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'description' => '<p><span>Perform </span><strong>MeDIP-seq </strong>experiments, <em>i.e.</em> m<span>ethylated DNA immunoprecipitation followed by next generation sequencing, to obtain region-resolution assessment of DNA methylation using a highly sensitive 5-mC-specific antibody. This technology provides a useful, reproducible, and affordable approach for high-resolution methylome research.</span></p>
<p>MeDIP-seq methods allow you to:</p>
<ul>
<li> Perform <span>genome-wide DNA methylation mapping</span></li>
<li> Detect and identify <span>differentially </span><span>methylated regions with high sensitivity</span></li>
<li> Get better insight of your epigenetics research</li>
</ul>
<p><span>Diagenode's <strong>MagMeDIP-seq package V2</strong> has been specifically developed and optimized to generate DNA libraries during the MagMeDIP assay from the <strong>lowest DNA amounts </strong><strong> </strong>and secure <strong>high-quality NGS data </strong>for DNA methylation analysis. <strong>Only 10 ng</strong> <strong>of sheared genomic DNA</strong> is required for IP enrichment and library generation, while preserving the efficiency of the enrichment. </span></p>
<p>The package <span>contains </span><strong>everything you need</strong><span><span> for your MeDIP-seq experiment, including highly specific antibody, fully validated reagents for library preparation from enriched methylated DNA, and external DNA controls.</span></span></p>
<h3>Content</h3>
<ul>
<li><a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns" target="_blank">MagMeDIP qPCR Kit</a><span> </span>(x10) including highly sensitive 5mC specific antibody (clone 33D3) for <strong>superior enrichment</strong> and external DNA controls and qPCR primer pairs for <strong>quality controls</strong></li>
<li><a href="https://www.diagenode.com/en/p/iDeal-DNA-IP-library-preparation-kit-x24" target="_blank">iDeal DNA IP library preparation kit </a>(x24) and <a href="https://www.diagenode.com/en/p/iDeal-24-Unique-Dual-Indexes-Set-A">iDeal UDI modules</a> (x24) for <strong>highest library yields</strong> and <strong>index hopping mitigation</strong></li>
<li><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24" target="_blank">IPure kit v2</a><span> </span>(x24) for <strong>highest quality purification</strong> before sequencing</li>
</ul>
<h3><span><span></span></span><span>Features</span></h3>
<ul>
<li><strong>All-in one </strong>MeDIP-seq kit, fully validated for <strong>NGS analysis</strong></li>
<li>Low DNA requirement:<b><span> </span></b>down to <b>10 ng per reaction</b></li>
<li><b>Robust </b>method<b>, <strong>superior</strong> </b>enrichment,<b> </b>and<b> easy-to-use </b>protocol</li>
<li><b>High reproducibility<span> </span></b>between replicates and repetitive experiments</li>
</ul>
<h3><span>Sequencing analysis</span></h3>
<div class="extra-spaced">
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<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig1.png" /></div>
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<p><strong></strong></p>
<p><strong>Figure 1. NGS data generated using Diagenode's MagMeDIP-seq Package V2 detects methylation at CpG shores. </strong><br />MeDIP-seq libraries were prepared from 50 ng of genomic DNA originating from human blood samples with Diagenode's MagMeDIP-seq Package V2. IP and corresponding INPUT samples were sequenced in paired-end 50 bp on Illumina NovaSeq instrument. Reads were mapped to generate a whole-genome DNA methylation profile. The image above shows two examples of DNA methylation being detected at CpG shores rather than in the CpG island itself. This data agrees with recent findings showing that a large portion of methylated sites occur in these regions that are adjacent to CpG islands.</p>
<p><strong>A.</strong> Coverage profile at the PTP42 locus. The protein encoded by this gene belongs to a small class of the protein tyrosine phosphatase (PTP) family. Overexpression of this gene in mammalian cells conferred a transformed phenotype, which suggested its role in tumorigenesis.</p>
<p><strong>B.</strong> Coverage profile at the CHD1L locus. The protein encoded by this gene is a calcium dependent cell-cell adhesion glycoprotein. Loss of function of this gene is thought to contribute to progression in cancer by increasing proliferation, invasion, and/or metastasis.</p>
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<p><strong></strong></p>
<p><strong>Figure 2. Excellent sequencing quality. </strong>Genomic DNA was extracted from human blood samples and sheared to a mean fragment length of 200 bp. MeDIP-seq libraries were prepared from different starting amounts of gDNA using Diagenode's MagMeDIP-seq Package V2 and sequenced in paired-end 50 bp on Illumina NovaSeq instrument generating around 60 million read pairs per sample. Sequencing statistics reveal that all samples performed well, with mean Phred scores above 30 along the entire reads 1 and 2 (data shown for 50 ng gDNA input after trimming).</p>
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<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 3. Saturation analysis.</strong> Clean reads were aligned to the human genome (hg19) using Burrows-Wheeler aligner (BWA) algorithm after which duplicated and unmapped reads were removed resulting in a mapping efficiency >98% for all samples. Quality and validity check of the mapped MeDIP-seq data was performed using MEDIPS R package. Saturation plots show that all sets of reads have sufficient complexity and depth to saturate the coverage profile of the reference genome and that this is reproducible <span>between replicates and repetitive experiments </span>(data shown for 50 ng gDNA input: left panel = replicate a, right panel = replicate b).</p>
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<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 4. Superior enrichment of methylated regions from nanograms of gDNA from human blood samples. </strong>MeDIP-seq measure the relative enrichment of methylated DNA between the samples and its corresponding input. Regions with significant (adjusted p-value <0.1) positive changes of the samples over the input are defined as peak and used for further downstream analysis. With Diagenode's MagMeDIP-seq V2 Package, a significant proportion of uniquely mapped reads corresponds to peaks, demonstrating a highly efficient enrichment even for low gDNA amounts.</p>
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<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 5. Annotation of significant methylated regions detected on human blood samples. </strong>The common peaks between replicates of the same condition were annotated with regards to CpG context and genomic features. Diagenode's MagMeDIP-seq package V2 allows a wide interrogation of methylated regions of the human genome, especially in low density CpG regions (data shown for 50 ng gDNA input).</p>
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<p><strong></strong></p>
<p><strong>Figure 6. Coverage profiles on the positive control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the TSH2B (H2BC1) locus (marked by blue boxes in the bottom track), which is a repressed region in blood cells and should be highly methylated, resulting in enrichment and reads accumulation following Diagenode's MagMeDIP-Seq V2 workflow. This methylated region was consistently detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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</div>
<div class="extra-spaced">
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<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig6.png" /></div>
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<p><strong></strong></p>
<p><strong>Figure 7. Coverage profiles on the negative control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the GADPH locus (marked by blue boxes in the bottom track), which is a highly active transcription region and should not be methylated, resulting in no reads accumulation following Diagenode's MagMeDIP-Seq V2 package. This non-methylated region was not detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<p><span style="font-weight: 400;">Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to </span><a href="../applications/dna-rna-shearing"><span style="font-weight: 400;">fragmented DNA or RNA</span></a><span style="font-weight: 400;"> prior to sequencing</span></p>
<p><span style="font-weight: 400;">After input DNA has been fragmented, it is end-repaired and blunt-ended</span><span style="font-weight: 400;">. The next step is a A-tailing in which dAMP is added to the 3´ end of the blunt phosphorylated DNA fragments to prevent concatemerization and to allow the ligation of adaptors with complementary dT overhangs. In addition, barcoded adapters can be incorporated to facilitate multiplexing prior to or during amplification.</span></p>
<center><img src="https://www.diagenode.com/img/categories/library-prep/flux.png" /></center>
<p><span style="font-weight: 400;">Diagenode offers a comprehensive product portfolio for library preparation:<br /></span></p>
<strong><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">D-Plex RNA-seq Library Preparation Kits</a></strong><br />
<p><span style="font-weight: 400;">Diagenode’s new RNA-sequencing solutions utilize the innovative c</span><span style="font-weight: 400;">apture and a</span><span style="font-weight: 400;">mplification by t</span><span style="font-weight: 400;">ailing and s</span><span style="font-weight: 400;">witching”</span><span style="font-weight: 400;">, a ligation-free method to produce DNA libraries for next generation sequencing from low input amounts of RNA. </span><span style="font-weight: 400;"></span><a href="../categories/Library-preparation-for-RNA-seq">Learn more</a></p>
<strong><a href="../categories/library-preparation-for-ChIP-seq">ChIP-seq and DNA sequencing library preparation solutions</a></strong><br />
<p><span style="font-weight: 400;">Our kits have been optimized for DNA library preparation used for next generation sequencing for a wide range of inputs. Using a simple three-step protocols, our</span><a href="http://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><span style="font-weight: 400;"> </span></a><span style="font-weight: 400;">kits are an optimal choice for library preparation from DNA inputs down to 50 pg. </span><a href="../categories/library-preparation-for-ChIP-seq">Learn more</a></p>
<a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span><strong>Bioruptor Pico - short fragments</strong></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">Our well-cited Bioruptor Pico is the shearing device of choice for chromatin and DNA fragmentation. Obtain uniform and tight fragment distributions between 150bp -2kb. </span><a href="../p/bioruptor-pico-sonication-device">Learn more</a></p>
<strong><a href="../p/megaruptor2-1-unit"><span href="../p/bioruptor-pico-sonication-device">Megaruptor</span>® - long fragments</a></strong><a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">The Megaruptor is designed to shear DNA from 3kb-75kb for long-read sequencing. <a href="../p/megaruptor2-1-unit">Learn more</a></span></p>
<span href="../p/bioruptor-pico-sonication-device"></span><span style="font-weight: 400;"></span></div>
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<div style="text-align: justify;" class="small-12 medium-8 large-8 columns">
<h2>Complete solutions for DNA methylation studies</h2>
<p>Whether you are experienced or new to the field of DNA methylation, Diagenode has everything you need to make your assay as easy and convenient as possible while ensuring consistent data between samples and experiments. Diagenode offers sonication instruments, reagent kits, high quality antibodies, and high-throughput automation capability to address all of your specific DNA methylation analysis requirements.</p>
</div>
<div class="small-12 medium-4 large-4 columns text-center"><a href="../landing-pages/dna-methylation-grant-applications"><img src="https://www.diagenode.com/img/banners/banner-dna-grant.png" alt="" /></a></div>
<div style="text-align: justify;" class="small-12 medium-12 large-12 columns">
<p>DNA methylation was the first discovered epigenetic mark and is the most widely studied topic in epigenetics. <em>In vivo</em>, DNA is methylated following DNA replication and is involved in a number of biological processes including the regulation of imprinted genes, X chromosome inactivation. and tumor suppressor gene silencing in cancer cells. Methylation often occurs in cytosine-guanine rich regions of DNA (CpG islands), which are commonly upstream of promoter regions.</p>
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<div class="small-12 medium-12 large-12 columns"><br /><br />
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#dnamethyl"><i class="fa fa-caret-right"></i> Learn more</a>
<div id="dnamethyl" class="content">5-methylcytosine (5-mC) has been known for a long time as the only modification of DNA for epigenetic regulation. In 2009, however, Kriaucionis discovered a second methylated cytosine, 5-hydroxymethylcytosine (5-hmC). The so-called 6th base, is generated by enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine by the TET family of oxygenases. Early reports suggested that 5-hmC may represent an intermediate of active demethylation in a new pathway which demethylates DNA, converting 5-mC to cytosine. Recent evidence fuel this hypothesis suggesting that further oxidation of the hydroxymethyl group leads to a formyl or carboxyl group followed by either deformylation or decarboxylation. The formyl and carboxyl groups of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) could be enzymatically removed without excision of the base.
