taq i New England Biolabs Search Results


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  • 94
    New England Biolabs r0149m
    Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved <t>Taq</t> α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .
    R0149m, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 58 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher sequencing invitrogen 450030 t4 dna ligase new england biolabs m0202s experimental models
    Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved <t>Taq</t> α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .
    Sequencing Invitrogen 450030 T4 Dna Ligase New England Biolabs M0202s Experimental Models, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Qiagen new england biolab s standard taq
    Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved <t>Taq</t> α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .
    New England Biolab S Standard Taq, supplied by Qiagen, used in various techniques. Bioz Stars score: 86/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    New England Biolabs lipofectamine 2000 transfection kit new england biolabs
    Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved <t>Taq</t> α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .
    Lipofectamine 2000 Transfection Kit New England Biolabs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs new englad biolabs
    Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved <t>Taq</t> α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .
    New Englad Biolabs, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    New England Biolabs taq i
    Genotyping of <t>phlD</t> -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.
    Taq I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 510 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs taq i restriction enzymes
    Selective and quantitative amplification of targets. ( A ) Selective amplification of <t>DNA</t> flanking Tn insertions. Genomic DNA of 16 individual mutants were used to amplify DNA fragments until nearby <t>Taq</t> I restriction sites, and resolved on a sequencing gel. The mutants analyzed were: lane 1, SSA1 (V45B4); lane 2, YDJ1 (V6A2); lane 3, DDR48 (V6G5); lane 4, SSA2 (V18E7); lane 5, SSA3 (V41F1); lane 6, SSA4 (V5E8); lane 7, SSB1 (V23F11); lane 8, SSB2 (V32E7); lane 9, HSP35 (V18D3); lane 10, SSA4 (V3B8); lane 11, SOD2 (V4D11); lane 12, SSB2 (V47A3); lane 13, UBI4 (V36G6); lane 14, TPS2 (V2C2); lane 15, HSP104 (V8D8); lane 16, HSP104 (V22A9). Two bands each are seen for most of the mutants, consistent with specific amplification of DNA from both sides of each Tn insertion. ( B ) Quantitative amplification of targets, demonstrated by a reconstruction experiment. Ten different Tn insertion mutants were grown individually and then mixed together in equal proportions to obtain a pool of eight mutants (pool A, lane 1) and two mutants (pool B, lane 2). These two pools were then mixed at different ratios such that the abundance of the two mutants from pool B, with respect to the other mutants, was the same (lane 3) or was decreased 2-fold (lane 4), 4-fold (lane 5), 8-fold (lane 6) or 16-fold (lane 7). Genomic DNA was isolated from all the pools immediately and processed to amplify the targets. Equal volumes of PCR products were loaded, except for lane 2 where it was one-fifth of other lanes. While the intensity of the bands from eight mutants remained constant in lanes 3–7, that of two mutants (arrows) decreased in proportion to the abundance of the mutants in the pools, confirming quantitative amplification of the targets.
    Taq I Restriction Enzymes, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 257 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs endonuclease taq i
