epimark methylated dna enrichment kit  (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:
    451
    Size:
    25 rxns
    Category:
    DNA Fragment Analysis Kits
    Score:
    85
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    Structured Review

    New England Biolabs epimark methylated dna enrichment kit
    EpiMark Methylated DNA Enrichment Kit
    EpiMark Methylated DNA Enrichment Kit 25 rxns
    https://www.bioz.com/result/epimark methylated dna enrichment kit/product/New England Biolabs
    Average 96 stars, based on 14 article reviews
    Price from $9.99 to $1999.99
    epimark methylated dna enrichment kit - by Bioz Stars, 2019-12
    96/100 stars

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    microbiome dna enrichment kit New England Biolabs

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    Related Articles

    Whole Genome Amplification:

    Article Title: Epigenome-wide DNA Methylation Analysis Implicates Neuronal and Inflammatory Signaling Pathways in Adult Murine Hepatic Tumorigenesis following Perinatal Exposure to Bisphenol A
    Article Snippet: Paragraph title: Enrichment and Whole Genome Amplification of Methylated DNA ... Methylated DNA fragments from one sonication aliquot per sample were enriched for methylcytosine using methyl-CpG binding domain-based capture (MBD-Cap) with the EpiMark Methylated DNA Enrichment Kit (New England BioLabs, Ipswich, Massachusetts).

    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.). .. 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.).

    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. .. 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.

    Incubation:

    Article Title: Epigenome-wide DNA Methylation Analysis Implicates Neuronal and Inflammatory Signaling Pathways in Adult Murine Hepatic Tumorigenesis following Perinatal Exposure to Bisphenol A
    Article Snippet: Methylated DNA fragments from one sonication aliquot per sample were enriched for methylcytosine using methyl-CpG binding domain-based capture (MBD-Cap) with the EpiMark Methylated DNA Enrichment Kit (New England BioLabs, Ipswich, Massachusetts). .. The EpiMark kit uses a fusion protein (MBD-Fc) containing the highly conserved methyl binding domain (MBD) of human MBD2 protein fused to the Fc tail of human IgG.

    Article Title: Pros and cons of methylation-based enrichment methods for ancient DNA
    Article Snippet: 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: DNA methylation regulates associative reward learning
    Article Snippet: To increase yields of methylated DNA, purified genomic DNA was pooled across 2 biological samples per IP for in vivo experiments. .. Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit). .. Methylation levels at selected DNA regions were assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15s and 58°C for 60s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    Article Title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia
    Article Snippet: The quality of DNA shearing was assessed by running 600 ng of sheared DNA in a 1% agarose gel. .. Sonicated DNA was incubated for 1 h with 4 μl 5-methylcytosine antibody and then methylated DNA was collected with protein A-coated magnetic beads (Invitrogen), washed (Bind Wash Buffer, Epimark kit, New England BioLabs), extracted for 2 h at 60°C with proteinase K in TE buffer with 1% SDS, and purified (QIAGEN PCR purification kit). .. Methylation at selected DNA regions was assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15 s and 60°C for 60 s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    Expressing:

    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: 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: 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.

    Over Expression:

    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. .. 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.

    Flow Cytometry:

    Article Title: Epigenome-wide DNA Methylation Analysis Implicates Neuronal and Inflammatory Signaling Pathways in Adult Murine Hepatic Tumorigenesis following Perinatal Exposure to Bisphenol A
    Article Snippet: Methylated DNA fragments from one sonication aliquot per sample were enriched for methylcytosine using methyl-CpG binding domain-based capture (MBD-Cap) with the EpiMark Methylated DNA Enrichment Kit (New England BioLabs, Ipswich, Massachusetts). .. The EpiMark kit uses a fusion protein (MBD-Fc) containing the highly conserved methyl binding domain (MBD) of human MBD2 protein fused to the Fc tail of human IgG.

    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: To confirm the methylation levels, MeDIP was performed using 3 μg of DNA isolated from the skeletal muscle. .. 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: Genomics of CpG Methylation in Developing and Developed Zebrafish
    Article Snippet: DNA was concentrated in a Speed Vac SC110 A. Methylation enrichment was performed using EpiMark DNA Enrichment kit (New England Biolabs). .. DNA was concentrated in a Speed Vac SC110 A. Methylation enrichment was performed using EpiMark DNA Enrichment kit (New England Biolabs).