<p class="text-center"><img src="https://www.diagenode.com/img/categories/kits_dna/dna_methylation_variants.jpg" /></p>
</div>
</li>
</ul>
<br />
<h2>Main DNA methylation technologies</h2>
<p style="text-align: justify;">Overview of the <span style="font-weight: 400;">three main approaches for studying DNA methylation.</span></p>
<div class="row">
<ol>
<li style="font-weight: 400;"><span style="font-weight: 400;">Chemical modification with bisulfite – Bisulfite conversion</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Enrichment of methylated DNA (including MeDIP and MBD)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Treatment with methylation-sensitive or dependent restriction enzymes</span></li>
</ol>
<p><span style="font-weight: 400;"> </span></p>
<div class="row">
<table>
<thead>
<tr>
<th></th>
<th>Description</th>
<th width="350">Features</th>
</tr>
</thead>
<tbody>
<tr>
<td><strong>Bisulfite conversion</strong></td>
<td><span style="font-weight: 400;">Chemical conversion of unmethylated cytosine to uracil. Methylated cytosines are protected from this conversion allowing to determine DNA methylation at single nucleotide resolution.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Single nucleotide resolution</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Quantitative analysis - methylation rate (%)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Gold standard and well studied</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><b>Methylated DNA enrichment</b></td>
<td><span style="font-weight: 400;">(Hydroxy-)Methylated DNA is enriched by using specific antibodies (hMeDIP or MeDIP) or proteins (MBD) that specifically bind methylated CpG sites in fragmented genomic DNA.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Resolution depends on the fragment size of the enriched methylated DNA (300 bp)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Qualitative analysis</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><strong>Restriction enzyme-based digestion</strong></td>
<td><span style="font-weight: 400;">Use of (hydroxy)methylation-sensitive or (hydroxy)methylation-dependent restriction enzymes for DNA methylation analysis at specific sites.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Determination of methylation status is limited by the enzyme recognition site</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Easy to use</span></li>
</ul>
</td>
</tr>
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<p style="text-align: justify;">Diagenode’s epigenetic reagents include:</p>
<ul>
<li style="text-align: justify;"><strong>DNA methylation kits and antibodies</strong> - Validated NGS-compatible kits for MeDIP, MBD pull-down, whole genome bisulfite sequencing, and reduced representation bisulfite sequencing. Official provider for the original clone for 5-mC 33D3.</li>
<li style="text-align: justify;"><strong>ChIP and ChIP-seq kits for industry-leading specificity and sensitivity</strong> - MicroChIP/MicroPlex Kit for ChIP-seq with only 10,000 cells and the iDeal ChIP-seq Kits optimized for both transcription factors and histones. Our kits feature full reagents for ChIP-seq including control primers, control antibodies, magnetics beads, and purification reagents.</li>
<li style="text-align: justify;"><strong>Library preparation kits</strong> tailored for your specific requirements. The MicroPlex Library Preparation Kit simplifies library preparation requiring only 3 simple steps and allowing inputs of only 50 pg. </li>
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<p><img src="https://www.diagenode.com/img/areas/cancer.jpg" /></p>
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<h2>Epigenetics and Cancer</h2>
<p>Epigenetic processes control the normal development and maintenance of gene expression in a number of organisms. However, disruption of epigenetic mechanisms may alter gene function, potentially leading to cellular transformations that lead to tumorigenesis. Cancer is a multistep process from a succession of processes that alter the growth of normal cells. In cancer, epigenetic reprogramming occurs at multiple levels including nuclear organization and nucleosome positioning, DNA methylation, modification of histones, alteration of epigenetic regulators such as transcription factor binding, and non-coding RNA, such as microRNA.</p>
<p>Epigenetic modifications are reversible and potential treatments could be geared to alter irregular transcription factor binding, DNA methylation or histone acetylation. Accurate study with a versatile number of tools is essential for the study of epigenetics including sound sample preparation and analysis methodologies for DNA methylation such as with immunoprecipitation or bisulfite sequencing, chromatin analysis with chromatin immunoprecipitation (ChIP) combined with qPCR or sequencing, and RNA modification study. As researchers elucidate the mechanisms and specific modifications associated with cancer, it may be possible to target abnormal modifications in cells with minimal damage to normal cells, making the prospect of epigenetic therapy increasingly promising.</p>
<h3>Diagenode products for your epigenomics research in Cancer</h3>
<div class="row">
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #099f92; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/chromatin-function">Chromatin analysis</a></h3>
<center><a href="https://www.diagenode.com/en/categories/chromatin-function"><img src="https://www.diagenode.com/img/cancer/chromatin-icon.png" /></a></center>
<p class="text-left">Understand the role of chromatin in cancer regulation</p>
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<ul>
<li>New to ChIP? <a href="https://www.diagenode.com/en/pages/portal/chip">Learn more</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin shearing optimization</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation">Chromatin Immunoprecipitation</a></li>
<li>Validated <a href="https://www.diagenode.com/en/categories/antibodies">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/library-preparation">Library preparation</a></li>
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</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #30415c; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/dna-methylation" style="color: #30415c;">DNA methylation</a></h3>
<center><a href="https://www.diagenode.com/en/categories/dna-methylation"><img src="https://www.diagenode.com/img/cancer/dna-icon.png" /></a></center>
<p class="text-left">Analyze DNA methylation and the effects on oncogenesis and tumor suppression</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/bisulfite-conversion">Bisulfite sequencing</a></li>
<li><a href="https://www.diagenode.com/en/categories/methylated-dna-immunoprecipitation">Methylated DNA immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/dna-methylation-profiling-services">DNA methylation services</a></li>
</ul>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #474546; height: 275px;">
<h3 class="text-center"><span class="darkgrey">Non-coding RNAs</span></h3>
<center><img src="https://www.diagenode.com/img/cancer/non-coding-icon.png" /></center>
<p class="text-left">Discover noncoding RNAs in cancer</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">RNA-seq using D-Plex</a> </li>
<li><a href="https://www.diagenode.com/en/categories/rna-seq-category">RNA-seq services</a></li>
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<a href="/cn/p/magmedip-seq-package-V2-x10"><img src="/img/grey-logo.jpg" alt="default alt" class="th"/></a> </div>
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<span class="success label" style="">C02010041</span>
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<h6 style="height:60px">MagMeDIP kit</h6>
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'name' => 'MagMeDIP kit',
'description' => '<p><span>Perform </span><strong>MeDIP-seq </strong>experiments, <em>i.e.</em> m<span>ethylated DNA immunoprecipitation followed by next generation sequencing, to obtain region-resolution assessment of DNA methylation using a highly sensitive 5-mC-specific antibody. This technology provides a useful, reproducible, and affordable approach for high-resolution methylome research.</span></p>
<p>MeDIP-seq methods allow you to:</p>
<ul>
<li> Perform <span>genome-wide DNA methylation mapping</span></li>
<li> Detect and identify <span>differentially </span><span>methylated regions with high sensitivity</span></li>
<li> Get better insight of your epigenetics research</li>
</ul>
<p><span>Diagenode's <strong>MagMeDIP-seq package V2</strong> has been specifically developed and optimized to generate DNA libraries during the MagMeDIP assay from the <strong>lowest DNA amounts </strong><strong> </strong>and secure <strong>high-quality NGS data </strong>for DNA methylation analysis. <strong>Only 10 ng</strong> <strong>of sheared genomic DNA</strong> is required for IP enrichment and library generation, while preserving the efficiency of the enrichment. </span></p>
<p>The package <span>contains </span><strong>everything you need</strong><span><span> for your MeDIP-seq experiment, including highly specific antibody, fully validated reagents for library preparation from enriched methylated DNA, and external DNA controls.</span></span></p>
<h3>Content</h3>
<ul>
<li><a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns" target="_blank">MagMeDIP qPCR Kit</a><span> </span>(x10) including highly sensitive 5mC specific antibody (clone 33D3) for <strong>superior enrichment</strong> and external DNA controls and qPCR primer pairs for <strong>quality controls</strong></li>
<li><a href="https://www.diagenode.com/en/p/iDeal-DNA-IP-library-preparation-kit-x24" target="_blank">iDeal DNA IP library preparation kit </a>(x24) and <a href="https://www.diagenode.com/en/p/iDeal-24-Unique-Dual-Indexes-Set-A">iDeal UDI modules</a> (x24) for <strong>highest library yields</strong> and <strong>index hopping mitigation</strong></li>
<li><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24" target="_blank">IPure kit v2</a><span> </span>(x24) for <strong>highest quality purification</strong> before sequencing</li>
</ul>
<h3><span><span></span></span><span>Features</span></h3>
<ul>
<li><strong>All-in one </strong>MeDIP-seq kit, fully validated for <strong>NGS analysis</strong></li>
<li>Low DNA requirement:<b><span> </span></b>down to <b>10 ng per reaction</b></li>
<li><b>Robust </b>method<b>, <strong>superior</strong> </b>enrichment,<b> </b>and<b> easy-to-use </b>protocol</li>
<li><b>High reproducibility<span> </span></b>between replicates and repetitive experiments</li>
</ul>
<h3><span>Sequencing analysis</span></h3>
<div class="extra-spaced">
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<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig1.png" /></div>
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 1. NGS data generated using Diagenode's MagMeDIP-seq Package V2 detects methylation at CpG shores. </strong><br />MeDIP-seq libraries were prepared from 50 ng of genomic DNA originating from human blood samples with Diagenode's MagMeDIP-seq Package V2. IP and corresponding INPUT samples were sequenced in paired-end 50 bp on Illumina NovaSeq instrument. Reads were mapped to generate a whole-genome DNA methylation profile. The image above shows two examples of DNA methylation being detected at CpG shores rather than in the CpG island itself. This data agrees with recent findings showing that a large portion of methylated sites occur in these regions that are adjacent to CpG islands.</p>
<p><strong>A.</strong> Coverage profile at the PTP42 locus. The protein encoded by this gene belongs to a small class of the protein tyrosine phosphatase (PTP) family. Overexpression of this gene in mammalian cells conferred a transformed phenotype, which suggested its role in tumorigenesis.</p>
<p><strong>B.</strong> Coverage profile at the CHD1L locus. The protein encoded by this gene is a calcium dependent cell-cell adhesion glycoprotein. Loss of function of this gene is thought to contribute to progression in cancer by increasing proliferation, invasion, and/or metastasis.</p>
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<div class="row">
<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig2.png" /></div>
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 2. Excellent sequencing quality. </strong>Genomic DNA was extracted from human blood samples and sheared to a mean fragment length of 200 bp. MeDIP-seq libraries were prepared from different starting amounts of gDNA using Diagenode's MagMeDIP-seq Package V2 and sequenced in paired-end 50 bp on Illumina NovaSeq instrument generating around 60 million read pairs per sample. Sequencing statistics reveal that all samples performed well, with mean Phred scores above 30 along the entire reads 1 and 2 (data shown for 50 ng gDNA input after trimming).</p>
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<div class="extra-spaced">
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<p><strong></strong></p>
<p><strong>Figure 3. Saturation analysis.</strong> Clean reads were aligned to the human genome (hg19) using Burrows-Wheeler aligner (BWA) algorithm after which duplicated and unmapped reads were removed resulting in a mapping efficiency >98% for all samples. Quality and validity check of the mapped MeDIP-seq data was performed using MEDIPS R package. Saturation plots show that all sets of reads have sufficient complexity and depth to saturate the coverage profile of the reference genome and that this is reproducible <span>between replicates and repetitive experiments </span>(data shown for 50 ng gDNA input: left panel = replicate a, right panel = replicate b).</p>
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<p><strong></strong></p>
<p><strong>Figure 4. Superior enrichment of methylated regions from nanograms of gDNA from human blood samples. </strong>MeDIP-seq measure the relative enrichment of methylated DNA between the samples and its corresponding input. Regions with significant (adjusted p-value <0.1) positive changes of the samples over the input are defined as peak and used for further downstream analysis. With Diagenode's MagMeDIP-seq V2 Package, a significant proportion of uniquely mapped reads corresponds to peaks, demonstrating a highly efficient enrichment even for low gDNA amounts.</p>
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<div class="extra-spaced">
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<p><strong></strong></p>
