adna extracts  (New England Biolabs)


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    Name:
    EpiMark Methylated DNA Enrichment Kit
    Description:
    EpiMark Methylated DNA Enrichment Kit 25 rxns
    Catalog Number:
    e2600s
    Price:
    465
    Size:
    25 rxns
    Category:
    DNA Fragment Analysis Kits
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    Structured Review

    New England Biolabs adna extracts
    EpiMark Methylated DNA Enrichment Kit
    EpiMark Methylated DNA Enrichment Kit 25 rxns
    https://www.bioz.com/result/adna extracts/product/New England Biolabs
    Average 84 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    adna extracts - by Bioz Stars, 2020-03
    84/100 stars

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    1) Product Images from "Pros and cons of methylation-based enrichment methods for ancient DNA"

    Article Title: Pros and cons of methylation-based enrichment methods for ancient DNA

    Journal: Scientific Reports

    doi: 10.1038/srep11826

    Properties of MBD enrichment for ancient DNA. The MBD+ fraction favors DNA templates with a longer size and a higher number of m CpGs. This represents a limited fraction of the molecules present in aDNA extracts. mtDNA is under-represented in the MBD+ fraction while higher coverage is observed for hyper-methylated regions of the nuclear genome, including TEs.
    Figure Legend Snippet: Properties of MBD enrichment for ancient DNA. The MBD+ fraction favors DNA templates with a longer size and a higher number of m CpGs. This represents a limited fraction of the molecules present in aDNA extracts. mtDNA is under-represented in the MBD+ fraction while higher coverage is observed for hyper-methylated regions of the nuclear genome, including TEs.

    Techniques Used: Ancient DNA Assay, Methylation

    Related Articles

    Quantitative RT-PCR:

    Article Title: DDX3 Represses Stemness by Epigenetically Modulating Tumor-suppressive miRNAs in Hepatocellular Carcinoma
    Article Snippet: Methylated DNA fragments were enriched by EpiMark Methylated DNA Enrichment Kit (New England BioLabs Inc., Ipswich, MA, USA) according to manufacturer’s instruction. .. Gene specific primer sets for qRT-PCR analysis are identical to ChIP-qRT-PCR analysis, which are summarized in .

    Article Title: DDX3 localizes to the centrosome and prevents multipolar mitosis by epigenetically and translationally modulating p53 expression
    Article Snippet: Fragmented DNA was subjected to methylated DNA enrichment reaction using EpiMARK Methylated DNA Enrichment Kit according to manufacturer’s instruction (New England BioLabs). .. DNA methylation status of the p53 promoter region R2, R2-3 and R3 were analyzed by qRT-PCR using the primer sets: F (R2) 5′-TCCCGGGAGGAGAGGCGAAC-3′, R (R2) 5′-GCGGGACTCGGTAGGGGGAG-3′, F (R2-3) 5′-CGCAGCAGGTCTTGCACCTC-3′, R (R2-3) 5′-GCTTTTGCGTTTGCTCTCAGC-3′, F (R3) 5′-TTTCCACCCCAAAATGTTAGTA-3′, R (R3) 5′-ATCAAGTTCAGTCAGGAGCTTA-3′.

    Real-time Polymerase Chain Reaction:

    Article Title: Electroacupuncture Reduces Weight in Diet-Induced Obese Rats via Hypothalamic Tsc1 Promoter Demethylation and Inhibition of the Activity of mTORC1 Signaling Pathway
    Article Snippet: CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs). .. The qPCR program was set to 95°C for 30 s and 40 cycles of 95°C for 5 s, 55°C for 30 s, 72°C for 30 s. Value of CT was analyzed with the Sequence Detection software version 1.2.3 (Applied Biopsy Stems Company).

    Article Title: miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle
    Article Snippet: Using an EpiMark Methylated DNA Enrichment Kit (New England Biolabs, USA) according to the manufacturer’s instructions, methylated DNA was isolated from fragmented genomic DNA by binding to the methyl-CpG binding domain of the MBD2 protein that was fused to the Fc tail of IgG1 (MBD2-Fc), which was coupled to paramagnetic hydrophilic protein A beads (MBC2-Fc/Protein A Magnetic Beads). .. Then, the DNA was subjected to standard qPCR.

