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    New England Biolabs hpaii
    Schema of methylation-sensitive SNP array. If allele-specific <t>DNA</t> methylation (ASM) around heterozygous SNP A/C exists (which is hypermethylated around A allele and hypomethylated around C allele), SNP is called A/C in micro array before digestion and A/A after digestion by MSREs. Thus, the probes heterozygous in uncut genomic DNA and homozygous in MSREs-digested DNA indicate ASM around SNP. Because we expect methylation skew between two alleles, all heterozygous SNPs which the ratio of signal intensities given two alleles changed after digestion should be extracted. SNP, single-nucleotide polymorphisms; MSREs, methylation-sensitive restriction enzymes, which contain <t>HpaII</t> ( 5′-CˆCGG-3′ ), HhaI ( 5′-GCGˆC-3′ ), and AciI ( 5′-CˆCGC-3′ ).
    Hpaii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hpaii/product/New England Biolabs
    Average 96 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hpaii - by Bioz Stars, 2022-05
    96/100 stars

    Images

    1) Product Images from "Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease"

    Article Title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0194036

    Schema of methylation-sensitive SNP array. If allele-specific DNA methylation (ASM) around heterozygous SNP A/C exists (which is hypermethylated around A allele and hypomethylated around C allele), SNP is called A/C in micro array before digestion and A/A after digestion by MSREs. Thus, the probes heterozygous in uncut genomic DNA and homozygous in MSREs-digested DNA indicate ASM around SNP. Because we expect methylation skew between two alleles, all heterozygous SNPs which the ratio of signal intensities given two alleles changed after digestion should be extracted. SNP, single-nucleotide polymorphisms; MSREs, methylation-sensitive restriction enzymes, which contain HpaII ( 5′-CˆCGG-3′ ), HhaI ( 5′-GCGˆC-3′ ), and AciI ( 5′-CˆCGC-3′ ).
    Figure Legend Snippet: Schema of methylation-sensitive SNP array. If allele-specific DNA methylation (ASM) around heterozygous SNP A/C exists (which is hypermethylated around A allele and hypomethylated around C allele), SNP is called A/C in micro array before digestion and A/A after digestion by MSREs. Thus, the probes heterozygous in uncut genomic DNA and homozygous in MSREs-digested DNA indicate ASM around SNP. Because we expect methylation skew between two alleles, all heterozygous SNPs which the ratio of signal intensities given two alleles changed after digestion should be extracted. SNP, single-nucleotide polymorphisms; MSREs, methylation-sensitive restriction enzymes, which contain HpaII ( 5′-CˆCGG-3′ ), HhaI ( 5′-GCGˆC-3′ ), and AciI ( 5′-CˆCGC-3′ ).

    Techniques Used: Methylation, DNA Methylation Assay, Microarray

    2) Product Images from "The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma"

    Article Title: The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma

    Journal: JCI Insight

    doi: 10.1172/jci.insight.120422

    Melanoma is characterized by widespread changes in DNA methylation. ( A . ( B ) Volcano plot showing difference of mean methylation and statistical significance of the difference, with the number of differentially methylated loci indicated. Numbers to the left indicate hypermethylated loci, and numbers to the right indicate Differentially methylated regions (DMRs) in melanoma. An FDR of less than 5% is used as a marker of significant differences. ( C ) Global methylation levels tested by the LUMA assay indicate loss of methylation in malignant melanoma samples ( n = 36) (unpaired t test, 2-tailed). ( D and E ) Predominantly hypomethylated loci are seen in primary tumors and nodal and distant metastasis. The single blue dot (located in the right upper quadrant) in the volcano plots indicate the CSF1R locus. ( F ) The genomic position of every HpaII-amplifiable fragment on the HELP array was compared with the location of known CpG islands, demonstrating demethylated DMRs enriched outside of CpG-islands (proportions test). ( G ) Box plots of mean DNA copy number alterations (gains + losses) for melanoma sample clusters based on methylation (M1, M2, and M3) (1-way ANOVA). ( H ) Global methylation (%5mC) and hydroxymethylation (%5HmC) in melanocytes ( n = 3), melanoma tumors ( n = 4), and cells ( n = 3) (1-way ANOVA).
    Figure Legend Snippet: Melanoma is characterized by widespread changes in DNA methylation. ( A . ( B ) Volcano plot showing difference of mean methylation and statistical significance of the difference, with the number of differentially methylated loci indicated. Numbers to the left indicate hypermethylated loci, and numbers to the right indicate Differentially methylated regions (DMRs) in melanoma. An FDR of less than 5% is used as a marker of significant differences. ( C ) Global methylation levels tested by the LUMA assay indicate loss of methylation in malignant melanoma samples ( n = 36) (unpaired t test, 2-tailed). ( D and E ) Predominantly hypomethylated loci are seen in primary tumors and nodal and distant metastasis. The single blue dot (located in the right upper quadrant) in the volcano plots indicate the CSF1R locus. ( F ) The genomic position of every HpaII-amplifiable fragment on the HELP array was compared with the location of known CpG islands, demonstrating demethylated DMRs enriched outside of CpG-islands (proportions test). ( G ) Box plots of mean DNA copy number alterations (gains + losses) for melanoma sample clusters based on methylation (M1, M2, and M3) (1-way ANOVA). ( H ) Global methylation (%5mC) and hydroxymethylation (%5HmC) in melanocytes ( n = 3), melanoma tumors ( n = 4), and cells ( n = 3) (1-way ANOVA).