<p><strong>Figure 5. Annotation of significant methylated regions detected on human blood samples. </strong>The common peaks between replicates of the same condition were annotated with regards to CpG context and genomic features. Diagenode's MagMeDIP-seq package V2 allows a wide interrogation of methylated regions of the human genome, especially in low density CpG regions (data shown for 50 ng gDNA input).</p>
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<p><strong>Figure 6. Coverage profiles on the positive control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the TSH2B (H2BC1) locus (marked by blue boxes in the bottom track), which is a repressed region in blood cells and should be highly methylated, resulting in enrichment and reads accumulation following Diagenode's MagMeDIP-Seq V2 workflow. This methylated region was consistently detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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'description' => '<p><span>Perform </span><strong>MeDIP-seq </strong>experiments, <em>i.e.</em> m<span>ethylated DNA immunoprecipitation followed by next generation sequencing, to obtain region-resolution assessment of DNA methylation using a highly sensitive 5-mC-specific antibody. This technology provides a useful, reproducible, and affordable approach for high-resolution methylome research.</span></p>
<p>MeDIP-seq methods allow you to:</p>
<ul>
<li> Perform <span>genome-wide DNA methylation mapping</span></li>
<li> Detect and identify <span>differentially </span><span>methylated regions with high sensitivity</span></li>
<li> Get better insight of your epigenetics research</li>
</ul>
<p><span>Diagenode's <strong>MagMeDIP-seq package V2</strong> has been specifically developed and optimized to generate DNA libraries during the MagMeDIP assay from the <strong>lowest DNA amounts </strong><strong> </strong>and secure <strong>high-quality NGS data </strong>for DNA methylation analysis. <strong>Only 10 ng</strong> <strong>of sheared genomic DNA</strong> is required for IP enrichment and library generation, while preserving the efficiency of the enrichment. </span></p>
<p>The package <span>contains </span><strong>everything you need</strong><span><span> for your MeDIP-seq experiment, including highly specific antibody, fully validated reagents for library preparation from enriched methylated DNA, and external DNA controls.</span></span></p>
<h3>Content</h3>
<ul>
<li><a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns" target="_blank">MagMeDIP qPCR Kit</a><span> </span>(x10) including highly sensitive 5mC specific antibody (clone 33D3) for <strong>superior enrichment</strong> and external DNA controls and qPCR primer pairs for <strong>quality controls</strong></li>
<li><a href="https://www.diagenode.com/en/p/iDeal-DNA-IP-library-preparation-kit-x24" target="_blank">iDeal DNA IP library preparation kit </a>(x24) and <a href="https://www.diagenode.com/en/p/iDeal-24-Unique-Dual-Indexes-Set-A">iDeal UDI modules</a> (x24) for <strong>highest library yields</strong> and <strong>index hopping mitigation</strong></li>
<li><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24" target="_blank">IPure kit v2</a><span> </span>(x24) for <strong>highest quality purification</strong> before sequencing</li>
</ul>
<h3><span><span></span></span><span>Features</span></h3>
<ul>
<li><strong>All-in one </strong>MeDIP-seq kit, fully validated for <strong>NGS analysis</strong></li>
<li>Low DNA requirement:<b><span> </span></b>down to <b>10 ng per reaction</b></li>
<li><b>Robust </b>method<b>, <strong>superior</strong> </b>enrichment,<b> </b>and<b> easy-to-use </b>protocol</li>
<li><b>High reproducibility<span> </span></b>between replicates and repetitive experiments</li>
</ul>
<h3><span>Sequencing analysis</span></h3>
<div class="extra-spaced">
<div class="row">
<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig1.png" /></div>
</div>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 1. NGS data generated using Diagenode's MagMeDIP-seq Package V2 detects methylation at CpG shores. </strong><br />MeDIP-seq libraries were prepared from 50 ng of genomic DNA originating from human blood samples with Diagenode's MagMeDIP-seq Package V2. IP and corresponding INPUT samples were sequenced in paired-end 50 bp on Illumina NovaSeq instrument. Reads were mapped to generate a whole-genome DNA methylation profile. The image above shows two examples of DNA methylation being detected at CpG shores rather than in the CpG island itself. This data agrees with recent findings showing that a large portion of methylated sites occur in these regions that are adjacent to CpG islands.</p>
<p><strong>A.</strong> Coverage profile at the PTP42 locus. The protein encoded by this gene belongs to a small class of the protein tyrosine phosphatase (PTP) family. Overexpression of this gene in mammalian cells conferred a transformed phenotype, which suggested its role in tumorigenesis.</p>
<p><strong>B.</strong> Coverage profile at the CHD1L locus. The protein encoded by this gene is a calcium dependent cell-cell adhesion glycoprotein. Loss of function of this gene is thought to contribute to progression in cancer by increasing proliferation, invasion, and/or metastasis.</p>
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<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 2. Excellent sequencing quality. </strong>Genomic DNA was extracted from human blood samples and sheared to a mean fragment length of 200 bp. MeDIP-seq libraries were prepared from different starting amounts of gDNA using Diagenode's MagMeDIP-seq Package V2 and sequenced in paired-end 50 bp on Illumina NovaSeq instrument generating around 60 million read pairs per sample. Sequencing statistics reveal that all samples performed well, with mean Phred scores above 30 along the entire reads 1 and 2 (data shown for 50 ng gDNA input after trimming).</p>
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<div class="extra-spaced">
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 3. Saturation analysis.</strong> Clean reads were aligned to the human genome (hg19) using Burrows-Wheeler aligner (BWA) algorithm after which duplicated and unmapped reads were removed resulting in a mapping efficiency >98% for all samples. Quality and validity check of the mapped MeDIP-seq data was performed using MEDIPS R package. Saturation plots show that all sets of reads have sufficient complexity and depth to saturate the coverage profile of the reference genome and that this is reproducible <span>between replicates and repetitive experiments </span>(data shown for 50 ng gDNA input: left panel = replicate a, right panel = replicate b).</p>
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<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 4. Superior enrichment of methylated regions from nanograms of gDNA from human blood samples. </strong>MeDIP-seq measure the relative enrichment of methylated DNA between the samples and its corresponding input. Regions with significant (adjusted p-value <0.1) positive changes of the samples over the input are defined as peak and used for further downstream analysis. With Diagenode's MagMeDIP-seq V2 Package, a significant proportion of uniquely mapped reads corresponds to peaks, demonstrating a highly efficient enrichment even for low gDNA amounts.</p>
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<div class="extra-spaced">
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<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 5. Annotation of significant methylated regions detected on human blood samples. </strong>The common peaks between replicates of the same condition were annotated with regards to CpG context and genomic features. Diagenode's MagMeDIP-seq package V2 allows a wide interrogation of methylated regions of the human genome, especially in low density CpG regions (data shown for 50 ng gDNA input).</p>
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<p><strong></strong></p>
<p><strong>Figure 6. Coverage profiles on the positive control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the TSH2B (H2BC1) locus (marked by blue boxes in the bottom track), which is a repressed region in blood cells and should be highly methylated, resulting in enrichment and reads accumulation following Diagenode's MagMeDIP-Seq V2 workflow. This methylated region was consistently detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<p><strong></strong></p>
<p><strong>Figure 7. Coverage profiles on the negative control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the GADPH locus (marked by blue boxes in the bottom track), which is a highly active transcription region and should not be methylated, resulting in no reads accumulation following Diagenode's MagMeDIP-Seq V2 package. This non-methylated region was not detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<p><span style="font-weight: 400;">Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to </span><a href="../applications/dna-rna-shearing"><span style="font-weight: 400;">fragmented DNA or RNA</span></a><span style="font-weight: 400;"> prior to sequencing</span></p>
<p><span style="font-weight: 400;">After input DNA has been fragmented, it is end-repaired and blunt-ended</span><span style="font-weight: 400;">. The next step is a A-tailing in which dAMP is added to the 3´ end of the blunt phosphorylated DNA fragments to prevent concatemerization and to allow the ligation of adaptors with complementary dT overhangs. In addition, barcoded adapters can be incorporated to facilitate multiplexing prior to or during amplification.</span></p>
<center><img src="https://www.diagenode.com/img/categories/library-prep/flux.png" /></center>
<p><span style="font-weight: 400;">Diagenode offers a comprehensive product portfolio for library preparation:<br /></span></p>
<strong><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">D-Plex RNA-seq Library Preparation Kits</a></strong><br />
<p><span style="font-weight: 400;">Diagenode’s new RNA-sequencing solutions utilize the innovative c</span><span style="font-weight: 400;">apture and a</span><span style="font-weight: 400;">mplification by t</span><span style="font-weight: 400;">ailing and s</span><span style="font-weight: 400;">witching”</span><span style="font-weight: 400;">, a ligation-free method to produce DNA libraries for next generation sequencing from low input amounts of RNA. </span><span style="font-weight: 400;"></span><a href="../categories/Library-preparation-for-RNA-seq">Learn more</a></p>
<strong><a href="../categories/library-preparation-for-ChIP-seq">ChIP-seq and DNA sequencing library preparation solutions</a></strong><br />
<p><span style="font-weight: 400;">Our kits have been optimized for DNA library preparation used for next generation sequencing for a wide range of inputs. Using a simple three-step protocols, our</span><a href="http://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><span style="font-weight: 400;"> </span></a><span style="font-weight: 400;">kits are an optimal choice for library preparation from DNA inputs down to 50 pg. </span><a href="../categories/library-preparation-for-ChIP-seq">Learn more</a></p>
<a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span><strong>Bioruptor Pico - short fragments</strong></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">Our well-cited Bioruptor Pico is the shearing device of choice for chromatin and DNA fragmentation. Obtain uniform and tight fragment distributions between 150bp -2kb. </span><a href="../p/bioruptor-pico-sonication-device">Learn more</a></p>
<strong><a href="../p/megaruptor2-1-unit"><span href="../p/bioruptor-pico-sonication-device">Megaruptor</span>® - long fragments</a></strong><a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">The Megaruptor is designed to shear DNA from 3kb-75kb for long-read sequencing. <a href="../p/megaruptor2-1-unit">Learn more</a></span></p>
<span href="../p/bioruptor-pico-sonication-device"></span><span style="font-weight: 400;"></span></div>
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<div class="large-12 columns">
<div style="text-align: justify;" class="small-12 medium-8 large-8 columns">
<h2>Complete solutions for DNA methylation studies</h2>
<p>Whether you are experienced or new to the field of DNA methylation, Diagenode has everything you need to make your assay as easy and convenient as possible while ensuring consistent data between samples and experiments. Diagenode offers sonication instruments, reagent kits, high quality antibodies, and high-throughput automation capability to address all of your specific DNA methylation analysis requirements.</p>
</div>
<div class="small-12 medium-4 large-4 columns text-center"><a href="../landing-pages/dna-methylation-grant-applications"><img src="https://www.diagenode.com/img/banners/banner-dna-grant.png" alt="" /></a></div>
<div style="text-align: justify;" class="small-12 medium-12 large-12 columns">
<p>DNA methylation was the first discovered epigenetic mark and is the most widely studied topic in epigenetics. <em>In vivo</em>, DNA is methylated following DNA replication and is involved in a number of biological processes including the regulation of imprinted genes, X chromosome inactivation. and tumor suppressor gene silencing in cancer cells. Methylation often occurs in cytosine-guanine rich regions of DNA (CpG islands), which are commonly upstream of promoter regions.</p>
</div>
<div class="small-12 medium-12 large-12 columns"><br /><br />
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#dnamethyl"><i class="fa fa-caret-right"></i> Learn more</a>
<div id="dnamethyl" class="content">5-methylcytosine (5-mC) has been known for a long time as the only modification of DNA for epigenetic regulation. In 2009, however, Kriaucionis discovered a second methylated cytosine, 5-hydroxymethylcytosine (5-hmC). The so-called 6th base, is generated by enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine by the TET family of oxygenases. Early reports suggested that 5-hmC may represent an intermediate of active demethylation in a new pathway which demethylates DNA, converting 5-mC to cytosine. Recent evidence fuel this hypothesis suggesting that further oxidation of the hydroxymethyl group leads to a formyl or carboxyl group followed by either deformylation or decarboxylation. The formyl and carboxyl groups of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) could be enzymatically removed without excision of the base.
