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msres  (New England Biolabs)


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    New England Biolabs msres
    If <t>allele-specific</t> <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 <t>MSREs.</t> 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′ ).
    Msres, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 2384 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/microarray+human+scleroderma+data+set/HpaII/pmc05856270-104-10-18
    Average 97 stars, based on 2384 article reviews
    msres - by Bioz Stars, 2026-10
    97/100 stars

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    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

    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: 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: DNA Methylation Assay, Microarray, Methylation

    SNP, single-nucleotide polymorphism; MSRE, methylation-sensitive restriction enzyme; RAS, relative allele score; IBD, inflammatory bowel disease; (G), genomic DNA; (D), DNA digested MSREs; (U), whole-genome-amplified fully unmethylated DNA digested MSREs.
    Figure Legend Snippet: SNP, single-nucleotide polymorphism; MSRE, methylation-sensitive restriction enzyme; RAS, relative allele score; IBD, inflammatory bowel disease; (G), genomic DNA; (D), DNA digested MSREs; (U), whole-genome-amplified fully unmethylated DNA digested MSREs.

    Techniques Used: Methylation, Amplification

    Related Articles

    Polymerase Chain Reaction:

    Article Title: Genetic Diversity of ‘Candidatus Phytoplasma solani’ in Plant Hosts and Insect Vectors in Winegrowing Regions in Germany
    Article Snippet: .. PCR products were subjected to restriction analysis using HpaII endonuclease (R0171S, New England Biolabs, Ipswich, USA). ..

    Article Title: Identification and validation of liquid biopsy-based methylation biomarkers for germ cell tumor subtypes.
    Article Snippet: .. Per experiment, PCR mastermixes were prepared containing APC/DPP7/GATA4/FBRS primer pairs (integrated DNA technologies), SYBR green dye (Thermofisher), Milli-Q, and either a total MSRE input of 1 unit (AciI + HhaI for APC, HpaII + HhaI for DPP7, HpaII for GATA4, and AciI + HpaII for FBRS) or Diluent A (all from New England Biolabs). ..

    Article Title: High-throughput analyses of Phocaeicola vulgatus reveal fitness determinants for gut colonization and during colitis
    Article Snippet: .. This PCR product was then digested with HpaII (NEB), which cuts asymmetrically within the invertible region so that the on fragment would produce 431 bp and 149 bp digestion products while the promoter off orientation would produce 313 bp and 267 bp cleavage products. ..

    SYBR Green Assay:

    Article Title: Identification and validation of liquid biopsy-based methylation biomarkers for germ cell tumor subtypes.
    Article Snippet: .. Per experiment, PCR mastermixes were prepared containing APC/DPP7/GATA4/FBRS primer pairs (integrated DNA technologies), SYBR green dye (Thermofisher), Milli-Q, and either a total MSRE input of 1 unit (AciI + HhaI for APC, HpaII + HhaI for DPP7, HpaII for GATA4, and AciI + HpaII for FBRS) or Diluent A (all from New England Biolabs). ..

    Methylation:

    Article Title: MeCP2 requires interactions with nucleosome linker DNA to read chromatin DNA methylation.
    Article Snippet: Fluorescent dyes, biotin tags and asymmetric methyl-cytosine bases were incorporated into HPLC pure primers used in amplification PCR steps (IDT technologies). .. Enzymatic methylation was added to DNA at CpG sites using methyltransferase enzymes M.HhaI or M.HpaII (NEB). .. Reactions were set up with 1 unit of methyltransferase per μg of DNA, 640 μM S-adenosylmethionine (SAM) (NEB) and 1x rCutsmart buffer (NEB).