    Microarray:

    Article Title: Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells
    Article Snippet: We used 9 μg of fragmented genomic DNA per culture, treatment and sampling point for enrichment of methylated DNA by magnetic beads coupled MBD2-Fc protein (Epimark Methylated DNA Enrichment Kit; NEB, Ipswich, MA, USA) according to the manufacturer´s protocol. .. After purification with silica columns, the DNA samples from the four replicate cultures of each time point were pooled before microarray analysis.

    Incubation:

    Article Title: Novel Epigenetic Biomarkers Mediating Bisphenol A Exposure and Metabolic Phenotypes in Female Mice
    Article Snippet: Methylated regions of fragmented DNA were enriched by methyl CpG-binding domain (MBD)–based capture by using the Methylated DNA Enrichment Kit (Epimark, New England BioLabs, Ipswich, MA). .. First, MBD2-Fc and beads were combined, incubated by rotation for 15 minutes at room temperature, and washed twice.

    Article Title: A simple bridging flocculation assay for rapid, sensitive and stringent detection of gene specific DNA methylation
    Article Snippet: Rapid high stringency MBD enrichment The Epimark Methylated DNA Enrichment kit (New England Biolabs) was used with major modifications to the recommended instructions. .. Briefly, 2 μg MDB2a-Fc protein was incubated with 10 μL of Protein A magnetic beads at room temperature for 15 minutes.

    Article Title: Pros and cons of methylation-based enrichment methods for ancient DNA
    Article Snippet: MBD enrichment MBD enrichment of the aDNA extracts was performed using either the EpiMark® Methylated DNA Enrichment Kit (catalogue number E2600, New England BioLabs) or the NEBNext® Microbiome DNA Enrichment Kit (E2612), with slight modifications ( ). .. A volume of 10 μL of washed beads was mixed with 21.25–50 μL of aDNA extract, 20 μL of 5X Bind/Wash Buffer and supplemented with sterile water up to 100 μL, before being incubated for 20 minutes at RT with agitation.

    Article Title: miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle
    Article Snippet: Using an EpiMark Methylated DNA Enrichment Kit (New England Biolabs, USA) according to the manufacturer’s instructions, methylated DNA was isolated from fragmented genomic DNA by binding to the methyl-CpG binding domain of the MBD2 protein that was fused to the Fc tail of IgG1 (MBD2-Fc), which was coupled to paramagnetic hydrophilic protein A beads (MBC2-Fc/Protein A Magnetic Beads). .. After simple washing steps, followed by magnetic capture, the enriched DNA sample was eluted in nuclease-free water by incubation at 65 °C.

    Expressing:

    Article Title: HDAC8-mediated epigenetic reprogramming plays a key role in resistance to anthrax lethal toxin-induced pyroptosis in macrophages
    Article Snippet: Among the main DNMTs, expression levels of DNMT1, but not DNMT3a and 3b, were correlated with the extents of TIR (Data not shown) and knocking down DNMT1 by siRNA sensitized TIR cells to LeTx ( ). .. Several approaches including direct sequencing of several CpG islands found in the promoter regions of BNIP3, BNIP3L and MLN64, and ChIP-sequencing using the EpiMark Methylated DNA Enrichment kit (New England Biolabs, MA) and the Illumina next generation sequencing, revealed no difference in methylation levels of these genomic regions.

    Modification:

    Article Title: A simple bridging flocculation assay for rapid, sensitive and stringent detection of gene specific DNA methylation
    Article Snippet: Rapid high stringency MBD enrichment The Epimark Methylated DNA Enrichment kit (New England Biolabs) was used with major modifications to the recommended instructions. .. 0.5 μL of the MBD/magnetic bead mix was then used for each 50 μL enrichment reaction in a 1× MBD buffer with NaCl modified to a concentration of 300 mM.

    DNA Methylation Assay:

    Article Title: HDAC8-mediated epigenetic reprogramming plays a key role in resistance to anthrax lethal toxin-induced pyroptosis in macrophages
    Article Snippet: In line with this note, global DNA methylation levels in wild-type and TIR cells were both very low (~1%) and indifferent (data not shown). .. Several approaches including direct sequencing of several CpG islands found in the promoter regions of BNIP3, BNIP3L and MLN64, and ChIP-sequencing using the EpiMark Methylated DNA Enrichment kit (New England Biolabs, MA) and the Illumina next generation sequencing, revealed no difference in methylation levels of these genomic regions.