<p class="text-center"><img src="https://www.diagenode.com/img/categories/kits_dna/dna_methylation_variants.jpg" /></p>
</div>
</li>
</ul>
<br />
<h2>Main DNA methylation technologies</h2>
<p style="text-align: justify;">Overview of the <span style="font-weight: 400;">three main approaches for studying DNA methylation.</span></p>
<div class="row">
<ol>
<li style="font-weight: 400;"><span style="font-weight: 400;">Chemical modification with bisulfite – Bisulfite conversion</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Enrichment of methylated DNA (including MeDIP and MBD)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Treatment with methylation-sensitive or dependent restriction enzymes</span></li>
</ol>
<p><span style="font-weight: 400;"> </span></p>
<div class="row">
<table>
<thead>
<tr>
<th></th>
<th>Description</th>
<th width="350">Features</th>
</tr>
</thead>
<tbody>
<tr>
<td><strong>Bisulfite conversion</strong></td>
<td><span style="font-weight: 400;">Chemical conversion of unmethylated cytosine to uracil. Methylated cytosines are protected from this conversion allowing to determine DNA methylation at single nucleotide resolution.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Single nucleotide resolution</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Quantitative analysis - methylation rate (%)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Gold standard and well studied</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><b>Methylated DNA enrichment</b></td>
<td><span style="font-weight: 400;">(Hydroxy-)Methylated DNA is enriched by using specific antibodies (hMeDIP or MeDIP) or proteins (MBD) that specifically bind methylated CpG sites in fragmented genomic DNA.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Resolution depends on the fragment size of the enriched methylated DNA (300 bp)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Qualitative analysis</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><strong>Restriction enzyme-based digestion</strong></td>
<td><span style="font-weight: 400;">Use of (hydroxy)methylation-sensitive or (hydroxy)methylation-dependent restriction enzymes for DNA methylation analysis at specific sites.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Determination of methylation status is limited by the enzyme recognition site</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Easy to use</span></li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="row"></div>
</div>
</div>
<div class="large-12 columns"></div>
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<p style="text-align: justify;">Diagenode’s epigenetic reagents include:</p>
<ul>
<li style="text-align: justify;"><strong>DNA methylation kits and antibodies</strong> - Validated NGS-compatible kits for MeDIP, MBD pull-down, whole genome bisulfite sequencing, and reduced representation bisulfite sequencing. Official provider for the original clone for 5-mC 33D3.</li>
<li style="text-align: justify;"><strong>ChIP and ChIP-seq kits for industry-leading specificity and sensitivity</strong> - MicroChIP/MicroPlex Kit for ChIP-seq with only 10,000 cells and the iDeal ChIP-seq Kits optimized for both transcription factors and histones. Our kits feature full reagents for ChIP-seq including control primers, control antibodies, magnetics beads, and purification reagents.</li>
<li style="text-align: justify;"><strong>Library preparation kits</strong> tailored for your specific requirements. The MicroPlex Library Preparation Kit simplifies library preparation requiring only 3 simple steps and allowing inputs of only 50 pg. </li>
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<p><img src="https://www.diagenode.com/img/areas/cancer.jpg" /></p>
</div>
<h2>Epigenetics and Cancer</h2>
<p>Epigenetic processes control the normal development and maintenance of gene expression in a number of organisms. However, disruption of epigenetic mechanisms may alter gene function, potentially leading to cellular transformations that lead to tumorigenesis. Cancer is a multistep process from a succession of processes that alter the growth of normal cells. In cancer, epigenetic reprogramming occurs at multiple levels including nuclear organization and nucleosome positioning, DNA methylation, modification of histones, alteration of epigenetic regulators such as transcription factor binding, and non-coding RNA, such as microRNA.</p>
<p>Epigenetic modifications are reversible and potential treatments could be geared to alter irregular transcription factor binding, DNA methylation or histone acetylation. Accurate study with a versatile number of tools is essential for the study of epigenetics including sound sample preparation and analysis methodologies for DNA methylation such as with immunoprecipitation or bisulfite sequencing, chromatin analysis with chromatin immunoprecipitation (ChIP) combined with qPCR or sequencing, and RNA modification study. As researchers elucidate the mechanisms and specific modifications associated with cancer, it may be possible to target abnormal modifications in cells with minimal damage to normal cells, making the prospect of epigenetic therapy increasingly promising.</p>
<h3>Diagenode products for your epigenomics research in Cancer</h3>
<div class="row">
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #099f92; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/chromatin-function">Chromatin analysis</a></h3>
<center><a href="https://www.diagenode.com/en/categories/chromatin-function"><img src="https://www.diagenode.com/img/cancer/chromatin-icon.png" /></a></center>
<p class="text-left">Understand the role of chromatin in cancer regulation</p>
</div>
<ul>
<li>New to ChIP? <a href="https://www.diagenode.com/en/pages/portal/chip">Learn more</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin shearing optimization</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation">Chromatin Immunoprecipitation</a></li>
<li>Validated <a href="https://www.diagenode.com/en/categories/antibodies">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/library-preparation">Library preparation</a></li>
</ul>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #30415c; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/dna-methylation" style="color: #30415c;">DNA methylation</a></h3>
<center><a href="https://www.diagenode.com/en/categories/dna-methylation"><img src="https://www.diagenode.com/img/cancer/dna-icon.png" /></a></center>
<p class="text-left">Analyze DNA methylation and the effects on oncogenesis and tumor suppression</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/bisulfite-conversion">Bisulfite sequencing</a></li>
<li><a href="https://www.diagenode.com/en/categories/methylated-dna-immunoprecipitation">Methylated DNA immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/dna-methylation-profiling-services">DNA methylation services</a></li>
</ul>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #474546; height: 275px;">
<h3 class="text-center"><span class="darkgrey">Non-coding RNAs</span></h3>
<center><img src="https://www.diagenode.com/img/cancer/non-coding-icon.png" /></center>
<p class="text-left">Discover noncoding RNAs in cancer</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">RNA-seq using D-Plex</a> </li>
<li><a href="https://www.diagenode.com/en/categories/rna-seq-category">RNA-seq services</a></li>
</ul>
</div>
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<a href="/cn/p/magmedip-seq-package-V2-x10"><img src="/img/grey-logo.jpg" alt="default alt" class="th"/></a> </div>
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<span class="success label" style="">C02010041</span>
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<h6 style="height:60px">MagMeDIP kit</h6>
</div>
</div>
</li>
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'id' => '3195',
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'name' => 'MagMeDIP kit',
'description' => '<p><span>Perform </span><strong>MeDIP-seq </strong>experiments, <em>i.e.</em> m<span>ethylated DNA immunoprecipitation followed by next generation sequencing, to obtain region-resolution assessment of DNA methylation using a highly sensitive 5-mC-specific antibody. This technology provides a useful, reproducible, and affordable approach for high-resolution methylome research.</span></p>
<p>MeDIP-seq methods allow you to:</p>
<ul>
<li> Perform <span>genome-wide DNA methylation mapping</span></li>
<li> Detect and identify <span>differentially </span><span>methylated regions with high sensitivity</span></li>
<li> Get better insight of your epigenetics research</li>
</ul>
<p><span>Diagenode's <strong>MagMeDIP-seq package V2</strong> has been specifically developed and optimized to generate DNA libraries during the MagMeDIP assay from the <strong>lowest DNA amounts </strong><strong> </strong>and secure <strong>high-quality NGS data </strong>for DNA methylation analysis. <strong>Only 10 ng</strong> <strong>of sheared genomic DNA</strong> is required for IP enrichment and library generation, while preserving the efficiency of the enrichment. </span></p>
<p>The package <span>contains </span><strong>everything you need</strong><span><span> for your MeDIP-seq experiment, including highly specific antibody, fully validated reagents for library preparation from enriched methylated DNA, and external DNA controls.</span></span></p>
<h3>Content</h3>
<ul>
<li><a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns" target="_blank">MagMeDIP qPCR Kit</a><span> </span>(x10) including highly sensitive 5mC specific antibody (clone 33D3) for <strong>superior enrichment</strong> and external DNA controls and qPCR primer pairs for <strong>quality controls</strong></li>
<li><a href="https://www.diagenode.com/en/p/iDeal-DNA-IP-library-preparation-kit-x24" target="_blank">iDeal DNA IP library preparation kit </a>(x24) and <a href="https://www.diagenode.com/en/p/iDeal-24-Unique-Dual-Indexes-Set-A">iDeal UDI modules</a> (x24) for <strong>highest library yields</strong> and <strong>index hopping mitigation</strong></li>
<li><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24" target="_blank">IPure kit v2</a><span> </span>(x24) for <strong>highest quality purification</strong> before sequencing</li>
</ul>
<h3><span><span></span></span><span>Features</span></h3>
<ul>
<li><strong>All-in one </strong>MeDIP-seq kit, fully validated for <strong>NGS analysis</strong></li>
<li>Low DNA requirement:<b><span> </span></b>down to <b>10 ng per reaction</b></li>
<li><b>Robust </b>method<b>, <strong>superior</strong> </b>enrichment,<b> </b>and<b> easy-to-use </b>protocol</li>
<li><b>High reproducibility<span> </span></b>between replicates and repetitive experiments</li>
</ul>
<h3><span>Sequencing analysis</span></h3>
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<p><strong>Figure 1. NGS data generated using Diagenode's MagMeDIP-seq Package V2 detects methylation at CpG shores. </strong><br />MeDIP-seq libraries were prepared from 50 ng of genomic DNA originating from human blood samples with Diagenode's MagMeDIP-seq Package V2. IP and corresponding INPUT samples were sequenced in paired-end 50 bp on Illumina NovaSeq instrument. Reads were mapped to generate a whole-genome DNA methylation profile. The image above shows two examples of DNA methylation being detected at CpG shores rather than in the CpG island itself. This data agrees with recent findings showing that a large portion of methylated sites occur in these regions that are adjacent to CpG islands.</p>
<p><strong>A.</strong> Coverage profile at the PTP42 locus. The protein encoded by this gene belongs to a small class of the protein tyrosine phosphatase (PTP) family. Overexpression of this gene in mammalian cells conferred a transformed phenotype, which suggested its role in tumorigenesis.</p>
<p><strong>B.</strong> Coverage profile at the CHD1L locus. The protein encoded by this gene is a calcium dependent cell-cell adhesion glycoprotein. Loss of function of this gene is thought to contribute to progression in cancer by increasing proliferation, invasion, and/or metastasis.</p>
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<p><strong>Figure 2. Excellent sequencing quality. </strong>Genomic DNA was extracted from human blood samples and sheared to a mean fragment length of 200 bp. MeDIP-seq libraries were prepared from different starting amounts of gDNA using Diagenode's MagMeDIP-seq Package V2 and sequenced in paired-end 50 bp on Illumina NovaSeq instrument generating around 60 million read pairs per sample. Sequencing statistics reveal that all samples performed well, with mean Phred scores above 30 along the entire reads 1 and 2 (data shown for 50 ng gDNA input after trimming).</p>
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<p><strong>Figure 3. Saturation analysis.</strong> Clean reads were aligned to the human genome (hg19) using Burrows-Wheeler aligner (BWA) algorithm after which duplicated and unmapped reads were removed resulting in a mapping efficiency >98% for all samples. Quality and validity check of the mapped MeDIP-seq data was performed using MEDIPS R package. Saturation plots show that all sets of reads have sufficient complexity and depth to saturate the coverage profile of the reference genome and that this is reproducible <span>between replicates and repetitive experiments </span>(data shown for 50 ng gDNA input: left panel = replicate a, right panel = replicate b).</p>
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<p><strong>Figure 4. Superior enrichment of methylated regions from nanograms of gDNA from human blood samples. </strong>MeDIP-seq measure the relative enrichment of methylated DNA between the samples and its corresponding input. Regions with significant (adjusted p-value <0.1) positive changes of the samples over the input are defined as peak and used for further downstream analysis. With Diagenode's MagMeDIP-seq V2 Package, a significant proportion of uniquely mapped reads corresponds to peaks, demonstrating a highly efficient enrichment even for low gDNA amounts.</p>
