taq α  (New England Biolabs)


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    Name:
    Taq alpha I
    Description:
    Taq alpha I 20 000 units
    Catalog Number:
    r0149l
    Price:
    257
    Size:
    20 000 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs taq α
    Taq alpha I
    Taq alpha I 20 000 units
    https://www.bioz.com/result/taq α/product/New England Biolabs
    Average 94 stars, based on 144 article reviews
    Price from $9.99 to $1999.99
    taq α - by Bioz Stars, 2020-09
    94/100 stars

    Images

    1) Product Images from "Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy"

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

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0087053

    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] .
    Figure Legend 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] .

    Techniques Used: 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.
    Figure Legend 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.

    Techniques Used: 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.
    Figure Legend 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.

    Techniques Used: Sequencing

    2) Product Images from "Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy"

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

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0087053

    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] .
    Figure Legend 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] .

    Techniques Used: 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.
    Figure Legend 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.

    Techniques Used: 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.
    Figure Legend 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.

    Techniques Used: Sequencing

    3) Product Images from "Assessing the allelotypic effect of two aminocyclopropane carboxylic acid synthase-encoding genes MdACS1 and MdACS3a on fruit ethylene production and softening in Malus"

    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

    Journal: Horticulture Research

    doi: 10.1038/hortres.2016.24

    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).
    Figure Legend 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).

    Techniques Used: 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.
    Figure Legend 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.

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

    4) Product Images from "A comprehensive look at transcription factor gene expression changes in colorectal adenomas"

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

    Journal: BMC Cancer

    doi: 10.1186/1471-2407-14-46

    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.
    Figure Legend 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.

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

    Related Articles

    Clone Assay:

    Article Title: Nocturnal Production of Endospores in Natural Populations of Epulopiscium-Like Surgeonfish Symbionts
    Article Snippet: .. Unique clones were selected based on restriction fragment length polymorphisms of digests of PCR-amplified inserts using HaeIII, HhaI, Taq α I, and MseI (New England Biolabs). .. Plasmid DNA from selected clones was isolated using the RPM kit (Q-BIOgene).

    Amplification:

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

    Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
    Article Snippet: .. PCR amplified and purified 2 μg library material was then digested overnight with 100 U of TaqI (NEB, cat#R0149S) in NEB buffer 4 in a final volume of 100 μL at 65 °C. ..

    Agarose Gel Electrophoresis:

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

    Synthesized:

    Article Title: Elk1 affects katanin and spastin proteins via differential transcriptional and post-transcriptional regulations
    Article Snippet: .. For this reaction, specific primers ( ) were synthesized by Alpha DNA and One Taq Enzyme System (NEB) was used as DNA polymerase and buffer solution. .. The amplified fragments were individually cloned into pGL3-basic luciferase reporter vector using SacI, HindIII, and XhoI cloning sites inside the vector.

    Purification:

    Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
    Article Snippet: .. PCR amplified and purified 2 μg library material was then digested overnight with 100 U of TaqI (NEB, cat#R0149S) in NEB buffer 4 in a final volume of 100 μL at 65 °C. ..

    Polymerase Chain Reaction:

    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
    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. .. The restricted PCR products were assayed by electrophoresis on 1.5% agarose gel and then stained with ethidium bromide for visualization and documentation as described previously.

    Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
    Article Snippet: .. PCR amplified and purified 2 μg library material was then digested overnight with 100 U of TaqI (NEB, cat#R0149S) in NEB buffer 4 in a final volume of 100 μL at 65 °C. ..

    Article Title: Nocturnal Production of Endospores in Natural Populations of Epulopiscium-Like Surgeonfish Symbionts
    Article Snippet: .. Unique clones were selected based on restriction fragment length polymorphisms of digests of PCR-amplified inserts using HaeIII, HhaI, Taq α I, and MseI (New England Biolabs). .. Plasmid DNA from selected clones was isolated using the RPM kit (Q-BIOgene).

    Staining:

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

    Chloramphenicol Acetyltransferase Assay:

    Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling
    Article Snippet: .. PCR amplified and purified 2 μg library material was then digested overnight with 100 U of TaqI (NEB, catR0149S) in NEB buffer 4 in a final volume of 100 μL at 65 °C. ..

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  • 94
    New England Biolabs taq α
    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] .
    Taq α, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taq α/product/New England Biolabs
    Average 94 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    taq α - by Bioz Stars, 2020-09
    94/100 stars
      Buy from Supplier

    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