    Concentration Assay:

    Article Title: A simple bridging flocculation assay for rapid, sensitive and stringent detection of gene specific DNA methylation
    Article Snippet: 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.). .. 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.).

    Methylation:

    Article Title: A simple bridging flocculation assay for rapid, sensitive and stringent detection of gene specific DNA methylation
    Article Snippet: After digestion, 2 μL of the reaction was used for each 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: 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. .. Eight washing steps were used to wash off unbound DNA.

    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: Then, the DNA was subjected to standard qPCR. .. Fragmented DNA untreated by the EpiMark Methylated DNA Enrichment Kit was used as the input ctrl to calculate the relative methylation level (MeDIP/input). .. miR-434-3p information was obtained from miRBase (ID: MIMAT0005315) .

    Article Title: DDX3 localizes to the centrosome and prevents multipolar mitosis by epigenetically and translationally modulating p53 expression
    Article Snippet: 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). .. 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: Epigenome-wide DNA Methylation Analysis Implicates Neuronal and Inflammatory Signaling Pathways in Adult Murine Hepatic Tumorigenesis following Perinatal Exposure to Bisphenol A
    Article Snippet: Matching sample aliquots were reserved as genomic input for co-hybridization with enriched fractions to microarrays. .. Methylated DNA fragments from one sonication aliquot per sample were enriched for methylcytosine using methyl-CpG binding domain-based capture (MBD-Cap) with the EpiMark Methylated DNA Enrichment Kit (New England BioLabs, Ipswich, Massachusetts). .. The EpiMark kit uses a fusion protein (MBD-Fc) containing the highly conserved methyl binding domain (MBD) of human MBD2 protein fused to the Fc tail of human IgG.

    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: To confirm the methylation levels, MeDIP was performed using 3 μg of DNA isolated from the skeletal muscle. .. 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: Electrochemical affinity biosensors for fast detection of gene-specific methylations with no need for bisulfite and amplification treatments
    Article Snippet: A Salivette® collection device (Sarstedt) was used for collecting the saliva samples. .. 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.). .. The following buffer solutions, prepared with Milli-Q water (18 MΩ cm at 25 °C) and sterilized after their preparation, were used: PBS consisting of 0.01 M phosphate buffer solution containing 137 mM NaCl and 2.7 mM KCl, pH 7.5, 0.1 M Tris–HCl, pH 7.2, 0.1 M phosphate buffer, pH 8.0; 0.025 M MES buffer, pH 5.0, B & W buffer consisting of 10 mM Tris–HCl solution containing 1 mM EDTA and 2 M NaCl, pH 7.5, Tris–EDTA buffer (TE) consisting of 0.01 M Tris–HCl solution containing 1 mM EDTA, pH 8.0 and 0.05 M phosphate buffer, pH 6.0.

    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. .. At this moment, how DNMT1 is involved in TIR is still elusive and warrants further extensive studies.

    Article Title: Pros and cons of methylation-based enrichment methods for ancient DNA
    Article Snippet: All aDNA extracts were stored at −20 °C before being subjected to 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 ( ). .. For each enrichment reaction, we coupled 10 μL of human MBD2 protein fused to the Fc tail of human IgG1 (MBD2−Fc) to 1 μL of paramagnetic protein A beads (MBD2−Fc/Protein A Magnetic Bead) by incubating with 11 μL of 1X Bind/Wash Buffer for 15 min at Room Temperature (RT) with agitation.

    Article Title: DDX3 Represses Stemness by Epigenetically Modulating Tumor-suppressive miRNAs in Hepatocellular Carcinoma
    Article Snippet: 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. .. Gene specific primer sets for qRT-PCR analysis are identical to ChIP-qRT-PCR analysis, which are summarized in .

    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. .. 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.

    Article Title: Genomics of CpG Methylation in Developing and Developed Zebrafish
    Article Snippet: No more than 10 µg gDNA was used per sonication reaction. .. DNA was concentrated in a Speed Vac SC110 A. Methylation enrichment was performed using EpiMark DNA Enrichment kit (New England Biolabs). .. Both the captured (methylated) DNA and flow-through (unmethylated) DNA were retained for downstream analysis.