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<p><strong>Figure 6. Coverage profiles on the positive control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the TSH2B (H2BC1) locus (marked by blue boxes in the bottom track), which is a repressed region in blood cells and should be highly methylated, resulting in enrichment and reads accumulation following Diagenode's MagMeDIP-Seq V2 workflow. This methylated region was consistently detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<p><strong>Figure 7. Coverage profiles on the negative control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the GADPH locus (marked by blue boxes in the bottom track), which is a highly active transcription region and should not be methylated, resulting in no reads accumulation following Diagenode's MagMeDIP-Seq V2 package. This non-methylated region was not detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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'description' => '<p><span>Perform </span><strong>MeDIP-seq </strong>experiments, <em>i.e.</em> m<span>ethylated DNA immunoprecipitation followed by next generation sequencing, to obtain region-resolution assessment of DNA methylation using a highly sensitive 5-mC-specific antibody. This technology provides a useful, reproducible, and affordable approach for high-resolution methylome research.</span></p>
<p>MeDIP-seq methods allow you to:</p>
<ul>
<li> Perform <span>genome-wide DNA methylation mapping</span></li>
<li> Detect and identify <span>differentially </span><span>methylated regions with high sensitivity</span></li>
<li> Get better insight of your epigenetics research</li>
</ul>
<p><span>Diagenode's <strong>MagMeDIP-seq package V2</strong> has been specifically developed and optimized to generate DNA libraries during the MagMeDIP assay from the <strong>lowest DNA amounts </strong><strong> </strong>and secure <strong>high-quality NGS data </strong>for DNA methylation analysis. <strong>Only 10 ng</strong> <strong>of sheared genomic DNA</strong> is required for IP enrichment and library generation, while preserving the efficiency of the enrichment. </span></p>
<p>The package <span>contains </span><strong>everything you need</strong><span><span> for your MeDIP-seq experiment, including highly specific antibody, fully validated reagents for library preparation from enriched methylated DNA, and external DNA controls.</span></span></p>
<h3>Content</h3>
<ul>
<li><a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns" target="_blank">MagMeDIP qPCR Kit</a><span> </span>(x10) including highly sensitive 5mC specific antibody (clone 33D3) for <strong>superior enrichment</strong> and external DNA controls and qPCR primer pairs for <strong>quality controls</strong></li>
<li><a href="https://www.diagenode.com/en/p/iDeal-DNA-IP-library-preparation-kit-x24" target="_blank">iDeal DNA IP library preparation kit </a>(x24) and <a href="https://www.diagenode.com/en/p/iDeal-24-Unique-Dual-Indexes-Set-A">iDeal UDI modules</a> (x24) for <strong>highest library yields</strong> and <strong>index hopping mitigation</strong></li>
<li><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24" target="_blank">IPure kit v2</a><span> </span>(x24) for <strong>highest quality purification</strong> before sequencing</li>
</ul>
<h3><span><span></span></span><span>Features</span></h3>
<ul>
<li><strong>All-in one </strong>MeDIP-seq kit, fully validated for <strong>NGS analysis</strong></li>
<li>Low DNA requirement:<b><span> </span></b>down to <b>10 ng per reaction</b></li>
<li><b>Robust </b>method<b>, <strong>superior</strong> </b>enrichment,<b> </b>and<b> easy-to-use </b>protocol</li>
<li><b>High reproducibility<span> </span></b>between replicates and repetitive experiments</li>
</ul>
<h3><span>Sequencing analysis</span></h3>
<div class="extra-spaced">
<div class="row">
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 1. NGS data generated using Diagenode's MagMeDIP-seq Package V2 detects methylation at CpG shores. </strong><br />MeDIP-seq libraries were prepared from 50 ng of genomic DNA originating from human blood samples with Diagenode's MagMeDIP-seq Package V2. IP and corresponding INPUT samples were sequenced in paired-end 50 bp on Illumina NovaSeq instrument. Reads were mapped to generate a whole-genome DNA methylation profile. The image above shows two examples of DNA methylation being detected at CpG shores rather than in the CpG island itself. This data agrees with recent findings showing that a large portion of methylated sites occur in these regions that are adjacent to CpG islands.</p>
<p><strong>A.</strong> Coverage profile at the PTP42 locus. The protein encoded by this gene belongs to a small class of the protein tyrosine phosphatase (PTP) family. Overexpression of this gene in mammalian cells conferred a transformed phenotype, which suggested its role in tumorigenesis.</p>
<p><strong>B.</strong> Coverage profile at the CHD1L locus. The protein encoded by this gene is a calcium dependent cell-cell adhesion glycoprotein. Loss of function of this gene is thought to contribute to progression in cancer by increasing proliferation, invasion, and/or metastasis.</p>
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<p><strong>Figure 2. Excellent sequencing quality. </strong>Genomic DNA was extracted from human blood samples and sheared to a mean fragment length of 200 bp. MeDIP-seq libraries were prepared from different starting amounts of gDNA using Diagenode's MagMeDIP-seq Package V2 and sequenced in paired-end 50 bp on Illumina NovaSeq instrument generating around 60 million read pairs per sample. Sequencing statistics reveal that all samples performed well, with mean Phred scores above 30 along the entire reads 1 and 2 (data shown for 50 ng gDNA input after trimming).</p>
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<p><strong>Figure 4. Superior enrichment of methylated regions from nanograms of gDNA from human blood samples. </strong>MeDIP-seq measure the relative enrichment of methylated DNA between the samples and its corresponding input. Regions with significant (adjusted p-value <0.1) positive changes of the samples over the input are defined as peak and used for further downstream analysis. With Diagenode's MagMeDIP-seq V2 Package, a significant proportion of uniquely mapped reads corresponds to peaks, demonstrating a highly efficient enrichment even for low gDNA amounts.</p>
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<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 5. Annotation of significant methylated regions detected on human blood samples. </strong>The common peaks between replicates of the same condition were annotated with regards to CpG context and genomic features. Diagenode's MagMeDIP-seq package V2 allows a wide interrogation of methylated regions of the human genome, especially in low density CpG regions (data shown for 50 ng gDNA input).</p>
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<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 6. Coverage profiles on the positive control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the TSH2B (H2BC1) locus (marked by blue boxes in the bottom track), which is a repressed region in blood cells and should be highly methylated, resulting in enrichment and reads accumulation following Diagenode's MagMeDIP-Seq V2 workflow. This methylated region was consistently detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<p><strong></strong></p>
<p><strong>Figure 7. Coverage profiles on the negative control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the GADPH locus (marked by blue boxes in the bottom track), which is a highly active transcription region and should not be methylated, resulting in no reads accumulation following Diagenode's MagMeDIP-Seq V2 package. This non-methylated region was not detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<div class="small-12 medium-12 large-12 columns">
<p><span style="font-weight: 400;">Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to </span><a href="../applications/dna-rna-shearing"><span style="font-weight: 400;">fragmented DNA or RNA</span></a><span style="font-weight: 400;"> prior to sequencing</span></p>
<p><span style="font-weight: 400;">After input DNA has been fragmented, it is end-repaired and blunt-ended</span><span style="font-weight: 400;">. The next step is a A-tailing in which dAMP is added to the 3´ end of the blunt phosphorylated DNA fragments to prevent concatemerization and to allow the ligation of adaptors with complementary dT overhangs. In addition, barcoded adapters can be incorporated to facilitate multiplexing prior to or during amplification.</span></p>
<center><img src="https://www.diagenode.com/img/categories/library-prep/flux.png" /></center>
<p><span style="font-weight: 400;">Diagenode offers a comprehensive product portfolio for library preparation:<br /></span></p>
<strong><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">D-Plex RNA-seq Library Preparation Kits</a></strong><br />
<p><span style="font-weight: 400;">Diagenode’s new RNA-sequencing solutions utilize the innovative c</span><span style="font-weight: 400;">apture and a</span><span style="font-weight: 400;">mplification by t</span><span style="font-weight: 400;">ailing and s</span><span style="font-weight: 400;">witching”</span><span style="font-weight: 400;">, a ligation-free method to produce DNA libraries for next generation sequencing from low input amounts of RNA. </span><span style="font-weight: 400;"></span><a href="../categories/Library-preparation-for-RNA-seq">Learn more</a></p>
<strong><a href="../categories/library-preparation-for-ChIP-seq">ChIP-seq and DNA sequencing library preparation solutions</a></strong><br />
<p><span style="font-weight: 400;">Our kits have been optimized for DNA library preparation used for next generation sequencing for a wide range of inputs. Using a simple three-step protocols, our</span><a href="http://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><span style="font-weight: 400;"> </span></a><span style="font-weight: 400;">kits are an optimal choice for library preparation from DNA inputs down to 50 pg. </span><a href="../categories/library-preparation-for-ChIP-seq">Learn more</a></p>
<a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span><strong>Bioruptor Pico - short fragments</strong></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">Our well-cited Bioruptor Pico is the shearing device of choice for chromatin and DNA fragmentation. Obtain uniform and tight fragment distributions between 150bp -2kb. </span><a href="../p/bioruptor-pico-sonication-device">Learn more</a></p>
<strong><a href="../p/megaruptor2-1-unit"><span href="../p/bioruptor-pico-sonication-device">Megaruptor</span>® - long fragments</a></strong><a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">The Megaruptor is designed to shear DNA from 3kb-75kb for long-read sequencing. <a href="../p/megaruptor2-1-unit">Learn more</a></span></p>
<span href="../p/bioruptor-pico-sonication-device"></span><span style="font-weight: 400;"></span></div>
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<div class="large-12 columns">
<div style="text-align: justify;" class="small-12 medium-8 large-8 columns">
<h2>Complete solutions for DNA methylation studies</h2>
<p>Whether you are experienced or new to the field of DNA methylation, Diagenode has everything you need to make your assay as easy and convenient as possible while ensuring consistent data between samples and experiments. Diagenode offers sonication instruments, reagent kits, high quality antibodies, and high-throughput automation capability to address all of your specific DNA methylation analysis requirements.</p>
</div>
<div class="small-12 medium-4 large-4 columns text-center"><a href="../landing-pages/dna-methylation-grant-applications"><img src="https://www.diagenode.com/img/banners/banner-dna-grant.png" alt="" /></a></div>
<div style="text-align: justify;" class="small-12 medium-12 large-12 columns">
<p>DNA methylation was the first discovered epigenetic mark and is the most widely studied topic in epigenetics. <em>In vivo</em>, DNA is methylated following DNA replication and is involved in a number of biological processes including the regulation of imprinted genes, X chromosome inactivation. and tumor suppressor gene silencing in cancer cells. Methylation often occurs in cytosine-guanine rich regions of DNA (CpG islands), which are commonly upstream of promoter regions.</p>
</div>
<div class="small-12 medium-12 large-12 columns"><br /><br />
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#dnamethyl"><i class="fa fa-caret-right"></i> Learn more</a>
<div id="dnamethyl" class="content">5-methylcytosine (5-mC) has been known for a long time as the only modification of DNA for epigenetic regulation. In 2009, however, Kriaucionis discovered a second methylated cytosine, 5-hydroxymethylcytosine (5-hmC). The so-called 6th base, is generated by enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine by the TET family of oxygenases. Early reports suggested that 5-hmC may represent an intermediate of active demethylation in a new pathway which demethylates DNA, converting 5-mC to cytosine. Recent evidence fuel this hypothesis suggesting that further oxidation of the hydroxymethyl group leads to a formyl or carboxyl group followed by either deformylation or decarboxylation. The formyl and carboxyl groups of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) could be enzymatically removed without excision of the base.