    Selective and quantitative amplification of targets. ( A ) Selective amplification of <t>DNA</t> flanking Tn insertions. Genomic DNA of 16 individual mutants were used to amplify DNA fragments until nearby <t>Taq</t> I restriction sites, and resolved on a sequencing gel. The mutants analyzed were: lane 1, SSA1 (V45B4); lane 2, YDJ1 (V6A2); lane 3, DDR48 (V6G5); lane 4, SSA2 (V18E7); lane 5, SSA3 (V41F1); lane 6, SSA4 (V5E8); lane 7, SSB1 (V23F11); lane 8, SSB2 (V32E7); lane 9, HSP35 (V18D3); lane 10, SSA4 (V3B8); lane 11, SOD2 (V4D11); lane 12, SSB2 (V47A3); lane 13, UBI4 (V36G6); lane 14, TPS2 (V2C2); lane 15, HSP104 (V8D8); lane 16, HSP104 (V22A9). Two bands each are seen for most of the mutants, consistent with specific amplification of DNA from both sides of each Tn insertion. ( B ) Quantitative amplification of targets, demonstrated by a reconstruction experiment. Ten different Tn insertion mutants were grown individually and then mixed together in equal proportions to obtain a pool of eight mutants (pool A, lane 1) and two mutants (pool B, lane 2). These two pools were then mixed at different ratios such that the abundance of the two mutants from pool B, with respect to the other mutants, was the same (lane 3) or was decreased 2-fold (lane 4), 4-fold (lane 5), 8-fold (lane 6) or 16-fold (lane 7). Genomic DNA was isolated from all the pools immediately and processed to amplify the targets. Equal volumes of PCR products were loaded, except for lane 2 where it was one-fifth of other lanes. While the intensity of the bands from eight mutants remained constant in lanes 3–7, that of two mutants (arrows) decreased in proportion to the abundance of the mutants in the pools, confirming quantitative amplification of the targets.
    Endonuclease Taq I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs dna taq
    Selective and quantitative amplification of targets. ( A ) Selective amplification of <t>DNA</t> flanking Tn insertions. Genomic DNA of 16 individual mutants were used to amplify DNA fragments until nearby <t>Taq</t> I restriction sites, and resolved on a sequencing gel. The mutants analyzed were: lane 1, SSA1 (V45B4); lane 2, YDJ1 (V6A2); lane 3, DDR48 (V6G5); lane 4, SSA2 (V18E7); lane 5, SSA3 (V41F1); lane 6, SSA4 (V5E8); lane 7, SSB1 (V23F11); lane 8, SSB2 (V32E7); lane 9, HSP35 (V18D3); lane 10, SSA4 (V3B8); lane 11, SOD2 (V4D11); lane 12, SSB2 (V47A3); lane 13, UBI4 (V36G6); lane 14, TPS2 (V2C2); lane 15, HSP104 (V8D8); lane 16, HSP104 (V22A9). Two bands each are seen for most of the mutants, consistent with specific amplification of DNA from both sides of each Tn insertion. ( B ) Quantitative amplification of targets, demonstrated by a reconstruction experiment. Ten different Tn insertion mutants were grown individually and then mixed together in equal proportions to obtain a pool of eight mutants (pool A, lane 1) and two mutants (pool B, lane 2). These two pools were then mixed at different ratios such that the abundance of the two mutants from pool B, with respect to the other mutants, was the same (lane 3) or was decreased 2-fold (lane 4), 4-fold (lane 5), 8-fold (lane 6) or 16-fold (lane 7). Genomic DNA was isolated from all the pools immediately and processed to amplify the targets. Equal volumes of PCR products were loaded, except for lane 2 where it was one-fifth of other lanes. While the intensity of the bands from eight mutants remained constant in lanes 3–7, that of two mutants (arrows) decreased in proportion to the abundance of the mutants in the pools, confirming quantitative amplification of the targets.
    Dna Taq, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    New England Biolabs restriction enzyme taq i
    Restriction enzyme digestion patterns obtained with <t>Taq</t> I. Digestion mixtures were electrophoresed on 1.5% agarose gels. On each panel, the gel is flanked by a 100-bp ladder (Invitrogen Life Technologies) (lane MW). (A) The three species illustrated are unambiguously identified by the <t>Taq</t> I pattern. However, for the species illustrated in panel B, the Taq I patterns are similar to one another, although clearly distinct from that of the species in panel A.
    Restriction Enzyme Taq I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 70 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs taq∝ i
    Restriction enzyme digestion patterns obtained with <t>Taq</t> I. Digestion mixtures were electrophoresed on 1.5% agarose gels. On each panel, the gel is flanked by a 100-bp ladder (Invitrogen Life Technologies) (lane MW). (A) The three species illustrated are unambiguously identified by the <t>Taq</t> I pattern. However, for the species illustrated in panel B, the Taq I patterns are similar to one another, although clearly distinct from that of the species in panel A.
    Taq∝ I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved Taq α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .

    Journal: PLoS ONE

    Article Title: Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

    doi: 10.1371/journal.pone.0087053

    Figure Lengend Snippet: Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved Taq α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .

    Article Snippet: One µg of Taq α I digested DNA was made blunt using the NEBNext End Repair Module (NEB) according to the manufacturer’s instructions.

    Techniques: Sequencing

    Manhattan plot of la1-mu1 Taq α I sequencing. ( A ) Manhattan plot showing the distribution of reads from la1-mu1 genomic DNA mapped throughout the B73 genome. Alternating colors represent each of the ten maize chromosomes. Each x-axis pixel represents a bin of 1 Mb and the logarithmic y-axis denotes the number of reads mapping to each bin. The red line represents the known genetic map position for the la1 reference mutation. Each triangle below the plot represents the approximate location of mapped MFS. ( B ) Expanded Manhattan plot of a 1 Mb interval corresponding to the approximate map position of la1 . Same as top with each x-axis pixel representing a bin of 1 kb. Filtered genes in the 1 Mb interval are shown as black rectangles. MFS mapping to this interval are shown as inverted red triangles.

    Journal: PLoS ONE

    Article Title: Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

    doi: 10.1371/journal.pone.0087053

    Figure Lengend Snippet: Manhattan plot of la1-mu1 Taq α I sequencing. ( A ) Manhattan plot showing the distribution of reads from la1-mu1 genomic DNA mapped throughout the B73 genome. Alternating colors represent each of the ten maize chromosomes. Each x-axis pixel represents a bin of 1 Mb and the logarithmic y-axis denotes the number of reads mapping to each bin. The red line represents the known genetic map position for the la1 reference mutation. Each triangle below the plot represents the approximate location of mapped MFS. ( B ) Expanded Manhattan plot of a 1 Mb interval corresponding to the approximate map position of la1 . Same as top with each x-axis pixel representing a bin of 1 kb. Filtered genes in the 1 Mb interval are shown as black rectangles. MFS mapping to this interval are shown as inverted red triangles.

    Article Snippet: One µg of Taq α I digested DNA was made blunt using the NEBNext End Repair Module (NEB) according to the manufacturer’s instructions.

    Techniques: Sequencing, Mutagenesis

    Mu - Taq α I Library Construction. Digesting genomic DNA with Taq α I creates a library of fragments. Fragments containing a Mu -MFS junction will all contain a degenerate 39 nt Mu TIR tag along with 31–35 nt of flanking genomic sequence at one end of the 2×75 nt paired-end read. These fragments are computationally identified and the Mu flanking sequence (MFS) is mapped to the maize reference genome.

    Journal: PLoS ONE

    Article Title: Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

    doi: 10.1371/journal.pone.0087053

    Figure Lengend Snippet: Mu - Taq α I Library Construction. Digesting genomic DNA with Taq α I creates a library of fragments. Fragments containing a Mu -MFS junction will all contain a degenerate 39 nt Mu TIR tag along with 31–35 nt of flanking genomic sequence at one end of the 2×75 nt paired-end read. These fragments are computationally identified and the Mu flanking sequence (MFS) is mapped to the maize reference genome.

    Article Snippet: One µg of Taq α I digested DNA was made blunt using the NEBNext End Repair Module (NEB) according to the manufacturer’s instructions.

    Techniques: Sequencing

    A chromatogram screenshot of the DNA sequence (partial) of MdACS3a encompassing SNPs G 866 /T 866 and C 870 /T 870 in six apple cultivars—‘Florina’, ’Fuji red sport’, ‘Gala’, ‘Golden Delicious’ and ‘Granny Smith’. The oval circles in brown and red indicate the homozygous or heterozygous status at the 866th and 870th nucleotides in the coding sequence of MdACS3a , respectively. The recognition sites of restriction enzymes Bst NI and Taq α I are provided to show that the mutation from G 866 to T 866 abolishes the restriction site of Bst NI while the mutation from C 870 to T 870 gives rise to a restriction site for Taq α I. The right panel shows allelotypes of MdACS3a as represented by the SNP alleles, where G 866 stands for allele MdACS3a (wild type), T 866 for MdACS3a-G289V (functional null allele), C 870 also for allele MdACS3a and T 870 for Mdacs3a (transcriptional null allele).

    Journal: Horticulture Research

    Article Title: Assessing the allelotypic effect of two aminocyclopropane carboxylic acid synthase-encoding genes MdACS1 and MdACS3a on fruit ethylene production and softening in Malus

    doi: 10.1038/hortres.2016.24

    Figure Lengend Snippet: A chromatogram screenshot of the DNA sequence (partial) of MdACS3a encompassing SNPs G 866 /T 866 and C 870 /T 870 in six apple cultivars—‘Florina’, ’Fuji red sport’, ‘Gala’, ‘Golden Delicious’ and ‘Granny Smith’. The oval circles in brown and red indicate the homozygous or heterozygous status at the 866th and 870th nucleotides in the coding sequence of MdACS3a , respectively. The recognition sites of restriction enzymes Bst NI and Taq α I are provided to show that the mutation from G 866 to T 866 abolishes the restriction site of Bst NI while the mutation from C 870 to T 870 gives rise to a restriction site for Taq α I. The right panel shows allelotypes of MdACS3a as represented by the SNP alleles, where G 866 stands for allele MdACS3a (wild type), T 866 for MdACS3a-G289V (functional null allele), C 870 also for allele MdACS3a and T 870 for Mdacs3a (transcriptional null allele).