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: To increase yields of methylated DNA, purified genomic DNA was pooled across 2 biological samples per IP for in vivo experiments. .. Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit). .. Methylation levels at selected DNA regions were assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15s and 58°C for 60s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    Article Title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia
    Article Snippet: The quality of DNA shearing was assessed by running 600 ng of sheared DNA in a 1% agarose gel. .. Sonicated DNA was incubated for 1 h with 4 μl 5-methylcytosine antibody and then methylated DNA was collected with protein A-coated magnetic beads (Invitrogen), washed (Bind Wash Buffer, Epimark kit, New England BioLabs), extracted for 2 h at 60°C with proteinase K in TE buffer with 1% SDS, and purified (QIAGEN PCR purification kit). .. Methylation at selected DNA regions was assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15 s and 60°C for 60 s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    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: 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). .. CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs).

    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. .. At this moment, how DNMT1 is involved in TIR is still elusive and warrants further extensive studies.

    Sonication:

    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 localizes to the centrosome and prevents multipolar mitosis by epigenetically and translationally modulating p53 expression
    Article Snippet: 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: Epigenome-wide DNA Methylation Analysis Implicates Neuronal and Inflammatory Signaling Pathways in Adult Murine Hepatic Tumorigenesis following Perinatal Exposure to Bisphenol A
    Article Snippet: Matching sample aliquots were reserved as genomic input for co-hybridization with enriched fractions to microarrays. .. Methylated DNA fragments from one sonication aliquot per sample were enriched for methylcytosine using methyl-CpG binding domain-based capture (MBD-Cap) with the EpiMark Methylated DNA Enrichment Kit (New England BioLabs, Ipswich, Massachusetts). .. The EpiMark kit uses a fusion protein (MBD-Fc) containing the highly conserved methyl binding domain (MBD) of human MBD2 protein fused to the Fc tail of human IgG.

    Article Title: DDX3 Represses Stemness by Epigenetically Modulating Tumor-suppressive miRNAs in Hepatocellular Carcinoma
    Article Snippet: 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: 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.

    Article Title: Genomics of CpG Methylation in Developing and Developed Zebrafish
    Article Snippet: No more than 10 µg gDNA was used per sonication reaction. .. DNA was concentrated in a Speed Vac SC110 A. Methylation enrichment was performed using EpiMark DNA Enrichment kit (New England Biolabs).

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: To increase yields of methylated DNA, purified genomic DNA was pooled across 2 biological samples per IP for in vivo experiments. .. Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit). .. Methylation levels at selected DNA regions were assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15s and 58°C for 60s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    Article Title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia
    Article Snippet: The quality of DNA shearing was assessed by running 600 ng of sheared DNA in a 1% agarose gel. .. Sonicated DNA was incubated for 1 h with 4 μl 5-methylcytosine antibody and then methylated DNA was collected with protein A-coated magnetic beads (Invitrogen), washed (Bind Wash Buffer, Epimark kit, New England BioLabs), extracted for 2 h at 60°C with proteinase K in TE buffer with 1% SDS, and purified (QIAGEN PCR purification kit). .. Methylation at selected DNA regions was assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15 s and 60°C for 60 s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    Binding Assay:

    Article Title: Epigenome-wide DNA Methylation Analysis Implicates Neuronal and Inflammatory Signaling Pathways in Adult Murine Hepatic Tumorigenesis following Perinatal Exposure to Bisphenol A
    Article Snippet: Matching sample aliquots were reserved as genomic input for co-hybridization with enriched fractions to microarrays. .. Methylated DNA fragments from one sonication aliquot per sample were enriched for methylcytosine using methyl-CpG binding domain-based capture (MBD-Cap) with the EpiMark Methylated DNA Enrichment Kit (New England BioLabs, Ipswich, Massachusetts). .. The EpiMark kit uses a fusion protein (MBD-Fc) containing the highly conserved methyl binding domain (MBD) of human MBD2 protein fused to the Fc tail of human IgG.

    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: To confirm the methylation levels, MeDIP was performed using 3 μg of DNA isolated from the skeletal muscle. .. 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: DNA methylation regulates associative reward learning
    Article Snippet: Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit). .. Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit).