<p class="text-center"><img src="https://www.diagenode.com/img/categories/kits_dna/dna_methylation_variants.jpg" /></p>
</div>
</li>
</ul>
<br />
<h2>Main DNA methylation technologies</h2>
<p style="text-align: justify;">Overview of the <span style="font-weight: 400;">three main approaches for studying DNA methylation.</span></p>
<div class="row">
<ol>
<li style="font-weight: 400;"><span style="font-weight: 400;">Chemical modification with bisulfite – Bisulfite conversion</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Enrichment of methylated DNA (including MeDIP and MBD)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Treatment with methylation-sensitive or dependent restriction enzymes</span></li>
</ol>
<p><span style="font-weight: 400;"> </span></p>
<div class="row">
<table>
<thead>
<tr>
<th></th>
<th>Description</th>
<th width="350">Features</th>
</tr>
</thead>
<tbody>
<tr>
<td><strong>Bisulfite conversion</strong></td>
<td><span style="font-weight: 400;">Chemical conversion of unmethylated cytosine to uracil. Methylated cytosines are protected from this conversion allowing to determine DNA methylation at single nucleotide resolution.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Single nucleotide resolution</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Quantitative analysis - methylation rate (%)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Gold standard and well studied</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><b>Methylated DNA enrichment</b></td>
<td><span style="font-weight: 400;">(Hydroxy-)Methylated DNA is enriched by using specific antibodies (hMeDIP or MeDIP) or proteins (MBD) that specifically bind methylated CpG sites in fragmented genomic DNA.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Resolution depends on the fragment size of the enriched methylated DNA (300 bp)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Qualitative analysis</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><strong>Restriction enzyme-based digestion</strong></td>
<td><span style="font-weight: 400;">Use of (hydroxy)methylation-sensitive or (hydroxy)methylation-dependent restriction enzymes for DNA methylation analysis at specific sites.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Determination of methylation status is limited by the enzyme recognition site</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Easy to use</span></li>
</ul>
</td>
</tr>
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<div class="row"></div>
</div>
</div>
<div class="large-12 columns"></div>
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<p style="text-align: justify;">Diagenode’s epigenetic reagents include:</p>
<ul>
<li style="text-align: justify;"><strong>DNA methylation kits and antibodies</strong> - Validated NGS-compatible kits for MeDIP, MBD pull-down, whole genome bisulfite sequencing, and reduced representation bisulfite sequencing. Official provider for the original clone for 5-mC 33D3.</li>
<li style="text-align: justify;"><strong>ChIP and ChIP-seq kits for industry-leading specificity and sensitivity</strong> - MicroChIP/MicroPlex Kit for ChIP-seq with only 10,000 cells and the iDeal ChIP-seq Kits optimized for both transcription factors and histones. Our kits feature full reagents for ChIP-seq including control primers, control antibodies, magnetics beads, and purification reagents.</li>
<li style="text-align: justify;"><strong>Library preparation kits</strong> tailored for your specific requirements. The MicroPlex Library Preparation Kit simplifies library preparation requiring only 3 simple steps and allowing inputs of only 50 pg. </li>
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<p><img src="https://www.diagenode.com/img/areas/cancer.jpg" /></p>
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<h2>Epigenetics and Cancer</h2>
<p>Epigenetic processes control the normal development and maintenance of gene expression in a number of organisms. However, disruption of epigenetic mechanisms may alter gene function, potentially leading to cellular transformations that lead to tumorigenesis. Cancer is a multistep process from a succession of processes that alter the growth of normal cells. In cancer, epigenetic reprogramming occurs at multiple levels including nuclear organization and nucleosome positioning, DNA methylation, modification of histones, alteration of epigenetic regulators such as transcription factor binding, and non-coding RNA, such as microRNA.</p>
<p>Epigenetic modifications are reversible and potential treatments could be geared to alter irregular transcription factor binding, DNA methylation or histone acetylation. Accurate study with a versatile number of tools is essential for the study of epigenetics including sound sample preparation and analysis methodologies for DNA methylation such as with immunoprecipitation or bisulfite sequencing, chromatin analysis with chromatin immunoprecipitation (ChIP) combined with qPCR or sequencing, and RNA modification study. As researchers elucidate the mechanisms and specific modifications associated with cancer, it may be possible to target abnormal modifications in cells with minimal damage to normal cells, making the prospect of epigenetic therapy increasingly promising.</p>
<h3>Diagenode products for your epigenomics research in Cancer</h3>
<div class="row">
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #099f92; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/chromatin-function">Chromatin analysis</a></h3>
<center><a href="https://www.diagenode.com/en/categories/chromatin-function"><img src="https://www.diagenode.com/img/cancer/chromatin-icon.png" /></a></center>
<p class="text-left">Understand the role of chromatin in cancer regulation</p>
</div>
<ul>
<li>New to ChIP? <a href="https://www.diagenode.com/en/pages/portal/chip">Learn more</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin shearing optimization</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation">Chromatin Immunoprecipitation</a></li>
<li>Validated <a href="https://www.diagenode.com/en/categories/antibodies">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/library-preparation">Library preparation</a></li>
</ul>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #30415c; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/dna-methylation" style="color: #30415c;">DNA methylation</a></h3>
<center><a href="https://www.diagenode.com/en/categories/dna-methylation"><img src="https://www.diagenode.com/img/cancer/dna-icon.png" /></a></center>
<p class="text-left">Analyze DNA methylation and the effects on oncogenesis and tumor suppression</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/bisulfite-conversion">Bisulfite sequencing</a></li>
<li><a href="https://www.diagenode.com/en/categories/methylated-dna-immunoprecipitation">Methylated DNA immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/dna-methylation-profiling-services">DNA methylation services</a></li>
</ul>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #474546; height: 275px;">
<h3 class="text-center"><span class="darkgrey">Non-coding RNAs</span></h3>
<center><img src="https://www.diagenode.com/img/cancer/non-coding-icon.png" /></center>
<p class="text-left">Discover noncoding RNAs in cancer</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">RNA-seq using D-Plex</a> </li>
<li><a href="https://www.diagenode.com/en/categories/rna-seq-category">RNA-seq services</a></li>
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<span class="success label" style="">C02010041</span>
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<!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a-->
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<h6 style="height:60px">MagMeDIP kit</h6>
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'description' => '<p><span>Perform </span><strong>MeDIP-seq </strong>experiments, <em>i.e.</em> m<span>ethylated DNA immunoprecipitation followed by next generation sequencing, to obtain region-resolution assessment of DNA methylation using a highly sensitive 5-mC-specific antibody. This technology provides a useful, reproducible, and affordable approach for high-resolution methylome research.</span></p>
<p>MeDIP-seq methods allow you to:</p>
<ul>
<li> Perform <span>genome-wide DNA methylation mapping</span></li>
<li> Detect and identify <span>differentially </span><span>methylated regions with high sensitivity</span></li>
<li> Get better insight of your epigenetics research</li>
</ul>
<p><span>Diagenode's <strong>MagMeDIP-seq package V2</strong> has been specifically developed and optimized to generate DNA libraries during the MagMeDIP assay from the <strong>lowest DNA amounts </strong><strong> </strong>and secure <strong>high-quality NGS data </strong>for DNA methylation analysis. <strong>Only 10 ng</strong> <strong>of sheared genomic DNA</strong> is required for IP enrichment and library generation, while preserving the efficiency of the enrichment. </span></p>
<p>The package <span>contains </span><strong>everything you need</strong><span><span> for your MeDIP-seq experiment, including highly specific antibody, fully validated reagents for library preparation from enriched methylated DNA, and external DNA controls.</span></span></p>
<h3>Content</h3>
<ul>
<li><a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns" target="_blank">MagMeDIP qPCR Kit</a><span> </span>(x10) including highly sensitive 5mC specific antibody (clone 33D3) for <strong>superior enrichment</strong> and external DNA controls and qPCR primer pairs for <strong>quality controls</strong></li>
<li><a href="https://www.diagenode.com/en/p/iDeal-DNA-IP-library-preparation-kit-x24" target="_blank">iDeal DNA IP library preparation kit </a>(x24) and <a href="https://www.diagenode.com/en/p/iDeal-24-Unique-Dual-Indexes-Set-A">iDeal UDI modules</a> (x24) for <strong>highest library yields</strong> and <strong>index hopping mitigation</strong></li>
<li><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24" target="_blank">IPure kit v2</a><span> </span>(x24) for <strong>highest quality purification</strong> before sequencing</li>
</ul>
<h3><span><span></span></span><span>Features</span></h3>
<ul>
<li><strong>All-in one </strong>MeDIP-seq kit, fully validated for <strong>NGS analysis</strong></li>
<li>Low DNA requirement:<b><span> </span></b>down to <b>10 ng per reaction</b></li>
<li><b>Robust </b>method<b>, <strong>superior</strong> </b>enrichment,<b> </b>and<b> easy-to-use </b>protocol</li>
<li><b>High reproducibility<span> </span></b>between replicates and repetitive experiments</li>
</ul>
<h3><span>Sequencing analysis</span></h3>
<div class="extra-spaced">
<div class="row">
<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig1.png" /></div>
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<p><strong></strong></p>
<p><strong>Figure 1. NGS data generated using Diagenode's MagMeDIP-seq Package V2 detects methylation at CpG shores. </strong><br />MeDIP-seq libraries were prepared from 50 ng of genomic DNA originating from human blood samples with Diagenode's MagMeDIP-seq Package V2. IP and corresponding INPUT samples were sequenced in paired-end 50 bp on Illumina NovaSeq instrument. Reads were mapped to generate a whole-genome DNA methylation profile. The image above shows two examples of DNA methylation being detected at CpG shores rather than in the CpG island itself. This data agrees with recent findings showing that a large portion of methylated sites occur in these regions that are adjacent to CpG islands.</p>
<p><strong>A.</strong> Coverage profile at the PTP42 locus. The protein encoded by this gene belongs to a small class of the protein tyrosine phosphatase (PTP) family. Overexpression of this gene in mammalian cells conferred a transformed phenotype, which suggested its role in tumorigenesis.</p>
<p><strong>B.</strong> Coverage profile at the CHD1L locus. The protein encoded by this gene is a calcium dependent cell-cell adhesion glycoprotein. Loss of function of this gene is thought to contribute to progression in cancer by increasing proliferation, invasion, and/or metastasis.</p>
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<p><strong>Figure 2. Excellent sequencing quality. </strong>Genomic DNA was extracted from human blood samples and sheared to a mean fragment length of 200 bp. MeDIP-seq libraries were prepared from different starting amounts of gDNA using Diagenode's MagMeDIP-seq Package V2 and sequenced in paired-end 50 bp on Illumina NovaSeq instrument generating around 60 million read pairs per sample. Sequencing statistics reveal that all samples performed well, with mean Phred scores above 30 along the entire reads 1 and 2 (data shown for 50 ng gDNA input after trimming).</p>
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<p><strong>Figure 3. Saturation analysis.</strong> Clean reads were aligned to the human genome (hg19) using Burrows-Wheeler aligner (BWA) algorithm after which duplicated and unmapped reads were removed resulting in a mapping efficiency >98% for all samples. Quality and validity check of the mapped MeDIP-seq data was performed using MEDIPS R package. Saturation plots show that all sets of reads have sufficient complexity and depth to saturate the coverage profile of the reference genome and that this is reproducible <span>between replicates and repetitive experiments </span>(data shown for 50 ng gDNA input: left panel = replicate a, right panel = replicate b).</p>
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'label2' => 'Validation: Peak search',
'info2' => '<div class="extra-spaced">
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<p><strong></strong></p>
<p><strong>Figure 4. Superior enrichment of methylated regions from nanograms of gDNA from human blood samples. </strong>MeDIP-seq measure the relative enrichment of methylated DNA between the samples and its corresponding input. Regions with significant (adjusted p-value <0.1) positive changes of the samples over the input are defined as peak and used for further downstream analysis. With Diagenode's MagMeDIP-seq V2 Package, a significant proportion of uniquely mapped reads corresponds to peaks, demonstrating a highly efficient enrichment even for low gDNA amounts.</p>
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<p><strong>Figure 5. Annotation of significant methylated regions detected on human blood samples. </strong>The common peaks between replicates of the same condition were annotated with regards to CpG context and genomic features. Diagenode's MagMeDIP-seq package V2 allows a wide interrogation of methylated regions of the human genome, especially in low density CpG regions (data shown for 50 ng gDNA input).</p>