    Article Snippet: To detect alleles MdACS3a-G289V and Mdacs3a , the PCR products were restricted with enzymes Bst NI and Taq α I (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s instruction, respectively.

    Techniques: Sequencing, Mutagenesis, Functional Assay

    Agarose gel analyses of markers ACS1 ( a ), CAPS 866 ( b ) and CAPS 870 ( c ). For marker ACS1, the PCR products amplified by primers ACS1–5F/R were directly analyzed. Allelotypes MdACS1-1/1 , MdACS1–2/2 and MdACS1-1/2 are denoted with ‘1/1’, ‘2/2’ and ‘1/2’, respectively. For marker CAPS 866 , the PCR products were first amplified by primers ACS3a-289F/R and then digested with enzyme Bst NI, which restricts the MdACS3a (G 866 ) allele into the two lower bands. Allelotypes MdACS3a / MdACS3a (G 866 /G 866 ), MdACS3a / MdACS3a-G289V (G 866 /T 866 ) and MdACS3a-G289V/G289V (T 866 /T 866 ) are noted with ‘G/G’, ‘G/T’ and ‘T/T’, respectively. For marker CAPS 870 , enzyme Taq α I restricts the Mdacs3a (T 870 ) allele into the two lower bands. Allelotypes MdACS3a / MdACS3a (C 870 /C 870 ), MdACS3a / mdacs3a (C 870 /T 870 ) and mdacs3a/mdacs3a (T 870 /T 870 ) are noted with ‘C/C’, ‘C/T’ and ‘T/T’, respectively.

    Journal: Horticulture Research

    Article Title: Assessing the allelotypic effect of two aminocyclopropane carboxylic acid synthase-encoding genes MdACS1 and MdACS3a on fruit ethylene production and softening in Malus

    doi: 10.1038/hortres.2016.24

    Figure Lengend Snippet: Agarose gel analyses of markers ACS1 ( a ), CAPS 866 ( b ) and CAPS 870 ( c ). For marker ACS1, the PCR products amplified by primers ACS1–5F/R were directly analyzed. Allelotypes MdACS1-1/1 , MdACS1–2/2 and MdACS1-1/2 are denoted with ‘1/1’, ‘2/2’ and ‘1/2’, respectively. For marker CAPS 866 , the PCR products were first amplified by primers ACS3a-289F/R and then digested with enzyme Bst NI, which restricts the MdACS3a (G 866 ) allele into the two lower bands. Allelotypes MdACS3a / MdACS3a (G 866 /G 866 ), MdACS3a / MdACS3a-G289V (G 866 /T 866 ) and MdACS3a-G289V/G289V (T 866 /T 866 ) are noted with ‘G/G’, ‘G/T’ and ‘T/T’, respectively. For marker CAPS 870 , enzyme Taq α I restricts the Mdacs3a (T 870 ) allele into the two lower bands. Allelotypes MdACS3a / MdACS3a (C 870 /C 870 ), MdACS3a / mdacs3a (C 870 /T 870 ) and mdacs3a/mdacs3a (T 870 /T 870 ) are noted with ‘C/C’, ‘C/T’ and ‘T/T’, respectively.

    Article Snippet: To detect alleles MdACS3a-G289V and Mdacs3a , the PCR products were restricted with enzymes Bst NI and Taq α I (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s instruction, respectively.