    Article Title: Electroacupuncture Reduces Weight in Diet-Induced Obese Rats via Hypothalamic Tsc1 Promoter Demethylation and Inhibition of the Activity of mTORC1 Signaling Pathway
    Article Snippet: Methylated DNA immunoprecipitation (MeDIP) PCR was used to detect the DNA methylation. .. CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs).

    Article Title: DDX3 localizes to the centrosome and prevents multipolar mitosis by epigenetically and translationally modulating p53 expression
    Article Snippet: Fragmented DNA was subjected to methylated DNA enrichment reaction using EpiMARK Methylated DNA Enrichment Kit according to manufacturer’s instruction (New England BioLabs). .. DNA methylation status of the p53 promoter region R2, R2-3 and R3 were analyzed by qRT-PCR using the primer sets: F (R2) 5′-TCCCGGGAGGAGAGGCGAAC-3′, R (R2) 5′-GCGGGACTCGGTAGGGGGAG-3′, F (R2-3) 5′-CGCAGCAGGTCTTGCACCTC-3′, R (R2-3) 5′-GCTTTTGCGTTTGCTCTCAGC-3′, F (R3) 5′-TTTCCACCCCAAAATGTTAGTA-3′, R (R3) 5′-ATCAAGTTCAGTCAGGAGCTTA-3′.

    Concentration Assay:

    Article Title: A simple bridging flocculation assay for rapid, sensitive and stringent detection of gene specific DNA methylation
    Article Snippet: Rapid high stringency MBD enrichment The Epimark Methylated DNA Enrichment kit (New England Biolabs) was used with major modifications to the recommended instructions. .. 0.5 μL of the MBD/magnetic bead mix was then used for each 50 μL enrichment reaction in a 1× MBD buffer with NaCl modified to a concentration of 300 mM.

    Methylation:

    Article Title: HDAC8-mediated epigenetic reprogramming plays a key role in resistance to anthrax lethal toxin-induced pyroptosis in macrophages
    Article Snippet: .. Several approaches including direct sequencing of several CpG islands found in the promoter regions of BNIP3, BNIP3L and MLN64, and ChIP-sequencing using the EpiMark Methylated DNA Enrichment kit (New England Biolabs, MA) and the Illumina next generation sequencing, revealed no difference in methylation levels of these genomic regions. ..

    Article Title: Transcriptional profiling identifies novel regulators of macrophage polarization
    Article Snippet: .. Sonicated genomic DNA (target modal size 200–500 bp) was enriched for methylated DNA using the EpiMark Methylated DNA Enrichment Kit (New England Biolabs) according to manufacturer’s protocol. ..

    Article Title: Novel Epigenetic Biomarkers Mediating Bisphenol A Exposure and Metabolic Phenotypes in Female Mice
    Article Snippet: .. Methylated regions of fragmented DNA were enriched by methyl CpG-binding domain (MBD)–based capture by using the Methylated DNA Enrichment Kit (Epimark, New England BioLabs, Ipswich, MA). .. Methylated DNA binds to the MBD of the human MBD2 protein, which is coupled to paramagnetic protein A beads.

    Article Title: A simple bridging flocculation assay for rapid, sensitive and stringent detection of gene specific DNA methylation
    Article Snippet: .. Rapid high stringency MBD enrichment The Epimark Methylated DNA Enrichment kit (New England Biolabs) was used with major modifications to the recommended instructions. .. Briefly, 2 μg MDB2a-Fc protein was incubated with 10 μL of Protein A magnetic beads at room temperature for 15 minutes.

    Article Title: Electrochemical affinity biosensors for fast detection of gene-specific methylations with no need for bisulfite and amplification treatments
    Article Snippet: .. Fragmented HeLa genomic DNA used as control in the cells experiments was a component of the EpiMark Methylated DNA Enrichment Kit (New England Biolabs, Inc.). ..

    Article Title: Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells
    Article Snippet: .. We used 9 μg of fragmented genomic DNA per culture, treatment and sampling point for enrichment of methylated DNA by magnetic beads coupled MBD2-Fc protein (Epimark Methylated DNA Enrichment Kit; NEB, Ipswich, MA, USA) according to the manufacturer´s protocol. ..