    Methylated DNA Immunoprecipitation:

    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: Then, the DNA was subjected to standard qPCR. .. Fragmented DNA untreated by the EpiMark Methylated DNA Enrichment Kit was used as the input ctrl to calculate the relative methylation level (MeDIP/input). .. miR-434-3p information was obtained from miRBase (ID: MIMAT0005315) .

    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: 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: DNA methylation regulates associative reward learning
    Article Snippet: Paragraph title: Methylated DNA immunoprecipitation (MeDIP) ... Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit).

    Article Title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia
    Article Snippet: Paragraph title: Methylated DNA immunoprecipitation (MeDIP). ... Sonicated DNA was incubated for 1 h with 4 μl 5-methylcytosine antibody and then methylated DNA was collected with protein A-coated magnetic beads (Invitrogen), washed (Bind Wash Buffer, Epimark kit, New England BioLabs), extracted for 2 h at 60°C with proteinase K in TE buffer with 1% SDS, and purified (QIAGEN PCR purification kit).

    In Vivo:

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: To increase yields of methylated DNA, purified genomic DNA was pooled across 2 biological samples per IP for in vivo experiments. .. Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit).

    Magnetic Beads:

    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. .. Eight washing steps were used to wash off unbound DNA.

    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: To confirm the methylation levels, MeDIP was performed using 3 μg of DNA isolated from the skeletal muscle. .. 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: Pros and cons of methylation-based enrichment methods for ancient DNA
    Article Snippet: 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 ( ). .. For each enrichment reaction, we coupled 10 μL of human MBD2 protein fused to the Fc tail of human IgG1 (MBD2−Fc) to 1 μL of paramagnetic protein A beads (MBD2−Fc/Protein A Magnetic Bead) by incubating with 11 μL of 1X Bind/Wash Buffer for 15 min at Room Temperature (RT) with agitation.

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: To increase yields of methylated DNA, purified genomic DNA was pooled across 2 biological samples per IP for in vivo experiments. .. Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit). .. Methylation levels at selected DNA regions were assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15s and 58°C for 60s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    Article Title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia
    Article Snippet: The quality of DNA shearing was assessed by running 600 ng of sheared DNA in a 1% agarose gel. .. Sonicated DNA was incubated for 1 h with 4 μl 5-methylcytosine antibody and then methylated DNA was collected with protein A-coated magnetic beads (Invitrogen), washed (Bind Wash Buffer, Epimark kit, New England BioLabs), extracted for 2 h at 60°C with proteinase K in TE buffer with 1% SDS, and purified (QIAGEN PCR purification kit). .. Methylation at selected DNA regions was assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15 s and 60°C for 60 s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    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: To confirm the methylation levels, MeDIP was performed using 3 μg of DNA isolated from the skeletal muscle. .. 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.

    Size-exclusion Chromatography:

    Article Title: Genomics of CpG Methylation in Developing and Developed Zebrafish
    Article Snippet: Genomic DNA was sonicated to 300-bp fragments with a Covaris S2 with the following settings: 10% duty cycle; 4 intensity; and 200 cycles/burst for 90 sec in 130 µl Tris-EDTA. .. DNA was concentrated in a Speed Vac SC110 A. Methylation enrichment was performed using EpiMark DNA Enrichment kit (New England Biolabs).

    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. .. 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: DNA methylation regulates associative reward learning
    Article Snippet: To increase yields of methylated DNA, purified genomic DNA was pooled across 2 biological samples per IP for in vivo experiments. .. Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit). .. Methylation levels at selected DNA regions were assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15s and 58°C for 60s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    Article Title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia
    Article Snippet: The quality of DNA shearing was assessed by running 600 ng of sheared DNA in a 1% agarose gel. .. Sonicated DNA was incubated for 1 h with 4 μl 5-methylcytosine antibody and then methylated DNA was collected with protein A-coated magnetic beads (Invitrogen), washed (Bind Wash Buffer, Epimark kit, New England BioLabs), extracted for 2 h at 60°C with proteinase K in TE buffer with 1% SDS, and purified (QIAGEN PCR purification kit). .. Methylation at selected DNA regions was assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15 s and 60°C for 60 s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    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.