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'label3' => 'Validation: Control regions',
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<p><strong>Figure 6. Coverage profiles on the positive control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the TSH2B (H2BC1) locus (marked by blue boxes in the bottom track), which is a repressed region in blood cells and should be highly methylated, resulting in enrichment and reads accumulation following Diagenode's MagMeDIP-Seq V2 workflow. This methylated region was consistently detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<p><strong>Figure 7. Coverage profiles on the negative control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the GADPH locus (marked by blue boxes in the bottom track), which is a highly active transcription region and should not be methylated, resulting in no reads accumulation following Diagenode's MagMeDIP-Seq V2 package. This non-methylated region was not detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<li> Detect and identify <span>differentially </span><span>methylated regions with high sensitivity</span></li>
<li> Get better insight of your epigenetics research</li>
</ul>
<p><span>Diagenode's <strong>MagMeDIP-seq package V2</strong> has been specifically developed and optimized to generate DNA libraries during the MagMeDIP assay from the <strong>lowest DNA amounts </strong><strong> </strong>and secure <strong>high-quality NGS data </strong>for DNA methylation analysis. <strong>Only 10 ng</strong> <strong>of sheared genomic DNA</strong> is required for IP enrichment and library generation, while preserving the efficiency of the enrichment. </span></p>
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<h3>Content</h3>
<ul>
<li><a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns" target="_blank">MagMeDIP qPCR Kit</a><span> </span>(x10) including highly sensitive 5mC specific antibody (clone 33D3) for <strong>superior enrichment</strong> and external DNA controls and qPCR primer pairs for <strong>quality controls</strong></li>
<li><a href="https://www.diagenode.com/en/p/iDeal-DNA-IP-library-preparation-kit-x24" target="_blank">iDeal DNA IP library preparation kit </a>(x24) and <a href="https://www.diagenode.com/en/p/iDeal-24-Unique-Dual-Indexes-Set-A">iDeal UDI modules</a> (x24) for <strong>highest library yields</strong> and <strong>index hopping mitigation</strong></li>
<li><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24" target="_blank">IPure kit v2</a><span> </span>(x24) for <strong>highest quality purification</strong> before sequencing</li>
</ul>
<h3><span><span></span></span><span>Features</span></h3>
<ul>
<li><strong>All-in one </strong>MeDIP-seq kit, fully validated for <strong>NGS analysis</strong></li>
<li>Low DNA requirement:<b><span> </span></b>down to <b>10 ng per reaction</b></li>
<li><b>Robust </b>method<b>, <strong>superior</strong> </b>enrichment,<b> </b>and<b> easy-to-use </b>protocol</li>
<li><b>High reproducibility<span> </span></b>between replicates and repetitive experiments</li>
</ul>
<h3><span>Sequencing analysis</span></h3>
<div class="extra-spaced">
<div class="row">
<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig1.png" /></div>
</div>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 1. NGS data generated using Diagenode's MagMeDIP-seq Package V2 detects methylation at CpG shores. </strong><br />MeDIP-seq libraries were prepared from 50 ng of genomic DNA originating from human blood samples with Diagenode's MagMeDIP-seq Package V2. IP and corresponding INPUT samples were sequenced in paired-end 50 bp on Illumina NovaSeq instrument. Reads were mapped to generate a whole-genome DNA methylation profile. The image above shows two examples of DNA methylation being detected at CpG shores rather than in the CpG island itself. This data agrees with recent findings showing that a large portion of methylated sites occur in these regions that are adjacent to CpG islands.</p>
<p><strong>A.</strong> Coverage profile at the PTP42 locus. The protein encoded by this gene belongs to a small class of the protein tyrosine phosphatase (PTP) family. Overexpression of this gene in mammalian cells conferred a transformed phenotype, which suggested its role in tumorigenesis.</p>
<p><strong>B.</strong> Coverage profile at the CHD1L locus. The protein encoded by this gene is a calcium dependent cell-cell adhesion glycoprotein. Loss of function of this gene is thought to contribute to progression in cancer by increasing proliferation, invasion, and/or metastasis.</p>
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<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 2. Excellent sequencing quality. </strong>Genomic DNA was extracted from human blood samples and sheared to a mean fragment length of 200 bp. MeDIP-seq libraries were prepared from different starting amounts of gDNA using Diagenode's MagMeDIP-seq Package V2 and sequenced in paired-end 50 bp on Illumina NovaSeq instrument generating around 60 million read pairs per sample. Sequencing statistics reveal that all samples performed well, with mean Phred scores above 30 along the entire reads 1 and 2 (data shown for 50 ng gDNA input after trimming).</p>
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<div class="extra-spaced">
<div class="row">
<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig3.png" /></div>
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 3. Saturation analysis.</strong> Clean reads were aligned to the human genome (hg19) using Burrows-Wheeler aligner (BWA) algorithm after which duplicated and unmapped reads were removed resulting in a mapping efficiency >98% for all samples. Quality and validity check of the mapped MeDIP-seq data was performed using MEDIPS R package. Saturation plots show that all sets of reads have sufficient complexity and depth to saturate the coverage profile of the reference genome and that this is reproducible <span>between replicates and repetitive experiments </span>(data shown for 50 ng gDNA input: left panel = replicate a, right panel = replicate b).</p>
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<div class="small-12 medium-12 large-12 columns" style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig4.png" /></div>
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 4. Superior enrichment of methylated regions from nanograms of gDNA from human blood samples. </strong>MeDIP-seq measure the relative enrichment of methylated DNA between the samples and its corresponding input. Regions with significant (adjusted p-value <0.1) positive changes of the samples over the input are defined as peak and used for further downstream analysis. With Diagenode's MagMeDIP-seq V2 Package, a significant proportion of uniquely mapped reads corresponds to peaks, demonstrating a highly efficient enrichment even for low gDNA amounts.</p>
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<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig5.png" /></div>
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 5. Annotation of significant methylated regions detected on human blood samples. </strong>The common peaks between replicates of the same condition were annotated with regards to CpG context and genomic features. Diagenode's MagMeDIP-seq package V2 allows a wide interrogation of methylated regions of the human genome, especially in low density CpG regions (data shown for 50 ng gDNA input).</p>
</div>
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<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig7.png" /></div>
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 6. Coverage profiles on the positive control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the TSH2B (H2BC1) locus (marked by blue boxes in the bottom track), which is a repressed region in blood cells and should be highly methylated, resulting in enrichment and reads accumulation following Diagenode's MagMeDIP-Seq V2 workflow. This methylated region was consistently detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<div class="extra-spaced">
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<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig6.png" /></div>
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 7. Coverage profiles on the negative control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the GADPH locus (marked by blue boxes in the bottom track), which is a highly active transcription region and should not be methylated, resulting in no reads accumulation following Diagenode's MagMeDIP-Seq V2 package. This non-methylated region was not detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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<div class="small-12 medium-12 large-12 columns">
<p><span style="font-weight: 400;">Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to </span><a href="../applications/dna-rna-shearing"><span style="font-weight: 400;">fragmented DNA or RNA</span></a><span style="font-weight: 400;"> prior to sequencing</span></p>
<p><span style="font-weight: 400;">After input DNA has been fragmented, it is end-repaired and blunt-ended</span><span style="font-weight: 400;">. The next step is a A-tailing in which dAMP is added to the 3´ end of the blunt phosphorylated DNA fragments to prevent concatemerization and to allow the ligation of adaptors with complementary dT overhangs. In addition, barcoded adapters can be incorporated to facilitate multiplexing prior to or during amplification.</span></p>
<center><img src="https://www.diagenode.com/img/categories/library-prep/flux.png" /></center>
<p><span style="font-weight: 400;">Diagenode offers a comprehensive product portfolio for library preparation:<br /></span></p>
<strong><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">D-Plex RNA-seq Library Preparation Kits</a></strong><br />
<p><span style="font-weight: 400;">Diagenode’s new RNA-sequencing solutions utilize the innovative c</span><span style="font-weight: 400;">apture and a</span><span style="font-weight: 400;">mplification by t</span><span style="font-weight: 400;">ailing and s</span><span style="font-weight: 400;">witching”</span><span style="font-weight: 400;">, a ligation-free method to produce DNA libraries for next generation sequencing from low input amounts of RNA. </span><span style="font-weight: 400;"></span><a href="../categories/Library-preparation-for-RNA-seq">Learn more</a></p>
<strong><a href="../categories/library-preparation-for-ChIP-seq">ChIP-seq and DNA sequencing library preparation solutions</a></strong><br />
<p><span style="font-weight: 400;">Our kits have been optimized for DNA library preparation used for next generation sequencing for a wide range of inputs. Using a simple three-step protocols, our</span><a href="http://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><span style="font-weight: 400;"> </span></a><span style="font-weight: 400;">kits are an optimal choice for library preparation from DNA inputs down to 50 pg. </span><a href="../categories/library-preparation-for-ChIP-seq">Learn more</a></p>
<a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span><strong>Bioruptor Pico - short fragments</strong></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">Our well-cited Bioruptor Pico is the shearing device of choice for chromatin and DNA fragmentation. Obtain uniform and tight fragment distributions between 150bp -2kb. </span><a href="../p/bioruptor-pico-sonication-device">Learn more</a></p>
<strong><a href="../p/megaruptor2-1-unit"><span href="../p/bioruptor-pico-sonication-device">Megaruptor</span>® - long fragments</a></strong><a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">The Megaruptor is designed to shear DNA from 3kb-75kb for long-read sequencing. <a href="../p/megaruptor2-1-unit">Learn more</a></span></p>
<span href="../p/bioruptor-pico-sonication-device"></span><span style="font-weight: 400;"></span></div>
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<div class="large-12 columns">
<div style="text-align: justify;" class="small-12 medium-8 large-8 columns">
<h2>Complete solutions for DNA methylation studies</h2>
<p>Whether you are experienced or new to the field of DNA methylation, Diagenode has everything you need to make your assay as easy and convenient as possible while ensuring consistent data between samples and experiments. Diagenode offers sonication instruments, reagent kits, high quality antibodies, and high-throughput automation capability to address all of your specific DNA methylation analysis requirements.</p>
</div>
<div class="small-12 medium-4 large-4 columns text-center"><a href="../landing-pages/dna-methylation-grant-applications"><img src="https://www.diagenode.com/img/banners/banner-dna-grant.png" alt="" /></a></div>
<div style="text-align: justify;" class="small-12 medium-12 large-12 columns">
<p>DNA methylation was the first discovered epigenetic mark and is the most widely studied topic in epigenetics. <em>In vivo</em>, DNA is methylated following DNA replication and is involved in a number of biological processes including the regulation of imprinted genes, X chromosome inactivation. and tumor suppressor gene silencing in cancer cells. Methylation often occurs in cytosine-guanine rich regions of DNA (CpG islands), which are commonly upstream of promoter regions.</p>
</div>
<div class="small-12 medium-12 large-12 columns"><br /><br />
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#dnamethyl"><i class="fa fa-caret-right"></i> Learn more</a>
<div id="dnamethyl" class="content">5-methylcytosine (5-mC) has been known for a long time as the only modification of DNA for epigenetic regulation. In 2009, however, Kriaucionis discovered a second methylated cytosine, 5-hydroxymethylcytosine (5-hmC). The so-called 6th base, is generated by enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine by the TET family of oxygenases. Early reports suggested that 5-hmC may represent an intermediate of active demethylation in a new pathway which demethylates DNA, converting 5-mC to cytosine. Recent evidence fuel this hypothesis suggesting that further oxidation of the hydroxymethyl group leads to a formyl or carboxyl group followed by either deformylation or decarboxylation. The formyl and carboxyl groups of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) could be enzymatically removed without excision of the base.