    Article Title: Electroacupuncture Reduces Weight in Diet-Induced Obese Rats via Hypothalamic Tsc1 Promoter Demethylation and Inhibition of the Activity of mTORC1 Signaling Pathway
    Article Snippet: .. CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs). .. Tsc1 promoter, total of 511 bp, from the 15628th base to the 16139th base of the Tsc1 gene sequence, was searched in NCBI database and found 11 CpG island sites.

    Article Title: miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle
    Article Snippet: .. Fragmented DNA untreated by the EpiMark Methylated DNA Enrichment Kit was used as the input ctrl to calculate the relative methylation level (MeDIP/input). ..

    Article Title: DDX3 Represses Stemness by Epigenetically Modulating Tumor-suppressive miRNAs in Hepatocellular Carcinoma
    Article Snippet: .. Methylated DNA fragments were enriched by EpiMark Methylated DNA Enrichment Kit (New England BioLabs Inc., Ipswich, MA, USA) according to manufacturer’s instruction. .. Gene specific primer sets for qRT-PCR analysis are identical to ChIP-qRT-PCR analysis, which are summarized in .

    Article Title: DDX3 localizes to the centrosome and prevents multipolar mitosis by epigenetically and translationally modulating p53 expression
    Article Snippet: .. Fragmented DNA was subjected to methylated DNA enrichment reaction using EpiMARK Methylated DNA Enrichment Kit according to manufacturer’s instruction (New England BioLabs). .. DNA methylation status of the p53 promoter region R2, R2-3 and R3 were analyzed by qRT-PCR using the primer sets: F (R2) 5′-TCCCGGGAGGAGAGGCGAAC-3′, R (R2) 5′-GCGGGACTCGGTAGGGGGAG-3′, F (R2-3) 5′-CGCAGCAGGTCTTGCACCTC-3′, R (R2-3) 5′-GCTTTTGCGTTTGCTCTCAGC-3′, F (R3) 5′-TTTCCACCCCAAAATGTTAGTA-3′, R (R3) 5′-ATCAAGTTCAGTCAGGAGCTTA-3′.

    Article Title: Pros and cons of methylation-based enrichment methods for ancient DNA
    Article Snippet: .. MBD enrichment MBD enrichment of the aDNA extracts was performed using either the EpiMark® Methylated DNA Enrichment Kit (catalogue number E2600, New England BioLabs) or the NEBNext® Microbiome DNA Enrichment Kit (E2612), with slight modifications ( ). ..

    Article Title: Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection
    Article Snippet: .. Enrichment of methylated genomic DNA The gDNA fragments containing CpG methylated fragments were enriched using the EpiMark® Methylated DNA Enrichment Kit (New England BioLabs, Ipswich, MA). .. This approach uses selective binding of double-stranded methyl-CpG DNA to the methyl-CpG binding domain of human MBD2 protein fused to the Fc tail of human IgG1.

    Article Title: Activation of HIV-1 expression in latently infected CD4+ T cells by the small molecule PKC412
    Article Snippet: .. The methylated DNA at HIV-1 LTR promoter and H19 imprinted control region (H19ICR) was detected using an EpiMark methylated DNA Enrichment kit (New England BioLabs, Ipswich, USA), according to manufacturer’s protocol. .. Briefly, 1 × 106 ACH2 cells were mock treated or treated with PKC412, 5-aza-2′deoxycytidine (5-azac) for 48 h. The DNA in the cells were fragmented and they bound to the methyl-CpG binding domain of human MBD2 protein fused to the Fc tail of human IgG1 (MBD2-Fc), which is coupled to protein A magnetic beads.

    Generated:

    Article Title: Activation of HIV-1 expression in latently infected CD4+ T cells by the small molecule PKC412
    Article Snippet: The copy of HIV-1 promoter DNA was determined by comparing the cycle threshold values of each reaction to a standard curve generated from HIV-1 provirus DNA and is reported as fold change relative to negative control. .. The methylated DNA at HIV-1 LTR promoter and H19 imprinted control region (H19ICR) was detected using an EpiMark methylated DNA Enrichment kit (New England BioLabs, Ipswich, USA), according to manufacturer’s protocol.

    Sequencing:

    Article Title: HDAC8-mediated epigenetic reprogramming plays a key role in resistance to anthrax lethal toxin-induced pyroptosis in macrophages
    Article Snippet: .. Several approaches including direct sequencing of several CpG islands found in the promoter regions of BNIP3, BNIP3L and MLN64, and ChIP-sequencing using the EpiMark Methylated DNA Enrichment kit (New England Biolabs, MA) and the Illumina next generation sequencing, revealed no difference in methylation levels of these genomic regions. ..