    Article Title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia
    Article Snippet: The quality of DNA shearing was assessed by running 600 ng of sheared DNA in a 1% agarose gel. .. Sonicated DNA was incubated for 1 h with 4 μl 5-methylcytosine antibody and then methylated DNA was collected with protein A-coated magnetic beads (Invitrogen), washed (Bind Wash Buffer, Epimark kit, New England BioLabs), extracted for 2 h at 60°C with proteinase K in TE buffer with 1% SDS, and purified (QIAGEN PCR purification kit). .. Methylation at selected DNA regions was assayed via qPCR on an iQ5 real-time PCR system (Bio-Rad) at 95°C for 5 min, followed by 45 cycles of 95°C for 15 s and 60°C for 60 s, and then incubation at 72°C for 10 min followed by real-time melt analysis to verify product specificity.

    Sampling:

    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. .. Eight washing steps were used to wash off unbound DNA.

    Chromatin Immunoprecipitation:

    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. .. 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.

    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). .. CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs).

    Real-time Polymerase Chain Reaction:

    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: 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). .. CGP DNA was extracted using EpiMark Methylated DNA Enrichment Kit (New England Biolabs).

    Article Title: Genomics of CpG Methylation in Developing and Developed Zebrafish
    Article Snippet: DNA was concentrated in a Speed Vac SC110 A. Methylation enrichment was performed using EpiMark DNA Enrichment kit (New England Biolabs). .. Both the captured (methylated) DNA and flow-through (unmethylated) DNA were retained for downstream analysis.

    Article Title: Methylome, transcriptome, and PPARγ cistrome analyses reveal two epigenetic transitions in fat cells
    Article Snippet: For selected DMRs between ADSCs and FatCs, we measured not only methylated cytosines but also hydroxymethylated cytosines using EpiMark kit (New England BioLabs). .. The method is a kind of (hydroxy) methylation-sensitive restriction enzyme and qPCR assay where hydroxymethylated sites are protected by glycosylation, and methylated sites are specifically cleaved by MspI, while unmethylated sites are specifically cleaved by HpaII.

    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.

    Agarose Gel Electrophoresis:

    Article Title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia
    Article Snippet: The quality of DNA shearing was assessed by running 600 ng of sheared DNA in a 1% agarose gel. .. Sonicated DNA was incubated for 1 h with 4 μl 5-methylcytosine antibody and then methylated DNA was collected with protein A-coated magnetic beads (Invitrogen), washed (Bind Wash Buffer, Epimark kit, New England BioLabs), extracted for 2 h at 60°C with proteinase K in TE buffer with 1% SDS, and purified (QIAGEN PCR purification kit).

    In Vitro:

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: 200ng (in vivo experiments) or 400ng (in vitro experiments) of DNA per sample was removed and sonicated (Fisher Sonic Dismembrator 120) to 200–1000bp fragments for methylation analysis. .. Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit).

    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: 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. .. At this moment, how DNMT1 is involved in TIR is still elusive and warrants further extensive studies.

    DNA Methylation Assay:

    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: 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: Genomics of CpG Methylation in Developing and Developed Zebrafish
    Article Snippet: DNA was concentrated in a Speed Vac SC110 A. Methylation enrichment was performed using EpiMark DNA Enrichment kit (New England Biolabs). .. Both the captured (methylated) DNA and flow-through (unmethylated) DNA were retained for downstream analysis.

    Immunoprecipitation:

    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: 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: 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.

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: Paragraph title: Methylated DNA immunoprecipitation (MeDIP) ... Sonicated DNA was incubated for 1 hour with 4µl mC antibody and then methylated DNA was collected with protein A coated magnetic beads (Invitrogen), washed (1× Bind Wash Buffer, Epimark kit, New England Biolabs), extracted for 2 hrs at 60° with proteinase K in TE buffer with 1% SDS, and purified (Qiagen DNA micro kit).

    Article Title: Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia
    Article Snippet: Paragraph title: Methylated DNA immunoprecipitation (MeDIP). ... Sonicated DNA was incubated for 1 h with 4 μl 5-methylcytosine antibody and then methylated DNA was collected with protein A-coated magnetic beads (Invitrogen), washed (Bind Wash Buffer, Epimark kit, New England BioLabs), extracted for 2 h at 60°C with proteinase K in TE buffer with 1% SDS, and purified (QIAGEN PCR purification kit).

    ChIP-sequencing:

    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. .. At this moment, how DNMT1 is involved in TIR is still elusive and warrants further extensive studies.

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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: 96/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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