<p class="text-center"><img src="https://www.diagenode.com/img/categories/kits_dna/dna_methylation_variants.jpg" /></p>
</div>
</li>
</ul>
<br />
<h2>Main DNA methylation technologies</h2>
<p style="text-align: justify;">Overview of the <span style="font-weight: 400;">three main approaches for studying DNA methylation.</span></p>
<div class="row">
<ol>
<li style="font-weight: 400;"><span style="font-weight: 400;">Chemical modification with bisulfite – Bisulfite conversion</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Enrichment of methylated DNA (including MeDIP and MBD)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Treatment with methylation-sensitive or dependent restriction enzymes</span></li>
</ol>
<p><span style="font-weight: 400;"> </span></p>
<div class="row">
<table>
<thead>
<tr>
<th></th>
<th>Description</th>
<th width="350">Features</th>
</tr>
</thead>
<tbody>
<tr>
<td><strong>Bisulfite conversion</strong></td>
<td><span style="font-weight: 400;">Chemical conversion of unmethylated cytosine to uracil. Methylated cytosines are protected from this conversion allowing to determine DNA methylation at single nucleotide resolution.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Single nucleotide resolution</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Quantitative analysis - methylation rate (%)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Gold standard and well studied</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><b>Methylated DNA enrichment</b></td>
<td><span style="font-weight: 400;">(Hydroxy-)Methylated DNA is enriched by using specific antibodies (hMeDIP or MeDIP) or proteins (MBD) that specifically bind methylated CpG sites in fragmented genomic DNA.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Resolution depends on the fragment size of the enriched methylated DNA (300 bp)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Qualitative analysis</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><strong>Restriction enzyme-based digestion</strong></td>
<td><span style="font-weight: 400;">Use of (hydroxy)methylation-sensitive or (hydroxy)methylation-dependent restriction enzymes for DNA methylation analysis at specific sites.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Determination of methylation status is limited by the enzyme recognition site</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Easy to use</span></li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="row"></div>
</div>
</div>
<div class="large-12 columns"></div>
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<p style="text-align: justify;">Diagenode’s epigenetic reagents include:</p>
<ul>
<li style="text-align: justify;"><strong>DNA methylation kits and antibodies</strong> - Validated NGS-compatible kits for MeDIP, MBD pull-down, whole genome bisulfite sequencing, and reduced representation bisulfite sequencing. Official provider for the original clone for 5-mC 33D3.</li>
<li style="text-align: justify;"><strong>ChIP and ChIP-seq kits for industry-leading specificity and sensitivity</strong> - MicroChIP/MicroPlex Kit for ChIP-seq with only 10,000 cells and the iDeal ChIP-seq Kits optimized for both transcription factors and histones. Our kits feature full reagents for ChIP-seq including control primers, control antibodies, magnetics beads, and purification reagents.</li>
<li style="text-align: justify;"><strong>Library preparation kits</strong> tailored for your specific requirements. The MicroPlex Library Preparation Kit simplifies library preparation requiring only 3 simple steps and allowing inputs of only 50 pg. </li>
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<p><img src="https://www.diagenode.com/img/areas/cancer.jpg" /></p>
</div>
<h2>Epigenetics and Cancer</h2>
<p>Epigenetic processes control the normal development and maintenance of gene expression in a number of organisms. However, disruption of epigenetic mechanisms may alter gene function, potentially leading to cellular transformations that lead to tumorigenesis. Cancer is a multistep process from a succession of processes that alter the growth of normal cells. In cancer, epigenetic reprogramming occurs at multiple levels including nuclear organization and nucleosome positioning, DNA methylation, modification of histones, alteration of epigenetic regulators such as transcription factor binding, and non-coding RNA, such as microRNA.</p>
<p>Epigenetic modifications are reversible and potential treatments could be geared to alter irregular transcription factor binding, DNA methylation or histone acetylation. Accurate study with a versatile number of tools is essential for the study of epigenetics including sound sample preparation and analysis methodologies for DNA methylation such as with immunoprecipitation or bisulfite sequencing, chromatin analysis with chromatin immunoprecipitation (ChIP) combined with qPCR or sequencing, and RNA modification study. As researchers elucidate the mechanisms and specific modifications associated with cancer, it may be possible to target abnormal modifications in cells with minimal damage to normal cells, making the prospect of epigenetic therapy increasingly promising.</p>
<h3>Diagenode products for your epigenomics research in Cancer</h3>
<div class="row">
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #099f92; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/chromatin-function">Chromatin analysis</a></h3>
<center><a href="https://www.diagenode.com/en/categories/chromatin-function"><img src="https://www.diagenode.com/img/cancer/chromatin-icon.png" /></a></center>
<p class="text-left">Understand the role of chromatin in cancer regulation</p>
</div>
<ul>
<li>New to ChIP? <a href="https://www.diagenode.com/en/pages/portal/chip">Learn more</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin shearing optimization</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation">Chromatin Immunoprecipitation</a></li>
<li>Validated <a href="https://www.diagenode.com/en/categories/antibodies">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/library-preparation">Library preparation</a></li>
</ul>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #30415c; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/dna-methylation" style="color: #30415c;">DNA methylation</a></h3>
<center><a href="https://www.diagenode.com/en/categories/dna-methylation"><img src="https://www.diagenode.com/img/cancer/dna-icon.png" /></a></center>
<p class="text-left">Analyze DNA methylation and the effects on oncogenesis and tumor suppression</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/bisulfite-conversion">Bisulfite sequencing</a></li>
<li><a href="https://www.diagenode.com/en/categories/methylated-dna-immunoprecipitation">Methylated DNA immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/dna-methylation-profiling-services">DNA methylation services</a></li>
</ul>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #474546; height: 275px;">
<h3 class="text-center"><span class="darkgrey">Non-coding RNAs</span></h3>
<center><img src="https://www.diagenode.com/img/cancer/non-coding-icon.png" /></center>
<p class="text-left">Discover noncoding RNAs in cancer</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">RNA-seq using D-Plex</a> </li>
<li><a href="https://www.diagenode.com/en/categories/rna-seq-category">RNA-seq services</a></li>
</ul>
</div>
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<div class="row">
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<a href="/cn/p/magmedip-seq-package-V2-x10"><img src="/img/grey-logo.jpg" alt="default alt" class="th"/></a> </div>
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<span class="success label" style="">C02010041</span>
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<h6 style="height:60px">MagMeDIP kit</h6>
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'description' => '<p><span>Perform </span><strong>MeDIP-seq </strong>experiments, <em>i.e.</em> m<span>ethylated DNA immunoprecipitation followed by next generation sequencing, to obtain region-resolution assessment of DNA methylation using a highly sensitive 5-mC-specific antibody. This technology provides a useful, reproducible, and affordable approach for high-resolution methylome research.</span></p>
<p>MeDIP-seq methods allow you to:</p>
<ul>
<li> Perform <span>genome-wide DNA methylation mapping</span></li>
<li> Detect and identify <span>differentially </span><span>methylated regions with high sensitivity</span></li>
<li> Get better insight of your epigenetics research</li>
</ul>
<p><span>Diagenode's <strong>MagMeDIP-seq package V2</strong> has been specifically developed and optimized to generate DNA libraries during the MagMeDIP assay from the <strong>lowest DNA amounts </strong><strong> </strong>and secure <strong>high-quality NGS data </strong>for DNA methylation analysis. <strong>Only 10 ng</strong> <strong>of sheared genomic DNA</strong> is required for IP enrichment and library generation, while preserving the efficiency of the enrichment. </span></p>
<p>The package <span>contains </span><strong>everything you need</strong><span><span> for your MeDIP-seq experiment, including highly specific antibody, fully validated reagents for library preparation from enriched methylated DNA, and external DNA controls.</span></span></p>
<h3>Content</h3>
<ul>
<li><a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns" target="_blank">MagMeDIP qPCR Kit</a><span> </span>(x10) including highly sensitive 5mC specific antibody (clone 33D3) for <strong>superior enrichment</strong> and external DNA controls and qPCR primer pairs for <strong>quality controls</strong></li>
<li><a href="https://www.diagenode.com/en/p/iDeal-DNA-IP-library-preparation-kit-x24" target="_blank">iDeal DNA IP library preparation kit </a>(x24) and <a href="https://www.diagenode.com/en/p/iDeal-24-Unique-Dual-Indexes-Set-A">iDeal UDI modules</a> (x24) for <strong>highest library yields</strong> and <strong>index hopping mitigation</strong></li>
<li><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24" target="_blank">IPure kit v2</a><span> </span>(x24) for <strong>highest quality purification</strong> before sequencing</li>
</ul>
<h3><span><span></span></span><span>Features</span></h3>
<ul>
<li><strong>All-in one </strong>MeDIP-seq kit, fully validated for <strong>NGS analysis</strong></li>
<li>Low DNA requirement:<b><span> </span></b>down to <b>10 ng per reaction</b></li>
<li><b>Robust </b>method<b>, <strong>superior</strong> </b>enrichment,<b> </b>and<b> easy-to-use </b>protocol</li>
<li><b>High reproducibility<span> </span></b>between replicates and repetitive experiments</li>
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<h3><span>Sequencing analysis</span></h3>
<div class="extra-spaced">
<div class="row">
<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig1.png" /></div>
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<p><strong></strong></p>
<p><strong>Figure 1. NGS data generated using Diagenode's MagMeDIP-seq Package V2 detects methylation at CpG shores. </strong><br />MeDIP-seq libraries were prepared from 50 ng of genomic DNA originating from human blood samples with Diagenode's MagMeDIP-seq Package V2. IP and corresponding INPUT samples were sequenced in paired-end 50 bp on Illumina NovaSeq instrument. Reads were mapped to generate a whole-genome DNA methylation profile. The image above shows two examples of DNA methylation being detected at CpG shores rather than in the CpG island itself. This data agrees with recent findings showing that a large portion of methylated sites occur in these regions that are adjacent to CpG islands.</p>
<p><strong>A.</strong> Coverage profile at the PTP42 locus. The protein encoded by this gene belongs to a small class of the protein tyrosine phosphatase (PTP) family. Overexpression of this gene in mammalian cells conferred a transformed phenotype, which suggested its role in tumorigenesis.</p>
<p><strong>B.</strong> Coverage profile at the CHD1L locus. The protein encoded by this gene is a calcium dependent cell-cell adhesion glycoprotein. Loss of function of this gene is thought to contribute to progression in cancer by increasing proliferation, invasion, and/or metastasis.</p>
</div>
</div>
</div>
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'label1' => 'Validation: Sequencing quality',
'info1' => '<div class="extra-spaced">
<div class="row">
<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig2.png" /></div>
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<p><strong></strong></p>
<p><strong>Figure 2. Excellent sequencing quality. </strong>Genomic DNA was extracted from human blood samples and sheared to a mean fragment length of 200 bp. MeDIP-seq libraries were prepared from different starting amounts of gDNA using Diagenode's MagMeDIP-seq Package V2 and sequenced in paired-end 50 bp on Illumina NovaSeq instrument generating around 60 million read pairs per sample. Sequencing statistics reveal that all samples performed well, with mean Phred scores above 30 along the entire reads 1 and 2 (data shown for 50 ng gDNA input after trimming).</p>
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<div class="extra-spaced">
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<p><strong></strong></p>
<p><strong>Figure 3. Saturation analysis.</strong> Clean reads were aligned to the human genome (hg19) using Burrows-Wheeler aligner (BWA) algorithm after which duplicated and unmapped reads were removed resulting in a mapping efficiency >98% for all samples. Quality and validity check of the mapped MeDIP-seq data was performed using MEDIPS R package. Saturation plots show that all sets of reads have sufficient complexity and depth to saturate the coverage profile of the reference genome and that this is reproducible <span>between replicates and repetitive experiments </span>(data shown for 50 ng gDNA input: left panel = replicate a, right panel = replicate b).</p>
</div>
</div>
</div>
<script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script>',
'label2' => 'Validation: Peak search',
'info2' => '<div class="extra-spaced">
<div class="row">
<div class="small-12 medium-12 large-12 columns" style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig4.png" /></div>
</div>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 4. Superior enrichment of methylated regions from nanograms of gDNA from human blood samples. </strong>MeDIP-seq measure the relative enrichment of methylated DNA between the samples and its corresponding input. Regions with significant (adjusted p-value <0.1) positive changes of the samples over the input are defined as peak and used for further downstream analysis. With Diagenode's MagMeDIP-seq V2 Package, a significant proportion of uniquely mapped reads corresponds to peaks, demonstrating a highly efficient enrichment even for low gDNA amounts.</p>
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</div>
<div class="extra-spaced">
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<div class="row">
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<p><strong></strong></p>
<p><strong>Figure 5. Annotation of significant methylated regions detected on human blood samples. </strong>The common peaks between replicates of the same condition were annotated with regards to CpG context and genomic features. Diagenode's MagMeDIP-seq package V2 allows a wide interrogation of methylated regions of the human genome, especially in low density CpG regions (data shown for 50 ng gDNA input).</p>
</div>
</div>
</div>
<script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script>',
'label3' => 'Validation: Control regions',
'info3' => '<div class="extra-spaced">
<div class="row">
<div class="small-12 medium-12 large-12 columns"><img src="https://www.diagenode.com/img/product/kits/C02010041-magmedip-fig7.png" /></div>
</div>
<div class="row">
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<p><strong></strong></p>
<p><strong>Figure 6. Coverage profiles on the positive control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the TSH2B (H2BC1) locus (marked by blue boxes in the bottom track), which is a repressed region in blood cells and should be highly methylated, resulting in enrichment and reads accumulation following Diagenode's MagMeDIP-Seq V2 workflow. This methylated region was consistently detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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</div>
</div>
<div class="extra-spaced">
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong></strong></p>
<p><strong>Figure 7. Coverage profiles on the negative control region from different starting amounts of DNA from human blood samples. </strong>IGV snapshots were taken at the GADPH locus (marked by blue boxes in the bottom track), which is a highly active transcription region and should not be methylated, resulting in no reads accumulation following Diagenode's MagMeDIP-Seq V2 package. This non-methylated region was not detected across the range of DNA amounts: 1 µg (green), 50 ng (red) and 10 ng (blue).</p>
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