    Article Title: MeCP2 requires interactions with nucleosome linker DNA to read chromatin DNA methylation.
    Article Snippet: .. Methylation state was checked by digestion with methylation sensitive HhaI or HpaII restriction enzymes (NEB). ..

    other:

    Article Title: The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains XP12 ATCC 35934-B1 T4gt New England Biolabs N/A Unmethylated Lambda phage gDNA Promega Cat# D1521 5mCpG pUC19 plasmid DNA New England Biolabs Cat# E7122AAVIAL E.coli K-12 DHB4 gDNA New England Biolabs GenBank accession: CP014270.1 T7 Express Competent E.coli New England Biolabs Cat# C2566H 7 Express lysY/Iq Competent E. coli New England Biolabs Cat# C3013 dcm-6 cell gDNA New England Biolabs ER3662, CGSC Strain#: 6475 Δdcm cell gDNA New England Biolabs ER2861 Natrinema pallidum BOL6-1 gDNA This study GCF_005890195.1 Biological samples Human GM12878 gDNA Coriell Institute Cat# NA12878 Human brain gDNA biochain Cat# D1234035, LOT# C607510 Single donor human blood derived plasma Innovative Research Cat# IPLASK2E2ML HCT116 cell line ATCC Cat# CCL-247 DNMT1 and DNMT3b DKO HCT116 cell line John Hopkins Medicine N/A Chemicals, peptides, and recombinant proteins Acetic acid, LC-MS grade Sigma Cat# 49199-50ML-F Ammonium acetate, LC-MS grade Sigma Cat# 73594-100G-F Deoxynucleotide (dNTP) Solution Set New England Biolabs Cat# N0446S Methanol, LC-MS grade Sigma Cat#EM-MX0486-1 5-methyl-dCTP New England Biolabs Cat# N0356S Nuclease-free water New England Biolabs Cat# B1500L Quick CIP New England Biolabs Cat# M0525S Water, LC-MS grade VWR/BDH Cat# BDH23595.400 BugBuster Master Mix Millipore Cat #70584-M NEBExpress® E. coli Lysis Reagent New England Biolabs Cat# P8116 PEG8000 Sigma P5413 NaCl powder Sigma P9888 1M Tris-HCl, pH7.5, ultra pure grade AMRESCO E691 1M Tris-HCl, pH8.0, ultra pure grade AMRESCO E199 HpaII New England Biolabs Cat# R0171S HaeIII New England Biolabs Cat# R0108S AluI New England Biolabs Cat# R0137S AciI New England Biolabs Cat# R0551S BfaI New England Biolabs Cat# R0568S HhaI New England Biolabs Cat# R0139S HpyCH4IV New England Biolabs Cat# R0619S HpyCH4V New England Biolabs Cat# R0620S NlaIII New England Biolabs Cat# R0125S 10x rCutSmart Buffer New England Biolabs Cat# E6004 Proteinase K New England Biolabs Cat# P8107 AMPure XP beads Beckman Coulter Cat# A63880 NEBNext Ultra II Q5 Master Mix New England Biolabs Cat# E7645 (Continued on next page) Molecular Cell 86, 1–16.e1–e11, May 7, 2026 e1



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    microarray human scleroderma data set  (Biotechnology Information)
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    Biotechnology Information microarray human scleroderma data set
    The IL-13 pathway is activated in SSc and sclGVHD skin. A: Gene expression data for the 491 IL-13–responsive genes identified in human dermal fibroblasts were extracted from the SSc skin data of Milano et al.4 SSc skin biopsy samples are ordered by intrinsic subset and genes are organized by hierarchical clustering. The centroid average of the IL-13–responsive gene signature at maximal induction (12 and 24 hours) is shown to the left of the heat map. Pearson's correlation coefficients between the centroid and individual patient sample are plotted below each array. B: Expression data for the 734 genes reported by Fulkerson et al26 as IL-13–inducible genes in mouse lung were extracted from the sclGVHD <t>microarray</t> data set obtained 2 weeks and 5 weeks after splenocyte transfer (n = 4 per group). Genes and arrays were organized by hierarchical clustering. The relative expression of IL-13–inducible genes (centroid) in lungs is shown to the left of the heat map. C: Representative IL-13 IHC on skin biopsies obtained from an SSc patient and a normal control subject. Arrowheads indicate IL-13+ cells. Original magnification, ×400. D: Blinded quantification of the number of IHC IL-13+ cells per high-power field (×600) in skin biopsies from SSc patients and normal control subjects. SSc, n = 18; control, n = 6; P = 0.0037. E: IL-13 ELISA on the tissue culture supernatants of skin explants from BALB/c Rag2−/− mice that received either syngeneic BALB/c (n = 3) or allogeneic B10.D2 (n = 3) splenocytes 2 weeks earlier (P = 0.002).
    Microarray Human Scleroderma Data Set, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/microarray+human+scleroderma+data+set/microarray+human+scleroderma+data+set/pmc03349888-203-2-18
    Average 90 stars, based on 1 article reviews
    microarray human scleroderma data set - by Bioz Stars, 2026-10
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    Image Search Results