    Article Title: Electroacupuncture Reduces Weight in Diet-Induced Obese Rats via Hypothalamic Tsc1 Promoter Demethylation and Inhibition of the Activity of mTORC1 Signaling Pathway
    Article Snippet: CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs). .. Tsc1 promoter, total of 511 bp, from the 15628th base to the 16139th base of the Tsc1 gene sequence, was searched in NCBI database and found 11 CpG island sites.

    Sonication:

    Article Title: Transcriptional profiling identifies novel regulators of macrophage polarization
    Article Snippet: .. Sonicated genomic DNA (target modal size 200–500 bp) was enriched for methylated DNA using the EpiMark Methylated DNA Enrichment Kit (New England Biolabs) according to manufacturer’s protocol. ..

    Article Title: Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells
    Article Snippet: Sonication was carried out in TE buffer for 20 s with 20 % amplitude while cooling the tubes in ice water, and repeated up to 12 times depending on the persistent presence of high molecular DNA on agarose TAE control gels. .. We used 9 μg of fragmented genomic DNA per culture, treatment and sampling point for enrichment of methylated DNA by magnetic beads coupled MBD2-Fc protein (Epimark Methylated DNA Enrichment Kit; NEB, Ipswich, MA, USA) according to the manufacturer´s protocol.

    Article Title: DDX3 Represses Stemness by Epigenetically Modulating Tumor-suppressive miRNAs in Hepatocellular Carcinoma
    Article Snippet: Methylated DNA enrichment assay Genomic DNA was extracted and fragmented using QIAamp DNA Mini Kit (QIAGEN) and Biorupto r Standard Sonication System (Diagenode Inc., Seraing, Belgium), respectively. .. Methylated DNA fragments were enriched by EpiMark Methylated DNA Enrichment Kit (New England BioLabs Inc., Ipswich, MA, USA) according to manufacturer’s instruction.

    Article Title: DDX3 localizes to the centrosome and prevents multipolar mitosis by epigenetically and translationally modulating p53 expression
    Article Snippet: Methylated DNA enrichment assay Genomic DNA was extracted using QIAamp® DNA Mini Kit (Qiagen) and sheared with the Bioruptor® UCD-200 Sonication System. .. Fragmented DNA was subjected to methylated DNA enrichment reaction using EpiMARK Methylated DNA Enrichment Kit according to manufacturer’s instruction (New England BioLabs).

    Article Title: Activation of HIV-1 expression in latently infected CD4+ T cells by the small molecule PKC412
    Article Snippet: Cells were lysed and the cross-linked chromatin was sonicated to fragment 500–1000 base pairs using a Bioruptor standard sonicator. .. The methylated DNA at HIV-1 LTR promoter and H19 imprinted control region (H19ICR) was detected using an EpiMark methylated DNA Enrichment kit (New England BioLabs, Ipswich, USA), according to manufacturer’s protocol.

    Binding Assay:

    Article Title: Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection
    Article Snippet: Enrichment of methylated genomic DNA The gDNA fragments containing CpG methylated fragments were enriched using the EpiMark® Methylated DNA Enrichment Kit (New England BioLabs, Ipswich, MA). .. This approach uses selective binding of double-stranded methyl-CpG DNA to the methyl-CpG binding domain of human MBD2 protein fused to the Fc tail of human IgG1.

    Article Title: miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle
    Article Snippet: .. Using an EpiMark Methylated DNA Enrichment Kit (New England Biolabs, USA) according to the manufacturer’s instructions, methylated DNA was isolated from fragmented genomic DNA by binding to the methyl-CpG binding domain of the MBD2 protein that was fused to the Fc tail of IgG1 (MBD2-Fc), which was coupled to paramagnetic hydrophilic protein A beads (MBC2-Fc/Protein A Magnetic Beads). .. After simple washing steps, followed by magnetic capture, the enriched DNA sample was eluted in nuclease-free water by incubation at 65 °C.

