assay was performed as described in Materials and Methods incubating the indicated amounts of Bsu Ku with 100 ng of supercoiled plasmid pUC19. Products were analysed on 0.7% agarose electrophoresis. One half of each reaction mixture was loaded directly onto the agarose gel (direct loading lanes), while the other half was being treated with Proteinase K. After proteolytic digestion, those samples were loaded in the same agarose gel (Proteinase K treatment lanes). The electrophoretical mobility of the pUC19 plasmid in each case is indicated. In lane c, DNA was incubated with 50 ng of BSA. Right panel , Bsu Ku binding to supercoiled and relaxed plasmid DNA. The assay was performed essentially as described above. ( B ) Bsu Ku AP lyase activity can act on circular substrates. The assay was performed as described in Materials and Methods, incubating either 142 nM of Bsu Ku with 100 ng of plasmid without AP sites (pcDNA3.1) or 18, 36, 72 and 142 nM of Bsu Ku with 100 ng of plasmid containing AP sites (pcDNA3.1-AP) (left panel). The absence and presence of the AP sites in pcDNA3.1 and pcDNA3.1-AP, respectively, was confirmed after digestion with h APE1. As a control of the linear form, plasmids were also digested with EcoRI. NC : nicked circles; SC : supercoiled; L : linear. The assay shown in the right panel was performed by incubating 100 ng of plasmid without (pUC19) or with (pUC19-AP) AP sites with either h APE1 or 142 nM of Bsu Ku, as indicated. Figure 5B , right panel is a composite image made from different parts of the same experiment.

    Article Snippet: Agarose gel retardation Two micrograms of supercoiled pUC19 plasmid (Fermentas) were incubated with 10 U of the nickase Nt.BStNBI to obtain nicked pUC19.

    Techniques: Binding Assay, Plasmid Preparation, Electrophoresis, Agarose Gel Electrophoresis, Incubation, Activity Assay, Activated Clotting Time Assay

    Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the pUC19 plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq DNA PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.

    Journal: PLoS ONE

    Article Title: A Bumpy Ride on the Diagnostic Bench of Massive Parallel Sequencing, the Case of the Mitochondrial Genome

    doi: 10.1371/journal.pone.0112950

    Figure Lengend Snippet: Genome Coverage plots. Representation of the MPS relative coverage of both strands (rc+: relative coverage of the plus strand, rc-: relative coverage of the negative strand) of the pUC19 plasmid, or mtDNA molecules obtained from the Ion Torrent PGM or MiSeq sequencing system. The outer circle symbolizes the pUC19 (A) or mtDNA (B, C, D) gene structure, respectively. 1A: Use of the Ion Torrent PGM standard protocol on the pUC19 plasmid. 1B: Use of three different fragmentation methods in combination with the Ion Torrent sequencing protocol on the mtDNA: Ion Shear Plus Reagents (enzymatic), NEBNext dsDNA Fragmentase (enzymatic) and Covaris (physical). 1C: Use of an Ion Torrent PGM protocol without PCR amplification in the library construction on the mtDNA. 1D: LR-PCR products of the mtDNA were Covaris (physical) or NEBNext dsDNA Fragmentase (enzymatic) sheared, followed by a TruSeq DNA PCR free protocol on a MiSeq instrument. The same six samples were processed with a Nextera XT kit (enzymatic shearing and PCR amplification in library preparation) prior to MiSeq analysis.

    Article Snippet: Taking the average of all ratios per position resulted in the average error rate of the pUC19 plasmid DNA.

    Techniques: Plasmid Preparation, Sequencing, Polymerase Chain Reaction, Amplification

    In vivo functionality of E. coli CD (CodA, in pQE70 expression vector) and the DNA fragments that were selected from four metagenomic libraries: KANOS, URA4, URA3, and Vcz (in pUC19 vector). Empty pQE70 vector was used as a negative control. Minimal medium (M9) was supplemented 100 mg/L ampicillin, 15 mg/L kanamycin, 0.1 mM IPTG, and either with 20 mg/L cytosine (M9 + C), isocytosine (M9 + isoC) or uracil (M9 + U, positive control).

    Journal: Frontiers in Microbiology

    Article Title: Discovery of Bacterial Deaminases That Convert 5-Fluoroisocytosine Into 5-Fluorouracil

    doi: 10.3389/fmicb.2018.02375

    Figure Lengend Snippet: In vivo functionality of E. coli CD (CodA, in pQE70 expression vector) and the DNA fragments that were selected from four metagenomic libraries: KANOS, URA4, URA3, and Vcz (in pUC19 vector). Empty pQE70 vector was used as a negative control. Minimal medium (M9) was supplemented 100 mg/L ampicillin, 15 mg/L kanamycin, 0.1 mM IPTG, and either with 20 mg/L cytosine (M9 + C), isocytosine (M9 + isoC) or uracil (M9 + U, positive control).

    Article Snippet: High copy number cloning vector pUC19 (Thermo Fisher Scientific) was used for the preparation of metagenomic libraries ( ).

    Techniques: In Vivo, Expressing, Plasmid Preparation, Negative Control, Positive Control

    In vivo DNA assembly and cloning in E . coli DH5α. ( A ) E . coli DH5α-mediated DNA assembly involves only two basic steps: 1) preparation of fragments with homologous ends and 2) introduction of the fragments into competent cells. This approach minimizes the time and reagents required for DNA assembly in comparison to other common methods, which contain a separate assembly step before the introduction of the constructed plasmid into a recombination-impaired cloning strain such as DH5α ( B-D ). Assembly is typically carried out either with added enzymes in vitro ( B ), or in vivo , using as a host S . cerevisiae ( C ) or specialized E . coli strains expressing the λ Red or RecET phage-based systems ( D ).

    Journal: PLoS ONE

    Article Title: Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies

    doi: 10.1371/journal.pone.0137466

    Figure Lengend Snippet: In vivo DNA assembly and cloning in E . coli DH5α. ( A ) E . coli DH5α-mediated DNA assembly involves only two basic steps: 1) preparation of fragments with homologous ends and 2) introduction of the fragments into competent cells. This approach minimizes the time and reagents required for DNA assembly in comparison to other common methods, which contain a separate assembly step before the introduction of the constructed plasmid into a recombination-impaired cloning strain such as DH5α ( B-D ). Assembly is typically carried out either with added enzymes in vitro ( B ), or in vivo , using as a host S . cerevisiae ( C ) or specialized E . coli strains expressing the λ Red or RecET phage-based systems ( D ).

    Article Snippet: Bacterial strains The following commercial products were used: Max Efficiency DH5α (Life Technologies, Carlsbad, CA; chemically competent, ~109 colony-forming unit or CFU / μg pUC19), High Efficiency NEB 5-alpha (New England Biolabs, Ipswich, MA; chemically competent, CFU ~109 /μg pUC19), and NEB 5-alpha Electrocompetent E . coli (New England Biolabs, CFU ~1010 /μg pUC19).

    Techniques: In Vivo, Clone Assay, Construct, Plasmid Preparation, In Vitro, Expressing