    Techniques Used: DNA Methylation Assay, Methylation, Marker

    3) Product Images from "Epstein-Barr Virus Rta-Mediated Accumulation of DNA Methylation Interferes with CTCF Binding in both Host and Viral Genomes"

    Article Title: Epstein-Barr Virus Rta-Mediated Accumulation of DNA Methylation Interferes with CTCF Binding in both Host and Viral Genomes

    Journal: Journal of Virology

    doi: 10.1128/JVI.00736-17

    EBV Rta expression increases DNA methylation and decreases CTCF binding in the promoter regions of MYC , CCND1 , and JUN . (A, left) Schematic diagrams of methylation-sensitive restriction enzyme sites, CTCF binding sites, and Rta binding sites in each target promoter region. These regions contain no EcoRI site, thus EcoRI served as an input control for AciI, HpaII, and HinP1I. The MYC gene body without Rta and CTCF binding sites served as a negative control (N.C.). Lengths of promoters are illustrated to scale. (Right) CpG methylation levels in the cellular promoters of 293TetLuc and 293TetER cells. Cellular DNAs of paired untreated and doxycycline (Dox)-treated (12 and 24 h) cells were extracted and subjected to restriction enzyme digestions. DNA fragments protected by each methylation-sensitive enzyme were quantified by real-time PCR. Fold changes of each restriction enzyme assessment denote the relative CpG methylation levels in the Dox-treated cells compared to their untreated counterparts. Error bars depict the means ± SD from four independent experiments. Student's t test was used to evaluate the significant difference between the indicated data set. ***, P
    Figure Legend Snippet: EBV Rta expression increases DNA methylation and decreases CTCF binding in the promoter regions of MYC , CCND1 , and JUN . (A, left) Schematic diagrams of methylation-sensitive restriction enzyme sites, CTCF binding sites, and Rta binding sites in each target promoter region. These regions contain no EcoRI site, thus EcoRI served as an input control for AciI, HpaII, and HinP1I. The MYC gene body without Rta and CTCF binding sites served as a negative control (N.C.). Lengths of promoters are illustrated to scale. (Right) CpG methylation levels in the cellular promoters of 293TetLuc and 293TetER cells. Cellular DNAs of paired untreated and doxycycline (Dox)-treated (12 and 24 h) cells were extracted and subjected to restriction enzyme digestions. DNA fragments protected by each methylation-sensitive enzyme were quantified by real-time PCR. Fold changes of each restriction enzyme assessment denote the relative CpG methylation levels in the Dox-treated cells compared to their untreated counterparts. Error bars depict the means ± SD from four independent experiments. Student's t test was used to evaluate the significant difference between the indicated data set. ***, P

    Techniques Used: Expressing, DNA Methylation Assay, Binding Assay, Methylation, Negative Control, CpG Methylation Assay, Real-time Polymerase Chain Reaction

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    New England Biolabs hpaii
    Schema of methylation-sensitive SNP array. If allele-specific <t>DNA</t> methylation (ASM) around heterozygous SNP A/C exists (which is hypermethylated around A allele and hypomethylated around C allele), SNP is called A/C in micro array before digestion and A/A after digestion by MSREs. Thus, the probes heterozygous in uncut genomic DNA and homozygous in MSREs-digested DNA indicate ASM around SNP. Because we expect methylation skew between two alleles, all heterozygous SNPs which the ratio of signal intensities given two alleles changed after digestion should be extracted. SNP, single-nucleotide polymorphisms; MSREs, methylation-sensitive restriction enzymes, which contain <t>HpaII</t> ( 5′-CˆCGG-3′ ), HhaI ( 5′-GCGˆC-3′ ), and AciI ( 5′-CˆCGC-3′ ).
    Hpaii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hpaii/product/New England Biolabs
    Average 96 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    hpaii - by Bioz Stars, 2022-05
    96/100 stars
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    Schema of methylation-sensitive SNP array. If allele-specific DNA methylation (ASM) around heterozygous SNP A/C exists (which is hypermethylated around A allele and hypomethylated around C allele), SNP is called A/C in micro array before digestion and A/A after digestion by MSREs. Thus, the probes heterozygous in uncut genomic DNA and homozygous in MSREs-digested DNA indicate ASM around SNP. Because we expect methylation skew between two alleles, all heterozygous SNPs which the ratio of signal intensities given two alleles changed after digestion should be extracted. SNP, single-nucleotide polymorphisms; MSREs, methylation-sensitive restriction enzymes, which contain HpaII ( 5′-CˆCGG-3′ ), HhaI ( 5′-GCGˆC-3′ ), and AciI ( 5′-CˆCGC-3′ ).

    Journal: PLoS ONE

    Article Title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease

    doi: 10.1371/journal.pone.0194036

    Figure Lengend Snippet: Schema of methylation-sensitive SNP array. If allele-specific DNA methylation (ASM) around heterozygous SNP A/C exists (which is hypermethylated around A allele and hypomethylated around C allele), SNP is called A/C in micro array before digestion and A/A after digestion by MSREs. Thus, the probes heterozygous in uncut genomic DNA and homozygous in MSREs-digested DNA indicate ASM around SNP. Because we expect methylation skew between two alleles, all heterozygous SNPs which the ratio of signal intensities given two alleles changed after digestion should be extracted. SNP, single-nucleotide polymorphisms; MSREs, methylation-sensitive restriction enzymes, which contain HpaII ( 5′-CˆCGG-3′ ), HhaI ( 5′-GCGˆC-3′ ), and AciI ( 5′-CˆCGC-3′ ).

    Article Snippet: DNA from patients was digested using a cocktail of three MSREs: HpaII (5′-CˆCGG-3′), HhaI (5′-GCGˆC-3′), and AciI (5′-CˆCGC-3′) (New England BioLabs, Ipswich, USA), which in combination interrogate the methylation status of ~32.4% of CpG sites in the human genome [ ].

    Techniques: Methylation, DNA Methylation Assay, Microarray

    Melanoma is characterized by widespread changes in DNA methylation. ( A . ( B ) Volcano plot showing difference of mean methylation and statistical significance of the difference, with the number of differentially methylated loci indicated. Numbers to the left indicate hypermethylated loci, and numbers to the right indicate Differentially methylated regions (DMRs) in melanoma. An FDR of less than 5% is used as a marker of significant differences. ( C ) Global methylation levels tested by the LUMA assay indicate loss of methylation in malignant melanoma samples ( n = 36) (unpaired t test, 2-tailed). ( D and E ) Predominantly hypomethylated loci are seen in primary tumors and nodal and distant metastasis. The single blue dot (located in the right upper quadrant) in the volcano plots indicate the CSF1R locus. ( F ) The genomic position of every HpaII-amplifiable fragment on the HELP array was compared with the location of known CpG islands, demonstrating demethylated DMRs enriched outside of CpG-islands (proportions test). ( G ) Box plots of mean DNA copy number alterations (gains + losses) for melanoma sample clusters based on methylation (M1, M2, and M3) (1-way ANOVA). ( H ) Global methylation (%5mC) and hydroxymethylation (%5HmC) in melanocytes ( n = 3), melanoma tumors ( n = 4), and cells ( n = 3) (1-way ANOVA).

    Journal: JCI Insight

    Article Title: The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma

    doi: 10.1172/jci.insight.120422

    Figure Lengend Snippet: Melanoma is characterized by widespread changes in DNA methylation. ( A . ( B ) Volcano plot showing difference of mean methylation and statistical significance of the difference, with the number of differentially methylated loci indicated. Numbers to the left indicate hypermethylated loci, and numbers to the right indicate Differentially methylated regions (DMRs) in melanoma. An FDR of less than 5% is used as a marker of significant differences. ( C ) Global methylation levels tested by the LUMA assay indicate loss of methylation in malignant melanoma samples ( n = 36) (unpaired t test, 2-tailed). ( D and E ) Predominantly hypomethylated loci are seen in primary tumors and nodal and distant metastasis. The single blue dot (located in the right upper quadrant) in the volcano plots indicate the CSF1R locus. ( F ) The genomic position of every HpaII-amplifiable fragment on the HELP array was compared with the location of known CpG islands, demonstrating demethylated DMRs enriched outside of CpG-islands (proportions test). ( G ) Box plots of mean DNA copy number alterations (gains + losses) for melanoma sample clusters based on methylation (M1, M2, and M3) (1-way ANOVA). ( H ) Global methylation (%5mC) and hydroxymethylation (%5HmC) in melanocytes ( n = 3), melanoma tumors ( n = 4), and cells ( n = 3) (1-way ANOVA).

    Article Snippet: Genomic DNA (1 μg)was digested overnight with either HpaII or MspI (New England Biolabs).

    Techniques: DNA Methylation Assay, Methylation, Marker