    Article Title: Activation of HIV-1 expression in latently infected CD4+ T cells by the small molecule PKC412
    Article Snippet: The methylated DNA at HIV-1 LTR promoter and H19 imprinted control region (H19ICR) was detected using an EpiMark methylated DNA Enrichment kit (New England BioLabs, Ipswich, USA), according to manufacturer’s protocol. .. Briefly, 1 × 106 ACH2 cells were mock treated or treated with PKC412, 5-aza-2′deoxycytidine (5-azac) for 48 h. The DNA in the cells were fragmented and they bound to the methyl-CpG binding domain of human MBD2 protein fused to the Fc tail of human IgG1 (MBD2-Fc), which is coupled to protein A magnetic beads.

    Methylated DNA Immunoprecipitation:

    Article Title: Electroacupuncture Reduces Weight in Diet-Induced Obese Rats via Hypothalamic Tsc1 Promoter Demethylation and Inhibition of the Activity of mTORC1 Signaling Pathway
    Article Snippet: Methylated DNA immunoprecipitation (MeDIP) PCR was used to detect the DNA methylation. .. CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs).

    Article Title: miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle
    Article Snippet: .. Fragmented DNA untreated by the EpiMark Methylated DNA Enrichment Kit was used as the input ctrl to calculate the relative methylation level (MeDIP/input). ..

    Article Title: miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle
    Article Snippet: Paragraph title: Methylated DNA immunoprecipitation (MeDIP) ... Using an EpiMark Methylated DNA Enrichment Kit (New England Biolabs, USA) according to the manufacturer’s instructions, methylated DNA was isolated from fragmented genomic DNA by binding to the methyl-CpG binding domain of the MBD2 protein that was fused to the Fc tail of IgG1 (MBD2-Fc), which was coupled to paramagnetic hydrophilic protein A beads (MBC2-Fc/Protein A Magnetic Beads).

    RNA Sequencing Assay:

    Article Title: Transcriptional profiling identifies novel regulators of macrophage polarization
    Article Snippet: Genomic DNA from the same biological replicates used for RNA-Seq was extracted using DNeasy Blood and Tissue Kit (Qiagen) and submitted for MBD-sequencing, which was also done by the SKCCC NGS Core (PMID: 28733453). .. Sonicated genomic DNA (target modal size 200–500 bp) was enriched for methylated DNA using the EpiMark Methylated DNA Enrichment Kit (New England Biolabs) according to manufacturer’s protocol.

    Magnetic Beads:

    Article Title: A simple bridging flocculation assay for rapid, sensitive and stringent detection of gene specific DNA methylation
    Article Snippet: Rapid high stringency MBD enrichment The Epimark Methylated DNA Enrichment kit (New England Biolabs) was used with major modifications to the recommended instructions. .. Briefly, 2 μg MDB2a-Fc protein was incubated with 10 μL of Protein A magnetic beads at room temperature for 15 minutes.

    Article Title: Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells
    Article Snippet: .. We used 9 μg of fragmented genomic DNA per culture, treatment and sampling point for enrichment of methylated DNA by magnetic beads coupled MBD2-Fc protein (Epimark Methylated DNA Enrichment Kit; NEB, Ipswich, MA, USA) according to the manufacturer´s protocol. ..

    Article Title: Pros and cons of methylation-based enrichment methods for ancient DNA
    Article Snippet: MBD enrichment MBD enrichment of the aDNA extracts was performed using either the EpiMark® Methylated DNA Enrichment Kit (catalogue number E2600, New England BioLabs) or the NEBNext® Microbiome DNA Enrichment Kit (E2612), with slight modifications ( ). .. MBD2−Fc/Protein A Magnetic Beads were then concentrated using a magnetic rack and washed twice using 1 mL 1X Bind/Wash Buffer before being re-suspended in 11 μL 1X Bind/Wash Buffer.

    Article Title: Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection
    Article Snippet: Enrichment of methylated genomic DNA The gDNA fragments containing CpG methylated fragments were enriched using the EpiMark® Methylated DNA Enrichment Kit (New England BioLabs, Ipswich, MA). .. The fused IgG1 (MBD2-Fc) antibody is coupled to paramagnetic hydrophilic protein A magnetic beads.

    Article Title: miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle
    Article Snippet: .. Using an EpiMark Methylated DNA Enrichment Kit (New England Biolabs, USA) according to the manufacturer’s instructions, methylated DNA was isolated from fragmented genomic DNA by binding to the methyl-CpG binding domain of the MBD2 protein that was fused to the Fc tail of IgG1 (MBD2-Fc), which was coupled to paramagnetic hydrophilic protein A beads (MBC2-Fc/Protein A Magnetic Beads). .. After simple washing steps, followed by magnetic capture, the enriched DNA sample was eluted in nuclease-free water by incubation at 65 °C.