    Techniques: Agarose Gel Electrophoresis, Marker, Polymerase Chain Reaction, Amplification

    Methylation analysis of the CpG island in the DACH1 promoter. (A) : Schematic depiction of the CpG islands located respectively 5’ upstream from the DACH1 transcription start site (CpG I) and in the first intron of the DACH1 gene (CpG II). (B) : Examples of CpG I COBRA analysis in colorectal cancers with intense (red), patchy (green), or no (blue) DACH1 protein immunostaining and in 4 colon cancer cell lines characterized by low (HT29 and Caco2) or very low (HCT116 and CO115) DACH1 expression (based on microarray-documented DACH1 mRNA expression levels - see also Additional file 9 ). Asterisks indicate Taq α I -digested DNA fragments representing methylated alleles; slower-migrating fragments correspond to undigested, unmethylated DNA. MW, molecular weight; bp, base pair.

    Journal: BMC Cancer

    Article Title: A comprehensive look at transcription factor gene expression changes in colorectal adenomas

    doi: 10.1186/1471-2407-14-46

    Figure Lengend Snippet: Methylation analysis of the CpG island in the DACH1 promoter. (A) : Schematic depiction of the CpG islands located respectively 5’ upstream from the DACH1 transcription start site (CpG I) and in the first intron of the DACH1 gene (CpG II). (B) : Examples of CpG I COBRA analysis in colorectal cancers with intense (red), patchy (green), or no (blue) DACH1 protein immunostaining and in 4 colon cancer cell lines characterized by low (HT29 and Caco2) or very low (HCT116 and CO115) DACH1 expression (based on microarray-documented DACH1 mRNA expression levels - see also Additional file 9 ). Asterisks indicate Taq α I -digested DNA fragments representing methylated alleles; slower-migrating fragments correspond to undigested, unmethylated DNA. MW, molecular weight; bp, base pair.

    Article Snippet: The amplified products were digested with the Taq α I restriction enzyme (New England Biolabs, Beverly, MA, USA) and subjected to 2% agarose gel electrophoresis and ethidium bromide staining.

    Techniques: Methylation, Combined Bisulfite Restriction Analysis Assay, Immunostaining, Expressing, Microarray, Molecular Weight

    Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.

    Journal: Applied and Environmental Microbiology

    Article Title: Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat

    doi: 10.1128/AEM.67.10.4414-4425.2001

    Figure Lengend Snippet: Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.

    Article Snippet: To determine the genotype of phlD + populations, amplification products were digested with Hae III or Taq I (New England Biolabs, Beverly, Mass.).

    Techniques: Amplification, Positive Control

    Selective and quantitative amplification of targets. ( A ) Selective amplification of DNA flanking Tn insertions. Genomic DNA of 16 individual mutants were used to amplify DNA fragments until nearby Taq I restriction sites, and resolved on a sequencing gel. The mutants analyzed were: lane 1, SSA1 (V45B4); lane 2, YDJ1 (V6A2); lane 3, DDR48 (V6G5); lane 4, SSA2 (V18E7); lane 5, SSA3 (V41F1); lane 6, SSA4 (V5E8); lane 7, SSB1 (V23F11); lane 8, SSB2 (V32E7); lane 9, HSP35 (V18D3); lane 10, SSA4 (V3B8); lane 11, SOD2 (V4D11); lane 12, SSB2 (V47A3); lane 13, UBI4 (V36G6); lane 14, TPS2 (V2C2); lane 15, HSP104 (V8D8); lane 16, HSP104 (V22A9). Two bands each are seen for most of the mutants, consistent with specific amplification of DNA from both sides of each Tn insertion. ( B ) Quantitative amplification of targets, demonstrated by a reconstruction experiment. Ten different Tn insertion mutants were grown individually and then mixed together in equal proportions to obtain a pool of eight mutants (pool A, lane 1) and two mutants (pool B, lane 2). These two pools were then mixed at different ratios such that the abundance of the two mutants from pool B, with respect to the other mutants, was the same (lane 3) or was decreased 2-fold (lane 4), 4-fold (lane 5), 8-fold (lane 6) or 16-fold (lane 7). Genomic DNA was isolated from all the pools immediately and processed to amplify the targets. Equal volumes of PCR products were loaded, except for lane 2 where it was one-fifth of other lanes. While the intensity of the bands from eight mutants remained constant in lanes 3–7, that of two mutants (arrows) decreased in proportion to the abundance of the mutants in the pools, confirming quantitative amplification of the targets.