    The IL-13 pathway is activated in SSc and sclGVHD skin. A: Gene expression data for the 491 IL-13–responsive genes identified in human dermal fibroblasts were extracted from the SSc skin data of Milano et al.4 SSc skin biopsy samples are ordered by intrinsic subset and genes are organized by hierarchical clustering. The centroid average of the IL-13–responsive gene signature at maximal induction (12 and 24 hours) is shown to the left of the heat map. Pearson's correlation coefficients between the centroid and individual patient sample are plotted below each array. B: Expression data for the 734 genes reported by Fulkerson et al26 as IL-13–inducible genes in mouse lung were extracted from the sclGVHD microarray data set obtained 2 weeks and 5 weeks after splenocyte transfer (n = 4 per group). Genes and arrays were organized by hierarchical clustering. The relative expression of IL-13–inducible genes (centroid) in lungs is shown to the left of the heat map. C: Representative IL-13 IHC on skin biopsies obtained from an SSc patient and a normal control subject. Arrowheads indicate IL-13+ cells. Original magnification, ×400. D: Blinded quantification of the number of IHC IL-13+ cells per high-power field (×600) in skin biopsies from SSc patients and normal control subjects. SSc, n = 18; control, n = 6; P = 0.0037. E: IL-13 ELISA on the tissue culture supernatants of skin explants from BALB/c Rag2−/− mice that received either syngeneic BALB/c (n = 3) or allogeneic B10.D2 (n = 3) splenocytes 2 weeks earlier (P = 0.002).

    Journal: The American Journal of Pathology

    Article Title: Interspecies Comparison of Human and Murine Scleroderma Reveals IL-13 and CCL2 as Disease Subset-Specific Targets

    doi: 10.1016/j.ajpath.2011.11.024

    Figure Lengend Snippet: The IL-13 pathway is activated in SSc and sclGVHD skin. A: Gene expression data for the 491 IL-13–responsive genes identified in human dermal fibroblasts were extracted from the SSc skin data of Milano et al.4 SSc skin biopsy samples are ordered by intrinsic subset and genes are organized by hierarchical clustering. The centroid average of the IL-13–responsive gene signature at maximal induction (12 and 24 hours) is shown to the left of the heat map. Pearson's correlation coefficients between the centroid and individual patient sample are plotted below each array. B: Expression data for the 734 genes reported by Fulkerson et al26 as IL-13–inducible genes in mouse lung were extracted from the sclGVHD microarray data set obtained 2 weeks and 5 weeks after splenocyte transfer (n = 4 per group). Genes and arrays were organized by hierarchical clustering. The relative expression of IL-13–inducible genes (centroid) in lungs is shown to the left of the heat map. C: Representative IL-13 IHC on skin biopsies obtained from an SSc patient and a normal control subject. Arrowheads indicate IL-13+ cells. Original magnification, ×400. D: Blinded quantification of the number of IHC IL-13+ cells per high-power field (×600) in skin biopsies from SSc patients and normal control subjects. SSc, n = 18; control, n = 6; P = 0.0037. E: IL-13 ELISA on the tissue culture supernatants of skin explants from BALB/c Rag2−/− mice that received either syngeneic BALB/c (n = 3) or allogeneic B10.D2 (n = 3) splenocytes 2 weeks earlier (P = 0.002).

    Article Snippet: The 75 microarray human scleroderma data set, previously described, 4 is publicly available at the National Center for Biotechnology Information GEO site ( http://www.ncbi.nlm.nih.gov/geo ; accession {"type":"entrez-geo","attrs":{"text":"GSE9285","term_id":"9285"}} GSE9285 ).

    Techniques: Gene Expression, Expressing, Microarray, Control, Enzyme-linked Immunosorbent Assay