    Article Title: Activation of HIV-1 expression in latently infected CD4+ T cells by the small molecule PKC412
    Article Snippet: The methylated DNA at HIV-1 LTR promoter and H19 imprinted control region (H19ICR) was detected using an EpiMark methylated DNA Enrichment kit (New England BioLabs, Ipswich, USA), according to manufacturer’s protocol. .. Briefly, 1 × 106 ACH2 cells were mock treated or treated with PKC412, 5-aza-2′deoxycytidine (5-azac) for 48 h. The DNA in the cells were fragmented and they bound to the methyl-CpG binding domain of human MBD2 protein fused to the Fc tail of human IgG1 (MBD2-Fc), which is coupled to protein A magnetic beads.

    Isolation:

    Article Title: miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle
    Article Snippet: .. Using an EpiMark Methylated DNA Enrichment Kit (New England Biolabs, USA) according to the manufacturer’s instructions, methylated DNA was isolated from fragmented genomic DNA by binding to the methyl-CpG binding domain of the MBD2 protein that was fused to the Fc tail of IgG1 (MBD2-Fc), which was coupled to paramagnetic hydrophilic protein A beads (MBC2-Fc/Protein A Magnetic Beads). .. After simple washing steps, followed by magnetic capture, the enriched DNA sample was eluted in nuclease-free water by incubation at 65 °C.

    Purification:

    Article Title: Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells
    Article Snippet: We used 9 μg of fragmented genomic DNA per culture, treatment and sampling point for enrichment of methylated DNA by magnetic beads coupled MBD2-Fc protein (Epimark Methylated DNA Enrichment Kit; NEB, Ipswich, MA, USA) according to the manufacturer´s protocol. .. After purification with silica columns, the DNA samples from the four replicate cultures of each time point were pooled before microarray analysis.

    Polymerase Chain Reaction:

    Article Title: Electroacupuncture Reduces Weight in Diet-Induced Obese Rats via Hypothalamic Tsc1 Promoter Demethylation and Inhibition of the Activity of mTORC1 Signaling Pathway
    Article Snippet: Methylated DNA immunoprecipitation (MeDIP) PCR was used to detect the DNA methylation. .. CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs).

    Article Title: Activation of HIV-1 expression in latently infected CD4+ T cells by the small molecule PKC412
    Article Snippet: PCR of immunoprecipitates was performed using primers targeting the Nuc1 region of HIV-1LTR. .. The methylated DNA at HIV-1 LTR promoter and H19 imprinted control region (H19ICR) was detected using an EpiMark methylated DNA Enrichment kit (New England BioLabs, Ipswich, USA), according to manufacturer’s protocol.

    Chromatin Immunoprecipitation:

    Article Title: DDX3 Represses Stemness by Epigenetically Modulating Tumor-suppressive miRNAs in Hepatocellular Carcinoma
    Article Snippet: Methylated DNA fragments were enriched by EpiMark Methylated DNA Enrichment Kit (New England BioLabs Inc., Ipswich, MA, USA) according to manufacturer’s instruction. .. Gene specific primer sets for qRT-PCR analysis are identical to ChIP-qRT-PCR analysis, which are summarized in .

    Software:

    Article Title: Electroacupuncture Reduces Weight in Diet-Induced Obese Rats via Hypothalamic Tsc1 Promoter Demethylation and Inhibition of the Activity of mTORC1 Signaling Pathway
    Article Snippet: CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs). .. The qPCR program was set to 95°C for 30 s and 40 cycles of 95°C for 5 s, 55°C for 30 s, 72°C for 30 s. Value of CT was analyzed with the Sequence Detection software version 1.2.3 (Applied Biopsy Stems Company).

    Enzyme-linked Immunosorbent Assay:

    Article Title: Electrochemical affinity biosensors for fast detection of gene-specific methylations with no need for bisulfite and amplification treatments
    Article Snippet: Fragmented HeLa genomic DNA used as control in the cells experiments was a component of the EpiMark Methylated DNA Enrichment Kit (New England Biolabs, Inc.). .. Commercial 5-mC ELISA Buffer (Cat. No.: D5325-2-250) and 10 × ELISA Buffer (Cat. No.: D5425-2-30) from Zymo Research were also used.

    Negative Control:

    Article Title: Activation of HIV-1 expression in latently infected CD4+ T cells by the small molecule PKC412
    Article Snippet: The copy of HIV-1 promoter DNA was determined by comparing the cycle threshold values of each reaction to a standard curve generated from HIV-1 provirus DNA and is reported as fold change relative to negative control. .. The methylated DNA at HIV-1 LTR promoter and H19 imprinted control region (H19ICR) was detected using an EpiMark methylated DNA Enrichment kit (New England BioLabs, Ipswich, USA), according to manufacturer’s protocol.

    Next-Generation Sequencing:

    Article Title: HDAC8-mediated epigenetic reprogramming plays a key role in resistance to anthrax lethal toxin-induced pyroptosis in macrophages
    Article Snippet: .. Several approaches including direct sequencing of several CpG islands found in the promoter regions of BNIP3, BNIP3L and MLN64, and ChIP-sequencing using the EpiMark Methylated DNA Enrichment kit (New England Biolabs, MA) and the Illumina next generation sequencing, revealed no difference in methylation levels of these genomic regions. ..

    Article Title: Transcriptional profiling identifies novel regulators of macrophage polarization
    Article Snippet: Genomic DNA from the same biological replicates used for RNA-Seq was extracted using DNeasy Blood and Tissue Kit (Qiagen) and submitted for MBD-sequencing, which was also done by the SKCCC NGS Core (PMID: 28733453). .. Sonicated genomic DNA (target modal size 200–500 bp) was enriched for methylated DNA using the EpiMark Methylated DNA Enrichment Kit (New England Biolabs) according to manufacturer’s protocol.

    Sampling:

    Article Title: Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells
    Article Snippet: .. We used 9 μg of fragmented genomic DNA per culture, treatment and sampling point for enrichment of methylated DNA by magnetic beads coupled MBD2-Fc protein (Epimark Methylated DNA Enrichment Kit; NEB, Ipswich, MA, USA) according to the manufacturer´s protocol. ..

    Immunoprecipitation:

    Article Title: Electroacupuncture Reduces Weight in Diet-Induced Obese Rats via Hypothalamic Tsc1 Promoter Demethylation and Inhibition of the Activity of mTORC1 Signaling Pathway
    Article Snippet: Methylated DNA immunoprecipitation (MeDIP) PCR was used to detect the DNA methylation. .. CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs).

    Article Title: miR-434-3p and DNA hypomethylation co-regulate eIF5A1 to increase AChRs and to improve plasticity in SCT rat skeletal muscle
    Article Snippet: Paragraph title: Methylated DNA immunoprecipitation (MeDIP) ... Using an EpiMark Methylated DNA Enrichment Kit (New England Biolabs, USA) according to the manufacturer’s instructions, methylated DNA was isolated from fragmented genomic DNA by binding to the methyl-CpG binding domain of the MBD2 protein that was fused to the Fc tail of IgG1 (MBD2-Fc), which was coupled to paramagnetic hydrophilic protein A beads (MBC2-Fc/Protein A Magnetic Beads).

    Article Title: Activation of HIV-1 expression in latently infected CD4+ T cells by the small molecule PKC412
    Article Snippet: Immunoprecipitation reaction was performed with 5 μg of anti-acetyl-histone H3 (Ac-H3 catalogue #17–615, Millipore, Darmstadt, Germany) or rabbit pre-immune immunoglobulin G (negative control). .. The methylated DNA at HIV-1 LTR promoter and H19 imprinted control region (H19ICR) was detected using an EpiMark methylated DNA Enrichment kit (New England BioLabs, Ipswich, USA), according to manufacturer’s protocol.

    ChIP-sequencing:

    Article Title: HDAC8-mediated epigenetic reprogramming plays a key role in resistance to anthrax lethal toxin-induced pyroptosis in macrophages
    Article Snippet: .. Several approaches including direct sequencing of several CpG islands found in the promoter regions of BNIP3, BNIP3L and MLN64, and ChIP-sequencing using the EpiMark Methylated DNA Enrichment kit (New England Biolabs, MA) and the Illumina next generation sequencing, revealed no difference in methylation levels of these genomic regions. ..

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    New England Biolabs epimark methylated dna enrichment kit
    Epimark Methylated Dna Enrichment Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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