    Journal: Nucleic Acids Research

    Article Title: Quantitative target display: a method to screen yeast mutants conferring quantitative phenotypes by 'mutant DNA fingerprints'

    doi:

    Figure Lengend Snippet: Selective and quantitative amplification of targets. ( A ) Selective amplification of DNA flanking Tn insertions. Genomic DNA of 16 individual mutants were used to amplify DNA fragments until nearby Taq I restriction sites, and resolved on a sequencing gel. The mutants analyzed were: lane 1, SSA1 (V45B4); lane 2, YDJ1 (V6A2); lane 3, DDR48 (V6G5); lane 4, SSA2 (V18E7); lane 5, SSA3 (V41F1); lane 6, SSA4 (V5E8); lane 7, SSB1 (V23F11); lane 8, SSB2 (V32E7); lane 9, HSP35 (V18D3); lane 10, SSA4 (V3B8); lane 11, SOD2 (V4D11); lane 12, SSB2 (V47A3); lane 13, UBI4 (V36G6); lane 14, TPS2 (V2C2); lane 15, HSP104 (V8D8); lane 16, HSP104 (V22A9). Two bands each are seen for most of the mutants, consistent with specific amplification of DNA from both sides of each Tn insertion. ( B ) Quantitative amplification of targets, demonstrated by a reconstruction experiment. Ten different Tn insertion mutants were grown individually and then mixed together in equal proportions to obtain a pool of eight mutants (pool A, lane 1) and two mutants (pool B, lane 2). These two pools were then mixed at different ratios such that the abundance of the two mutants from pool B, with respect to the other mutants, was the same (lane 3) or was decreased 2-fold (lane 4), 4-fold (lane 5), 8-fold (lane 6) or 16-fold (lane 7). Genomic DNA was isolated from all the pools immediately and processed to amplify the targets. Equal volumes of PCR products were loaded, except for lane 2 where it was one-fifth of other lanes. While the intensity of the bands from eight mutants remained constant in lanes 3–7, that of two mutants (arrows) decreased in proportion to the abundance of the mutants in the pools, confirming quantitative amplification of the targets.

    Article Snippet: A typical 10 µl ligation reaction contained 250 ng of DNA fragments, 5 µM Taq I adapters, 25 mM Tris–HCl (pH 7.5), 5 mM MgCl2 , 5 mM dithiothreitol, 500 µΜ ATP, 12.5 µg/ml BSA and 200 cohesive-end units of T4 DNA ligase (New England Biolabs) and was incubated at 16°C for 12–16 h. Primary PCR was done in a 25 µl reaction volume containing 200 µM each dNTP, 40 nM each primer (Taq1-N 5′-ATGAGTCCTGACCGA, and Tn3-O2, 5′-TTAACGTGAGTTTTCGTTCCACTG), 2 mM MgSO4 and 1 U Taq DNA polymerase (Promega) in 1× PCR buffer (20 mM Tris–HCl pH 9.2, 10 mM KCl, 10 mM ammonium sulfate, 0.1% Triton X-100) and adapter-ligated DNA.

    Techniques: Amplification, Sequencing, Isolation, Polymerase Chain Reaction

    Restriction enzyme digestion patterns obtained with Taq I. Digestion mixtures were electrophoresed on 1.5% agarose gels. On each panel, the gel is flanked by a 100-bp ladder (Invitrogen Life Technologies) (lane MW). (A) The three species illustrated are unambiguously identified by the Taq I pattern. However, for the species illustrated in panel B, the Taq I patterns are similar to one another, although clearly distinct from that of the species in panel A.

    Journal: Journal of Clinical Microbiology

    Article Title: Detection and Identification of Bartonella Species Pathogenic for Humans by PCR Amplification Targeting the Riboflavin Synthase Gene (ribC)

    doi: 10.1128/JCM.41.3.1069-1072.2003

    Figure Lengend Snippet: Restriction enzyme digestion patterns obtained with Taq I. Digestion mixtures were electrophoresed on 1.5% agarose gels. On each panel, the gel is flanked by a 100-bp ladder (Invitrogen Life Technologies) (lane MW). (A) The three species illustrated are unambiguously identified by the Taq I pattern. However, for the species illustrated in panel B, the Taq I patterns are similar to one another, although clearly distinct from that of the species in panel A.

    Article Snippet: Each reaction mixture in which amplicons were detected was subjected to digestion with the restriction enzyme Taq I (New England Biolabs).

    Techniques: