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Auto MagMeDIP kit

Catalog Number

Format

Price

C02010014

48 rxns

Other format

C02010013

10 rxns

DISCONTINUED

Perform Automated MeDIP (seq) (Methylated DNA Immunoprecipitation sequencing) with Diagenode´s Auto MagMeDIP kit to estimate DNA methylation status of your sample using the 5-methylcytosine antibody. For further information about MeDIP-seq workflow, please consult "Protocols" section. Diagenode’s Auto MagMeDIP kit is available in two formats (10 and 48 IPs) and has been optimized on the SX-8G IP-Star® Automated System enabling highly reproducible results and allowing for high throughput assays.

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Human mitochondrial DNA is extensively methylated in a non-CpG context
Patil Vibha, Cuenin Cyrille, Chung Felicia, Aguilera Jesus R Rodriguez, Fernandez-Jimenez Nora, Romero-Garmendia Irati, Bilbao Jose Ramon, Cahais Vincent, Rothwell Joseph, Herceg Zdenko
Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global and site-specific methylation of the mitochondrial genome has been desc...

Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues.
Amorim BR, Dos Santos PAC, de Lima CL, Andia DC, Mazzeu JF, Acevedo AC
This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification meth...

Molecular Signatures of Regression of the Canine Transmissible Venereal Tumor.
Frampton D, Schwenzer H, Marino G, Butcher LM, Pollara G, Kriston-Vizi J, Venturini C, Austin R, de Castro KF, Ketteler R, Chain B, Goldstein RA, Weiss RA, Beck S, Fassati A
The canine transmissible venereal tumor (CTVT) is a clonally transmissible cancer that regresses spontaneously or after treatment with vincristine, but we know little about the regression mechanisms. We performed global transcriptional, methylation, and functional pathway analyses on serial biopsies of vincristine-t...

Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing
Staunstrup N.H. et al.
Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest i...

Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples
Bak S.T. et al.
We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), co...

Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots
Nicklas H. Staunstrup et al.
Background In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarke...

Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection
Sharma G et al.
A mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative conditions and cardiovascular diseases have been documented. Here we sho...

関連商品
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			'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010021',
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<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation) <span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> </span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
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			'description' => '<p><span>The Auro hMeDIP kit is designed for enrichment of hydroxymethylated DNA from fragmented&nbsp;genomic DNA&nbsp;samples for use in genome-wide methylation analysis. It features</span><span>&nbsp;a highly specific monoclonal antibody against&nbsp;</span><span>5-hydroxymethylcytosine (5-hmC) for the immunoprecipitation of hydroxymethylated DNA</span><span>. It includes&nbsp;control DNA and primers to assess the effiency of the assay.&nbsp;</span><span>Performing hydroxymethylation profiling with the hMeDIP kit is fast,&nbsp;reliable and&nbsp;highly specific.</span></p>',
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<li><span>Robust enrichment &amp; immunoprecipitation of hydroxymethylated DNA</span></li>
<li>Highly specific monoclonal antibody against 5-hmC<span>&nbsp;for reliable, reproducible results</span></li>
<li>Including&nbsp;control DNA and primers to&nbsp;<span>monitor the&nbsp;efficiency of the assay</span>
<ul style="list-style-type: circle;">
<li>5-hmC, 5-mC and unmethylated DNA sequences and primer pairs</li>
<li>Mouse primer pairs against Sfi1 targeting hydroxymethylated gene in mouse</li>
</ul>
</li>
</ul>
<ul style="list-style-type: disc;">
<li>Improved single-tube, magnetic bead-based protocol</li>
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			'name' => 'Auto MethylCap kit',
			'description' => '<p>The Auto MethylCap kit allows to specifically capture DNA fragments containing methylated CpGs. The assay is based on the affinity purification of methylated DNA using methyl-CpG-binding domain (MBD) of human MeCP2 protein. This procedure has been optimized to perform automated immunoprecipitation of chromatin using the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star&reg; Compact Automated System</a> enabling highly reproducible results and allowing for high throughput.</p>',
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<li><strong>Fast &amp; sensitive capture</strong> of methylated DNA</li>
<li><strong>High capture efficiency</strong></li>
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<li><strong>Automation compatibility</strong><strong></strong>
<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>F</strong><strong>igure 1.</strong><span>&nbsp;</span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
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			'description' => '<p>Diagenode's Premium Bisulfite Kit rapidly converts DNA through bisulfite treatment. Our conversion reagent is added directly to DNA, requires no intermediate steps, and results in high yields of DNA ready for downstream analysis methods including PCR and Next-Generation Sequencing.</p>',
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			'info1' => '<p><strong>Bisulfite Conversion efficiency in TERTBS1 and CTS56 genomic regions.</strong></p>
<p>The figure shows the conversion efficiency in TERTBS1 and CTS56 genomic regions when using 1 &mu;g, 500ng and 100 ng of genomic DNA. Between 1 and 5 clones were analyzed for the different amounts of genomic DNA</p>
<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
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<p>The DNA methylation control package includes one methylated and&nbsp;one unmethylated&nbsp;spike-in controls together with their corresponding qPCR primer sets for assessing the efficiency of your non-plant MeDIP experiments (Methylated DNA Immunoprecipitation)&nbsp;carried out with Diagenode&rsquo;s <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">MagMeDIP qPCR&nbsp;Kit</a> and <a href="https://www.diagenode.com/en/p/auto-magmedip-kit-x48-48-rxns" target="_blank">Auto MagMeDIP qPCR Kit</a>.</p>
<p><span>Those spike-in controls are made from&nbsp;<em>A. thaliana</em><span>. Therefore, they can interfere with DNA samples derived from plant species.</span></span></p>
<p><em><strong>CAUTION</strong>: These spike-in controls are compatible with <span>Diagenode&rsquo;s&nbsp;</span><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">MagMeDIP qPCR&nbsp;Kit</a><span><span>&nbsp;</span>and<span>&nbsp;</span></span><a href="https://www.diagenode.com/en/p/auto-magmedip-kit-x48-48-rxns" target="_blank">Auto MagMeDIP qPCR Kit</a><span>. However</span>, those are not the ones directly provided&nbsp;in the kits.&nbsp;The spike-in controls provided in the kits are available separately with the <a href="https://www.diagenode.com/en/p/dna-methylation-control-package-V2-48-rxns">DNA methylation control package V2</a>.</em></p>',
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			'description' => '<p><span></span>The reference&nbsp;C02010014 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">C02010021</a><span>.&nbsp;</span>&nbsp;</p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation) <span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> </span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
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<div class="small-12 medium-3 large-3 columns"><center><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank"><img src="https://www.diagenode.com/img/banners/banner-nature-publication-580.png" /></a></center></div>
<div class="small-12 medium-9 large-9 columns">
<h3>Sensitive tumour detection and classification using plasma cell-free DNA methylomes<br /><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank">Read the publication</a></h3>
<h3 class="c-article-title u-h1" data-test="article-title" itemprop="name headline">Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA<br /><a href="https://www.nature.com/articles/s41596-019-0202-2" target="_blank" title="cfMeDIP-seq Nature Method">Read the method</a></h3>
</div>
</div>
<div class="row">
<div class="large-12 columns"><span>The Methylated DNA Immunoprecipitation is based on the affinity purification of methylated and hydroxymethylated DNA using, respectively, an antibody directed against 5-methylcytosine (5-mC) in the case of MeDIP or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP.</span><br />
<h2></h2>
<h2>How it works</h2>
<p>In brief, Methyl DNA IP is performed as follows: Genomic DNA from cultured cells or tissues is prepared, sheared, and then denatured. Then, immunoselection and immunoprecipitation can take place using the antibody directed against 5 methylcytosine and antibody binding beads. After isolation and purification is performed, the IP&rsquo;d methylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or next generation sequencing.</p>
<h2>Applications</h2>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> qPCR analysis</a></div>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-seq-package-V2-x10" class="center alert radius button"> NGS analysis </a></div>
<h2>Advantages</h2>
<ul style="font-size: 19px;" class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <strong>Unaffected</strong> DNA</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>High enrichment</strong> yield</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>Robust</strong> &amp; <strong>reproducible</strong> techniques</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li>
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<h2></h2>
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<p>The Methylated DNA Immunoprecipitation is based on the affinity purification of methylated and hydroxymethylated DNA using, respectively, an antibody directed against 5-methylcytosine (5-mC) in the case of MeDIP or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP.</p>
<h2>How it works</h2>
<p>In brief, Methyl DNA IP is performed as follows: Genomic DNA from cultured cells or tissues is prepared, sheared, and then denatured. Then, immunoselection and immunoprecipitation can take place using the antibody directed against 5 methylcytosine and antibody binding beads. After isolation and purification is performed, the IP&rsquo;d methylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or next generation sequencing.</p>
<h2>Applications</h2>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> qPCR analysis</a></div>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> NGS analysis </a></div>
<h2>Advantages</h2>
<ul style="font-size: 19px;" class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <strong>Unaffected</strong> DNA</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>High enrichment</strong> yield</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>Robust</strong> &amp; <strong>reproducible</strong> techniques</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li>
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<div class="section">
<div class="layoutArea">
<div class="column">
<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #15 and&nbsp;before;</strong></li>
<li><strong>MagMeDIP x10 batch #7 and&nbsp;before</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP). </span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</div>
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<div class="layoutArea">
<div class="column">
<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #16 and after;</strong></li>
<li><strong>MagMeDIP x10 batch #7A and after.</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP).</span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
<p><span><span>MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</span></span></p>
<p><span></span></p>
<p><span></span></p>
</div>
</div>
</div>
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			'authors' => 'Patil Vibha, Cuenin Cyrille, Chung Felicia, Aguilera Jesus R Rodriguez, Fernandez-Jimenez Nora, Romero-Garmendia Irati, Bilbao Jose Ramon, Cahais Vincent, Rothwell Joseph, Herceg Zdenko',
			'description' => '<p>Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global and site-specific methylation of the mitochondrial genome has been described. Investigation of any functional consequences however remains unclear and debated due to insufficient evidence of the quantitative degree and frequency of mitochondrial DNA (mtDNA) methylation. This study uses WGBS to provide the first quantitative report of mtDNA methylation at single base pair resolution. The data show that mitochondrial genomes are extensively methylated predominantly at non-CpG sites. Importantly, these methylation patterns display notable differences between normal and cancer cells. Furthermore, knockdown of DNA methyltransferase enzymes resulted in a marked global reduction of mtDNA methylation levels, indicating these enzymes may be associated with the establishment and/or maintenance of mtDNA methylation. DNMT3B knockdown cells displayed a comparatively pronounced global reduction in mtDNA methylation with concomitant increases in gene expression, suggesting a potential functional link between methylation and gene expression. Together these results demonstrate reproducible, non-random methylation patterns of mtDNA and challenge the notion that mtDNA is lowlymethylated. This study discusses key differences in methodology that suggest future investigations must allow for techniques that assess both CpG and non-CpG methylation.</p>',
			'date' => '2019-08-23',
			'pmid' => 'https://academic.oup.com/nar/article/47/19/10072/5563943?login=false',
			'doi' => '10.1093/nar/gkz762',
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			'authors' => 'Amorim BR, Dos Santos PAC, de Lima CL, Andia DC, Mazzeu JF, Acevedo AC',
			'description' => '<p>This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification methods are detailed. In addition, protocols for cell culture establishment and characterization from patients with inherited dental anomalies are described.</p>',
			'date' => '2019-01-01',
			'pmid' => 'http://www.pubmed.gov/30838595',
			'doi' => '10.1007/978-1-4939-9012-2_37,',
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			'description' => '<p>The canine transmissible venereal tumor (CTVT) is a clonally transmissible cancer that regresses spontaneously or after treatment with vincristine, but we know little about the regression mechanisms. We performed global transcriptional, methylation, and functional pathway analyses on serial biopsies of vincristine-treated CTVTs and found that regression occurs in sequential steps; activation of the innate immune system and host epithelial tissue remodeling followed by immune infiltration of the tumor, arrest in the cell cycle, and repair of tissue damage. We identified CCL5 as a possible driver of CTVT regression. Changes in gene expression are associated with methylation changes at specific intragenic sites. Our results underscore the critical role of host innate immunity in triggering cancer regression.</p>',
			'date' => '2018-04-09',
			'pmid' => 'http://www.pubmed.gov/29634949',
			'doi' => '10.1016/j.ccell.2018.03.003',
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			'name' => 'Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing',
			'authors' => 'Staunstrup N.H. et al.',
			'description' => '<p><b></b>Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest in peripheral surrogate tissues. Whereas most work has been conducted on blood, saliva is now becoming recognized as an interesting alternative due to the simple and non-invasive manner of collection allowing for self-sampling. Results: In this study we have evaluated if saliva samples are suitable for DNA methylation studies using methylated DNA immunoprecipitation coupled to next-generation sequencing (MeDIP-seq). This was done by comparing the DNA methylation profile in saliva against the benchmark profile of peripheral blood from three individuals. We show that the output, quality, and depth of paired-end 50 bp sequencing reads are comparable between saliva and peripheral blood and, moreover, that the distribution of reads along genomic regions are similar and follow canonical methylation patterns. Conclusion: In summary, we show that high-quality MeDIP-seq data can be generated using saliva, thus supporting the future use of saliva in the generation of DNA methylation information at annotated genes, non-RefSeq genes, and repetitive elements relevant to human disease.</p>',
			'date' => '2017-10-19',
			'pmid' => 'http://www.mdpi.com/2075-4655/1/3/14',
			'doi' => '',
			'modified' => '2018-01-04 09:57:38',
			'created' => '2018-01-04 09:57:38',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '3108',
			'name' => 'Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples',
			'authors' => 'Bak S.T. et al.',
			'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>',
			'date' => '2016-12-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571',
			'doi' => '',
			'modified' => '2017-01-04 10:19:32',
			'created' => '2017-01-04 10:19:32',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '2991',
			'name' => 'Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots',
			'authors' => 'Nicklas H. Staunstrup et al.',
			'description' => '<p><strong>Background</strong> In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.</p>
<p><strong>Results</strong> Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.</p>
<p><strong>Conclusions</strong> In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.</p>',
			'date' => '2016-07-26',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27462375',
			'doi' => '10.1186/s13148-016-0242-1',
			'modified' => '2016-08-03 10:40:55',
			'created' => '2016-08-03 10:38:24',
			'ProductsPublication' => array(
				[maximum depth reached]
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		),
		(int) 6 => array(
			'id' => '2920',
			'name' => 'Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection',
			'authors' => 'Sharma G et al.',
			'description' => '<p>A mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative conditions and cardiovascular diseases have been documented. Here we show genome-wide DNA methylation changes in macrophages infected with the pathogen <i>M. tuberculosis</i>. Majority of the affected genomic loci were hypermethylated in <i>M. tuberculosis</i> infected THP1 macrophages. Hotspots of differential DNA methylation were enriched in genes involved in immune response and chromatin reorganization. Importantly, DNA methylation changes were observed predominantly for cytosines present in non-CpG dinucleotide context. This observation was consistent with our previous finding that the mycobacterial DNA methyltransferase, Rv2966c, targets non-CpG dinucleotides in the host DNA during <i>M. tuberculosis</i> infection and reiterates the hypothesis that pathogenic bacteria use non-canonical epigenetic strategies during infection.</p>',
			'date' => '2016-04-26',
			'pmid' => 'http://www.nature.com/articles/srep25006',
			'doi' => '10.1038/srep25006',
			'modified' => '2016-05-13 15:17:18',
			'created' => '2016-05-13 14:03:23',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		)
	),
	'Testimonial' => array(),
	'Area' => array(),
	'SafetySheet' => array()
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		'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010020 ',
		'description' => '<p><span>The reference&nbsp;C02010013 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns">C02010020</a>.</span></p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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	'antibody_id' => null,
	'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010020 ',
	'description' => '<p><span>The reference&nbsp;C02010013 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns">C02010020</a>.</span></p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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            </div>

        </div>
        <div class="small-12 columns" >
            <h6 style="height:60px">DNA Methylation control package</h6>
        </div>

    </div>
</li>
<li>
    <div class="row">
        <div class="small-12 columns">
                         <a href="/jp/p/auto-magmedip-kit-x48-48-rxns"><img src="/img/product/kits/methyl-kit-icon.png" alt="Methylation kit icon" class="th"/></a>        </div>



        <div class="small-12 columns">
            <div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px">
                <span class="success label" style="">C02010014</span>
            </div>
            <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px">
                <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a-->
                
            </div>

        </div>
        <div class="small-12 columns" >
            <h6 style="height:60px">Auto MagMeDIP kit</h6>
        </div>

    </div>
</li>
'
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	'description' => '<p><span></span>The reference&nbsp;C02010014 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">C02010021</a><span>.&nbsp;</span>&nbsp;</p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation) <span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> </span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
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	'description' => '<p><span>The reference&nbsp;C02010013 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns">C02010020</a>.</span></p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #16 and after;</strong></li>
<li><strong>MagMeDIP x10 batch #7A and after.</strong></li>
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<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP).</span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
<p><span><span>MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</span></span></p>
<p><span></span></p>
<p><span></span></p>
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			'description' => '<p><span></span>The reference&nbsp;C02010014 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">C02010021</a><span>.&nbsp;</span>&nbsp;</p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation) <span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> </span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
<p></p>',
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			'slug' => 'auto-magmedip-kit-x48-48-rxns',
			'meta_title' => 'Auto MagMeDIP qPCR Kit x48',
			'meta_keywords' => '',
			'meta_description' => 'Auto MagMeDIP qPCR Kit x48',
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			'id' => '1885',
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			'name' => 'Auto hMeDIP kit x16 (monoclonal mouse antibody)',
			'description' => '<p><span>The Auro hMeDIP kit is designed for enrichment of hydroxymethylated DNA from fragmented&nbsp;genomic DNA&nbsp;samples for use in genome-wide methylation analysis. It features</span><span>&nbsp;a highly specific monoclonal antibody against&nbsp;</span><span>5-hydroxymethylcytosine (5-hmC) for the immunoprecipitation of hydroxymethylated DNA</span><span>. It includes&nbsp;control DNA and primers to assess the effiency of the assay.&nbsp;</span><span>Performing hydroxymethylation profiling with the hMeDIP kit is fast,&nbsp;reliable and&nbsp;highly specific.</span></p>',
			'label1' => ' Characteristics',
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<li><span>Robust enrichment &amp; immunoprecipitation of hydroxymethylated DNA</span></li>
<li>Highly specific monoclonal antibody against 5-hmC<span>&nbsp;for reliable, reproducible results</span></li>
<li>Including&nbsp;control DNA and primers to&nbsp;<span>monitor the&nbsp;efficiency of the assay</span>
<ul style="list-style-type: circle;">
<li>5-hmC, 5-mC and unmethylated DNA sequences and primer pairs</li>
<li>Mouse primer pairs against Sfi1 targeting hydroxymethylated gene in mouse</li>
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<li>Improved single-tube, magnetic bead-based protocol</li>
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			'meta_description' => 'Auto hMeDIP kit x16 (monoclonal mouse antibody)',
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			'name' => 'Auto MethylCap kit',
			'description' => '<p>The Auto MethylCap kit allows to specifically capture DNA fragments containing methylated CpGs. The assay is based on the affinity purification of methylated DNA using methyl-CpG-binding domain (MBD) of human MeCP2 protein. This procedure has been optimized to perform automated immunoprecipitation of chromatin using the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star&reg; Compact Automated System</a> enabling highly reproducible results and allowing for high throughput.</p>',
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<li><strong>Fast &amp; sensitive capture</strong> of methylated DNA</li>
<li><strong>High capture efficiency</strong></li>
<li><strong>Differential fractionation</strong> of methylated DNA by CpG density (3 eluted fractions)</li>
<li><strong>Automation compatibility</strong><strong></strong>
<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>F</strong><strong>igure 1.</strong><span>&nbsp;</span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
</li>
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			'meta_title' => 'Auto MethylCap kit x48',
			'meta_keywords' => '',
			'meta_description' => 'Auto MethylCap kit x48',
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			'name' => 'Auto Premium Bisulfite kit',
			'description' => '<p>Diagenode's Premium Bisulfite Kit rapidly converts DNA through bisulfite treatment. Our conversion reagent is added directly to DNA, requires no intermediate steps, and results in high yields of DNA ready for downstream analysis methods including PCR and Next-Generation Sequencing.</p>',
			'label1' => 'Characteristics',
			'info1' => '<p><strong>Bisulfite Conversion efficiency in TERTBS1 and CTS56 genomic regions.</strong></p>
<p>The figure shows the conversion efficiency in TERTBS1 and CTS56 genomic regions when using 1 &mu;g, 500ng and 100 ng of genomic DNA. Between 1 and 5 clones were analyzed for the different amounts of genomic DNA</p>
<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
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			'price_EUR' => '255',
			'price_USD' => '240',
			'price_GBP' => '230',
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			'name' => 'DNA methylation control package',
			'description' => '<p><a href="https://www.diagenode.com/files/products/kits/Datasheet_DNA_methylation_control_package.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>The DNA methylation control package includes one methylated and&nbsp;one unmethylated&nbsp;spike-in controls together with their corresponding qPCR primer sets for assessing the efficiency of your non-plant MeDIP experiments (Methylated DNA Immunoprecipitation)&nbsp;carried out with Diagenode&rsquo;s <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">MagMeDIP qPCR&nbsp;Kit</a> and <a href="https://www.diagenode.com/en/p/auto-magmedip-kit-x48-48-rxns" target="_blank">Auto MagMeDIP qPCR Kit</a>.</p>
<p><span>Those spike-in controls are made from&nbsp;<em>A. thaliana</em><span>. Therefore, they can interfere with DNA samples derived from plant species.</span></span></p>
<p><em><strong>CAUTION</strong>: These spike-in controls are compatible with <span>Diagenode&rsquo;s&nbsp;</span><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">MagMeDIP qPCR&nbsp;Kit</a><span><span>&nbsp;</span>and<span>&nbsp;</span></span><a href="https://www.diagenode.com/en/p/auto-magmedip-kit-x48-48-rxns" target="_blank">Auto MagMeDIP qPCR Kit</a><span>. However</span>, those are not the ones directly provided&nbsp;in the kits.&nbsp;The spike-in controls provided in the kits are available separately with the <a href="https://www.diagenode.com/en/p/dna-methylation-control-package-V2-48-rxns">DNA methylation control package V2</a>.</em></p>',
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			'id' => '2945',
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			'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010021',
			'description' => '<p><span></span>The reference&nbsp;C02010014 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">C02010021</a><span>.&nbsp;</span>&nbsp;</p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation) <span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> </span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
<p></p>',
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		(int) 0 => array(
			'id' => '7',
			'position' => '10',
			'parent_id' => '1',
			'name' => 'Methylated DNA immunoprecipitation',
			'description' => '<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns"><center><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank"><img src="https://www.diagenode.com/img/banners/banner-nature-publication-580.png" /></a></center></div>
<div class="small-12 medium-9 large-9 columns">
<h3>Sensitive tumour detection and classification using plasma cell-free DNA methylomes<br /><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank">Read the publication</a></h3>
<h3 class="c-article-title u-h1" data-test="article-title" itemprop="name headline">Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA<br /><a href="https://www.nature.com/articles/s41596-019-0202-2" target="_blank" title="cfMeDIP-seq Nature Method">Read the method</a></h3>
</div>
</div>
<div class="row">
<div class="large-12 columns"><span>The Methylated DNA Immunoprecipitation is based on the affinity purification of methylated and hydroxymethylated DNA using, respectively, an antibody directed against 5-methylcytosine (5-mC) in the case of MeDIP or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP.</span><br />
<h2></h2>
<h2>How it works</h2>
<p>In brief, Methyl DNA IP is performed as follows: Genomic DNA from cultured cells or tissues is prepared, sheared, and then denatured. Then, immunoselection and immunoprecipitation can take place using the antibody directed against 5 methylcytosine and antibody binding beads. After isolation and purification is performed, the IP&rsquo;d methylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or next generation sequencing.</p>
<h2>Applications</h2>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> qPCR analysis</a></div>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-seq-package-V2-x10" class="center alert radius button"> NGS analysis </a></div>
<h2>Advantages</h2>
<ul style="font-size: 19px;" class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <strong>Unaffected</strong> DNA</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>High enrichment</strong> yield</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>Robust</strong> &amp; <strong>reproducible</strong> techniques</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li>
</ul>
<h2></h2>
</div>
</div>
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			'name' => 'Methylated DNA immunoprecipitation',
			'description' => '<p><a href="https://www.diagenode.com/en/p/magmedip-seq-package-V2-x10"><img src="https://www.diagenode.com/img/product/kits/b-email-magmedip.png" /></a></p>
<p>The Methylated DNA Immunoprecipitation is based on the affinity purification of methylated and hydroxymethylated DNA using, respectively, an antibody directed against 5-methylcytosine (5-mC) in the case of MeDIP or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP.</p>
<h2>How it works</h2>
<p>In brief, Methyl DNA IP is performed as follows: Genomic DNA from cultured cells or tissues is prepared, sheared, and then denatured. Then, immunoselection and immunoprecipitation can take place using the antibody directed against 5 methylcytosine and antibody binding beads. After isolation and purification is performed, the IP&rsquo;d methylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or next generation sequencing.</p>
<h2>Applications</h2>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> qPCR analysis</a></div>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> NGS analysis </a></div>
<h2>Advantages</h2>
<ul style="font-size: 19px;" class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <strong>Unaffected</strong> DNA</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>High enrichment</strong> yield</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>Robust</strong> &amp; <strong>reproducible</strong> techniques</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li>
</ul>
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<div class="section">
<div class="layoutArea">
<div class="column">
<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #15 and&nbsp;before;</strong></li>
<li><strong>MagMeDIP x10 batch #7 and&nbsp;before</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP). </span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</div>
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<div class="column">
<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #16 and after;</strong></li>
<li><strong>MagMeDIP x10 batch #7A and after.</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP).</span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
<p><span><span>MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</span></span></p>
<p><span></span></p>
<p><span></span></p>
</div>
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			'name' => 'Human mitochondrial DNA is extensively methylated in a non-CpG context',
			'authors' => 'Patil Vibha, Cuenin Cyrille, Chung Felicia, Aguilera Jesus R Rodriguez, Fernandez-Jimenez Nora, Romero-Garmendia Irati, Bilbao Jose Ramon, Cahais Vincent, Rothwell Joseph, Herceg Zdenko',
			'description' => '<p>Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global and site-specific methylation of the mitochondrial genome has been described. Investigation of any functional consequences however remains unclear and debated due to insufficient evidence of the quantitative degree and frequency of mitochondrial DNA (mtDNA) methylation. This study uses WGBS to provide the first quantitative report of mtDNA methylation at single base pair resolution. The data show that mitochondrial genomes are extensively methylated predominantly at non-CpG sites. Importantly, these methylation patterns display notable differences between normal and cancer cells. Furthermore, knockdown of DNA methyltransferase enzymes resulted in a marked global reduction of mtDNA methylation levels, indicating these enzymes may be associated with the establishment and/or maintenance of mtDNA methylation. DNMT3B knockdown cells displayed a comparatively pronounced global reduction in mtDNA methylation with concomitant increases in gene expression, suggesting a potential functional link between methylation and gene expression. Together these results demonstrate reproducible, non-random methylation patterns of mtDNA and challenge the notion that mtDNA is lowlymethylated. This study discusses key differences in methodology that suggest future investigations must allow for techniques that assess both CpG and non-CpG methylation.</p>',
			'date' => '2019-08-23',
			'pmid' => 'https://academic.oup.com/nar/article/47/19/10072/5563943?login=false',
			'doi' => '10.1093/nar/gkz762',
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			'name' => 'Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues.',
			'authors' => 'Amorim BR, Dos Santos PAC, de Lima CL, Andia DC, Mazzeu JF, Acevedo AC',
			'description' => '<p>This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification methods are detailed. In addition, protocols for cell culture establishment and characterization from patients with inherited dental anomalies are described.</p>',
			'date' => '2019-01-01',
			'pmid' => 'http://www.pubmed.gov/30838595',
			'doi' => '10.1007/978-1-4939-9012-2_37,',
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			'authors' => 'Frampton D, Schwenzer H, Marino G, Butcher LM, Pollara G, Kriston-Vizi J, Venturini C, Austin R, de Castro KF, Ketteler R, Chain B, Goldstein RA, Weiss RA, Beck S, Fassati A',
			'description' => '<p>The canine transmissible venereal tumor (CTVT) is a clonally transmissible cancer that regresses spontaneously or after treatment with vincristine, but we know little about the regression mechanisms. We performed global transcriptional, methylation, and functional pathway analyses on serial biopsies of vincristine-treated CTVTs and found that regression occurs in sequential steps; activation of the innate immune system and host epithelial tissue remodeling followed by immune infiltration of the tumor, arrest in the cell cycle, and repair of tissue damage. We identified CCL5 as a possible driver of CTVT regression. Changes in gene expression are associated with methylation changes at specific intragenic sites. Our results underscore the critical role of host innate immunity in triggering cancer regression.</p>',
			'date' => '2018-04-09',
			'pmid' => 'http://www.pubmed.gov/29634949',
			'doi' => '10.1016/j.ccell.2018.03.003',
			'modified' => '2018-12-31 11:57:33',
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			'name' => 'Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing',
			'authors' => 'Staunstrup N.H. et al.',
			'description' => '<p><b></b>Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest in peripheral surrogate tissues. Whereas most work has been conducted on blood, saliva is now becoming recognized as an interesting alternative due to the simple and non-invasive manner of collection allowing for self-sampling. Results: In this study we have evaluated if saliva samples are suitable for DNA methylation studies using methylated DNA immunoprecipitation coupled to next-generation sequencing (MeDIP-seq). This was done by comparing the DNA methylation profile in saliva against the benchmark profile of peripheral blood from three individuals. We show that the output, quality, and depth of paired-end 50 bp sequencing reads are comparable between saliva and peripheral blood and, moreover, that the distribution of reads along genomic regions are similar and follow canonical methylation patterns. Conclusion: In summary, we show that high-quality MeDIP-seq data can be generated using saliva, thus supporting the future use of saliva in the generation of DNA methylation information at annotated genes, non-RefSeq genes, and repetitive elements relevant to human disease.</p>',
			'date' => '2017-10-19',
			'pmid' => 'http://www.mdpi.com/2075-4655/1/3/14',
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			'authors' => 'Bak S.T. et al.',
			'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>',
			'date' => '2016-12-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571',
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			'authors' => 'Nicklas H. Staunstrup et al.',
			'description' => '<p><strong>Background</strong> In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.</p>
<p><strong>Results</strong> Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.</p>
<p><strong>Conclusions</strong> In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.</p>',
			'date' => '2016-07-26',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27462375',
			'doi' => '10.1186/s13148-016-0242-1',
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			'name' => 'Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection',
			'authors' => 'Sharma G et al.',
			'description' => '<p>A mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative conditions and cardiovascular diseases have been documented. Here we show genome-wide DNA methylation changes in macrophages infected with the pathogen <i>M. tuberculosis</i>. Majority of the affected genomic loci were hypermethylated in <i>M. tuberculosis</i> infected THP1 macrophages. Hotspots of differential DNA methylation were enriched in genes involved in immune response and chromatin reorganization. Importantly, DNA methylation changes were observed predominantly for cytosines present in non-CpG dinucleotide context. This observation was consistent with our previous finding that the mycobacterial DNA methyltransferase, Rv2966c, targets non-CpG dinucleotides in the host DNA during <i>M. tuberculosis</i> infection and reiterates the hypothesis that pathogenic bacteria use non-canonical epigenetic strategies during infection.</p>',
			'date' => '2016-04-26',
			'pmid' => 'http://www.nature.com/articles/srep25006',
			'doi' => '10.1038/srep25006',
			'modified' => '2016-05-13 15:17:18',
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		'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010020 ',
		'description' => '<p><span>The reference&nbsp;C02010013 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns">C02010020</a>.</span></p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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	'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010020 ',
	'description' => '<p><span>The reference&nbsp;C02010013 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns">C02010020</a>.</span></p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
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<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
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<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
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<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
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<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #16 and after;</strong></li>
<li><strong>MagMeDIP x10 batch #7A and after.</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP).</span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
<p><span><span>MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</span></span></p>
<p><span></span></p>
<p><span></span></p>
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	'name' => 'Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection',
	'authors' => 'Sharma G et al.',
	'description' => '<p>A mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative conditions and cardiovascular diseases have been documented. Here we show genome-wide DNA methylation changes in macrophages infected with the pathogen <i>M. tuberculosis</i>. Majority of the affected genomic loci were hypermethylated in <i>M. tuberculosis</i> infected THP1 macrophages. Hotspots of differential DNA methylation were enriched in genes involved in immune response and chromatin reorganization. Importantly, DNA methylation changes were observed predominantly for cytosines present in non-CpG dinucleotide context. This observation was consistent with our previous finding that the mycobacterial DNA methyltransferase, Rv2966c, targets non-CpG dinucleotides in the host DNA during <i>M. tuberculosis</i> infection and reiterates the hypothesis that pathogenic bacteria use non-canonical epigenetic strategies during infection.</p>',
	'date' => '2016-04-26',
	'pmid' => 'http://www.nature.com/articles/srep25006',
	'doi' => '10.1038/srep25006',
	'modified' => '2016-05-13 15:17:18',
	'created' => '2016-05-13 14:03:23',
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$externalLink = ' <a href="http://www.nature.com/articles/srep25006" target="_blank"><i class="fa fa-external-link"></i></a>'
include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118

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<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation) <span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> </span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
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<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
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<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
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<p><strong>F</strong><strong>igure 1.</strong><span>&nbsp;</span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
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<p>The DNA methylation control package includes one methylated and&nbsp;one unmethylated&nbsp;spike-in controls together with their corresponding qPCR primer sets for assessing the efficiency of your non-plant MeDIP experiments (Methylated DNA Immunoprecipitation)&nbsp;carried out with Diagenode&rsquo;s <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">MagMeDIP qPCR&nbsp;Kit</a> and <a href="https://www.diagenode.com/en/p/auto-magmedip-kit-x48-48-rxns" target="_blank">Auto MagMeDIP qPCR Kit</a>.</p>
<p><span>Those spike-in controls are made from&nbsp;<em>A. thaliana</em><span>. Therefore, they can interfere with DNA samples derived from plant species.</span></span></p>
<p><em><strong>CAUTION</strong>: These spike-in controls are compatible with <span>Diagenode&rsquo;s&nbsp;</span><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">MagMeDIP qPCR&nbsp;Kit</a><span><span>&nbsp;</span>and<span>&nbsp;</span></span><a href="https://www.diagenode.com/en/p/auto-magmedip-kit-x48-48-rxns" target="_blank">Auto MagMeDIP qPCR Kit</a><span>. However</span>, those are not the ones directly provided&nbsp;in the kits.&nbsp;The spike-in controls provided in the kits are available separately with the <a href="https://www.diagenode.com/en/p/dna-methylation-control-package-V2-48-rxns">DNA methylation control package V2</a>.</em></p>',
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			'description' => '<p><span></span>The reference&nbsp;C02010014 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">C02010021</a><span>.&nbsp;</span>&nbsp;</p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation) <span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> </span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
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<div class="small-12 medium-3 large-3 columns"><center><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank"><img src="https://www.diagenode.com/img/banners/banner-nature-publication-580.png" /></a></center></div>
<div class="small-12 medium-9 large-9 columns">
<h3>Sensitive tumour detection and classification using plasma cell-free DNA methylomes<br /><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank">Read the publication</a></h3>
<h3 class="c-article-title u-h1" data-test="article-title" itemprop="name headline">Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA<br /><a href="https://www.nature.com/articles/s41596-019-0202-2" target="_blank" title="cfMeDIP-seq Nature Method">Read the method</a></h3>
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<div class="large-12 columns"><span>The Methylated DNA Immunoprecipitation is based on the affinity purification of methylated and hydroxymethylated DNA using, respectively, an antibody directed against 5-methylcytosine (5-mC) in the case of MeDIP or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP.</span><br />
<h2></h2>
<h2>How it works</h2>
<p>In brief, Methyl DNA IP is performed as follows: Genomic DNA from cultured cells or tissues is prepared, sheared, and then denatured. Then, immunoselection and immunoprecipitation can take place using the antibody directed against 5 methylcytosine and antibody binding beads. After isolation and purification is performed, the IP&rsquo;d methylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or next generation sequencing.</p>
<h2>Applications</h2>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> qPCR analysis</a></div>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-seq-package-V2-x10" class="center alert radius button"> NGS analysis </a></div>
<h2>Advantages</h2>
<ul style="font-size: 19px;" class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <strong>Unaffected</strong> DNA</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>High enrichment</strong> yield</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>Robust</strong> &amp; <strong>reproducible</strong> techniques</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li>
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<p>The Methylated DNA Immunoprecipitation is based on the affinity purification of methylated and hydroxymethylated DNA using, respectively, an antibody directed against 5-methylcytosine (5-mC) in the case of MeDIP or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP.</p>
<h2>How it works</h2>
<p>In brief, Methyl DNA IP is performed as follows: Genomic DNA from cultured cells or tissues is prepared, sheared, and then denatured. Then, immunoselection and immunoprecipitation can take place using the antibody directed against 5 methylcytosine and antibody binding beads. After isolation and purification is performed, the IP&rsquo;d methylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or next generation sequencing.</p>
<h2>Applications</h2>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> qPCR analysis</a></div>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> NGS analysis </a></div>
<h2>Advantages</h2>
<ul style="font-size: 19px;" class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <strong>Unaffected</strong> DNA</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>High enrichment</strong> yield</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>Robust</strong> &amp; <strong>reproducible</strong> techniques</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li>
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<div class="layoutArea">
<div class="column">
<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #15 and&nbsp;before;</strong></li>
<li><strong>MagMeDIP x10 batch #7 and&nbsp;before</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP). </span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</div>
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<div class="section">
<div class="layoutArea">
<div class="column">
<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #16 and after;</strong></li>
<li><strong>MagMeDIP x10 batch #7A and after.</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP).</span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
<p><span><span>MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</span></span></p>
<p><span></span></p>
<p><span></span></p>
</div>
</div>
</div>
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			'name' => 'Human mitochondrial DNA is extensively methylated in a non-CpG context',
			'authors' => 'Patil Vibha, Cuenin Cyrille, Chung Felicia, Aguilera Jesus R Rodriguez, Fernandez-Jimenez Nora, Romero-Garmendia Irati, Bilbao Jose Ramon, Cahais Vincent, Rothwell Joseph, Herceg Zdenko',
			'description' => '<p>Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global and site-specific methylation of the mitochondrial genome has been described. Investigation of any functional consequences however remains unclear and debated due to insufficient evidence of the quantitative degree and frequency of mitochondrial DNA (mtDNA) methylation. This study uses WGBS to provide the first quantitative report of mtDNA methylation at single base pair resolution. The data show that mitochondrial genomes are extensively methylated predominantly at non-CpG sites. Importantly, these methylation patterns display notable differences between normal and cancer cells. Furthermore, knockdown of DNA methyltransferase enzymes resulted in a marked global reduction of mtDNA methylation levels, indicating these enzymes may be associated with the establishment and/or maintenance of mtDNA methylation. DNMT3B knockdown cells displayed a comparatively pronounced global reduction in mtDNA methylation with concomitant increases in gene expression, suggesting a potential functional link between methylation and gene expression. Together these results demonstrate reproducible, non-random methylation patterns of mtDNA and challenge the notion that mtDNA is lowlymethylated. This study discusses key differences in methodology that suggest future investigations must allow for techniques that assess both CpG and non-CpG methylation.</p>',
			'date' => '2019-08-23',
			'pmid' => 'https://academic.oup.com/nar/article/47/19/10072/5563943?login=false',
			'doi' => '10.1093/nar/gkz762',
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			'name' => 'Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues.',
			'authors' => 'Amorim BR, Dos Santos PAC, de Lima CL, Andia DC, Mazzeu JF, Acevedo AC',
			'description' => '<p>This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification methods are detailed. In addition, protocols for cell culture establishment and characterization from patients with inherited dental anomalies are described.</p>',
			'date' => '2019-01-01',
			'pmid' => 'http://www.pubmed.gov/30838595',
			'doi' => '10.1007/978-1-4939-9012-2_37,',
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			'description' => '<p>The canine transmissible venereal tumor (CTVT) is a clonally transmissible cancer that regresses spontaneously or after treatment with vincristine, but we know little about the regression mechanisms. We performed global transcriptional, methylation, and functional pathway analyses on serial biopsies of vincristine-treated CTVTs and found that regression occurs in sequential steps; activation of the innate immune system and host epithelial tissue remodeling followed by immune infiltration of the tumor, arrest in the cell cycle, and repair of tissue damage. We identified CCL5 as a possible driver of CTVT regression. Changes in gene expression are associated with methylation changes at specific intragenic sites. Our results underscore the critical role of host innate immunity in triggering cancer regression.</p>',
			'date' => '2018-04-09',
			'pmid' => 'http://www.pubmed.gov/29634949',
			'doi' => '10.1016/j.ccell.2018.03.003',
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			'name' => 'Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing',
			'authors' => 'Staunstrup N.H. et al.',
			'description' => '<p><b></b>Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest in peripheral surrogate tissues. Whereas most work has been conducted on blood, saliva is now becoming recognized as an interesting alternative due to the simple and non-invasive manner of collection allowing for self-sampling. Results: In this study we have evaluated if saliva samples are suitable for DNA methylation studies using methylated DNA immunoprecipitation coupled to next-generation sequencing (MeDIP-seq). This was done by comparing the DNA methylation profile in saliva against the benchmark profile of peripheral blood from three individuals. We show that the output, quality, and depth of paired-end 50 bp sequencing reads are comparable between saliva and peripheral blood and, moreover, that the distribution of reads along genomic regions are similar and follow canonical methylation patterns. Conclusion: In summary, we show that high-quality MeDIP-seq data can be generated using saliva, thus supporting the future use of saliva in the generation of DNA methylation information at annotated genes, non-RefSeq genes, and repetitive elements relevant to human disease.</p>',
			'date' => '2017-10-19',
			'pmid' => 'http://www.mdpi.com/2075-4655/1/3/14',
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			'name' => 'Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples',
			'authors' => 'Bak S.T. et al.',
			'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>',
			'date' => '2016-12-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571',
			'doi' => '',
			'modified' => '2017-01-04 10:19:32',
			'created' => '2017-01-04 10:19:32',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '2991',
			'name' => 'Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots',
			'authors' => 'Nicklas H. Staunstrup et al.',
			'description' => '<p><strong>Background</strong> In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.</p>
<p><strong>Results</strong> Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.</p>
<p><strong>Conclusions</strong> In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.</p>',
			'date' => '2016-07-26',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27462375',
			'doi' => '10.1186/s13148-016-0242-1',
			'modified' => '2016-08-03 10:40:55',
			'created' => '2016-08-03 10:38:24',
			'ProductsPublication' => array(
				[maximum depth reached]
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		),
		(int) 6 => array(
			'id' => '2920',
			'name' => 'Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection',
			'authors' => 'Sharma G et al.',
			'description' => '<p>A mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative conditions and cardiovascular diseases have been documented. Here we show genome-wide DNA methylation changes in macrophages infected with the pathogen <i>M. tuberculosis</i>. Majority of the affected genomic loci were hypermethylated in <i>M. tuberculosis</i> infected THP1 macrophages. Hotspots of differential DNA methylation were enriched in genes involved in immune response and chromatin reorganization. Importantly, DNA methylation changes were observed predominantly for cytosines present in non-CpG dinucleotide context. This observation was consistent with our previous finding that the mycobacterial DNA methyltransferase, Rv2966c, targets non-CpG dinucleotides in the host DNA during <i>M. tuberculosis</i> infection and reiterates the hypothesis that pathogenic bacteria use non-canonical epigenetic strategies during infection.</p>',
			'date' => '2016-04-26',
			'pmid' => 'http://www.nature.com/articles/srep25006',
			'doi' => '10.1038/srep25006',
			'modified' => '2016-05-13 15:17:18',
			'created' => '2016-05-13 14:03:23',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		)
	),
	'Testimonial' => array(),
	'Area' => array(),
	'SafetySheet' => array()
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	(int) 12 => 'DE',
	(int) 13 => 'CH',
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		'id' => '2944',
		'antibody_id' => null,
		'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010020 ',
		'description' => '<p><span>The reference&nbsp;C02010013 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns">C02010020</a>.</span></p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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		'slug' => 'auto-magmedip-kit-x10-10-rxns',
		'meta_title' => 'Auto MagMeDIP qPCR Kit x10',
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	'antibody_id' => null,
	'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010020 ',
	'description' => '<p><span>The reference&nbsp;C02010013 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns">C02010020</a>.</span></p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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	'price_CNY' => '/',
	'price_AUD' => '900',
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'
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<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation) <span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> </span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
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<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #16 and after;</strong></li>
<li><strong>MagMeDIP x10 batch #7A and after.</strong></li>
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<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP).</span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
<p><span><span>MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</span></span></p>
<p><span></span></p>
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<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
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			'name' => 'Auto hMeDIP kit x16 (monoclonal mouse antibody)',
			'description' => '<p><span>The Auro hMeDIP kit is designed for enrichment of hydroxymethylated DNA from fragmented&nbsp;genomic DNA&nbsp;samples for use in genome-wide methylation analysis. It features</span><span>&nbsp;a highly specific monoclonal antibody against&nbsp;</span><span>5-hydroxymethylcytosine (5-hmC) for the immunoprecipitation of hydroxymethylated DNA</span><span>. It includes&nbsp;control DNA and primers to assess the effiency of the assay.&nbsp;</span><span>Performing hydroxymethylation profiling with the hMeDIP kit is fast,&nbsp;reliable and&nbsp;highly specific.</span></p>',
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<li>Including&nbsp;control DNA and primers to&nbsp;<span>monitor the&nbsp;efficiency of the assay</span>
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<li>5-hmC, 5-mC and unmethylated DNA sequences and primer pairs</li>
<li>Mouse primer pairs against Sfi1 targeting hydroxymethylated gene in mouse</li>
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			'description' => '<p>The Auto MethylCap kit allows to specifically capture DNA fragments containing methylated CpGs. The assay is based on the affinity purification of methylated DNA using methyl-CpG-binding domain (MBD) of human MeCP2 protein. This procedure has been optimized to perform automated immunoprecipitation of chromatin using the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star&reg; Compact Automated System</a> enabling highly reproducible results and allowing for high throughput.</p>',
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<li><strong>High capture efficiency</strong></li>
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<li><strong>Automation compatibility</strong><strong></strong>
<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>F</strong><strong>igure 1.</strong><span>&nbsp;</span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
</li>
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			'meta_title' => 'Auto MethylCap kit x48',
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			'meta_description' => 'Auto MethylCap kit x48',
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			'description' => '<p>Diagenode's Premium Bisulfite Kit rapidly converts DNA through bisulfite treatment. Our conversion reagent is added directly to DNA, requires no intermediate steps, and results in high yields of DNA ready for downstream analysis methods including PCR and Next-Generation Sequencing.</p>',
			'label1' => 'Characteristics',
			'info1' => '<p><strong>Bisulfite Conversion efficiency in TERTBS1 and CTS56 genomic regions.</strong></p>
<p>The figure shows the conversion efficiency in TERTBS1 and CTS56 genomic regions when using 1 &mu;g, 500ng and 100 ng of genomic DNA. Between 1 and 5 clones were analyzed for the different amounts of genomic DNA</p>
<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
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<p>The DNA methylation control package includes one methylated and&nbsp;one unmethylated&nbsp;spike-in controls together with their corresponding qPCR primer sets for assessing the efficiency of your non-plant MeDIP experiments (Methylated DNA Immunoprecipitation)&nbsp;carried out with Diagenode&rsquo;s <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">MagMeDIP qPCR&nbsp;Kit</a> and <a href="https://www.diagenode.com/en/p/auto-magmedip-kit-x48-48-rxns" target="_blank">Auto MagMeDIP qPCR Kit</a>.</p>
<p><span>Those spike-in controls are made from&nbsp;<em>A. thaliana</em><span>. Therefore, they can interfere with DNA samples derived from plant species.</span></span></p>
<p><em><strong>CAUTION</strong>: These spike-in controls are compatible with <span>Diagenode&rsquo;s&nbsp;</span><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">MagMeDIP qPCR&nbsp;Kit</a><span><span>&nbsp;</span>and<span>&nbsp;</span></span><a href="https://www.diagenode.com/en/p/auto-magmedip-kit-x48-48-rxns" target="_blank">Auto MagMeDIP qPCR Kit</a><span>. However</span>, those are not the ones directly provided&nbsp;in the kits.&nbsp;The spike-in controls provided in the kits are available separately with the <a href="https://www.diagenode.com/en/p/dna-methylation-control-package-V2-48-rxns">DNA methylation control package V2</a>.</em></p>',
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			'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010021',
			'description' => '<p><span></span>The reference&nbsp;C02010014 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns">C02010021</a><span>.&nbsp;</span>&nbsp;</p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation) <span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> </span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p style="text-align: justify;"><em><strong>Figure<span>&nbsp;</span>2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>
<p></p>',
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			'name' => 'Methylated DNA immunoprecipitation',
			'description' => '<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns"><center><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank"><img src="https://www.diagenode.com/img/banners/banner-nature-publication-580.png" /></a></center></div>
<div class="small-12 medium-9 large-9 columns">
<h3>Sensitive tumour detection and classification using plasma cell-free DNA methylomes<br /><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank">Read the publication</a></h3>
<h3 class="c-article-title u-h1" data-test="article-title" itemprop="name headline">Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA<br /><a href="https://www.nature.com/articles/s41596-019-0202-2" target="_blank" title="cfMeDIP-seq Nature Method">Read the method</a></h3>
</div>
</div>
<div class="row">
<div class="large-12 columns"><span>The Methylated DNA Immunoprecipitation is based on the affinity purification of methylated and hydroxymethylated DNA using, respectively, an antibody directed against 5-methylcytosine (5-mC) in the case of MeDIP or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP.</span><br />
<h2></h2>
<h2>How it works</h2>
<p>In brief, Methyl DNA IP is performed as follows: Genomic DNA from cultured cells or tissues is prepared, sheared, and then denatured. Then, immunoselection and immunoprecipitation can take place using the antibody directed against 5 methylcytosine and antibody binding beads. After isolation and purification is performed, the IP&rsquo;d methylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or next generation sequencing.</p>
<h2>Applications</h2>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> qPCR analysis</a></div>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-seq-package-V2-x10" class="center alert radius button"> NGS analysis </a></div>
<h2>Advantages</h2>
<ul style="font-size: 19px;" class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <strong>Unaffected</strong> DNA</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>High enrichment</strong> yield</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>Robust</strong> &amp; <strong>reproducible</strong> techniques</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li>
</ul>
<h2></h2>
</div>
</div>
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			'meta_title' => 'Methylated DNA immunoprecipitation(MeDIP) - Dna methylation | Diagenode',
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<p>The Methylated DNA Immunoprecipitation is based on the affinity purification of methylated and hydroxymethylated DNA using, respectively, an antibody directed against 5-methylcytosine (5-mC) in the case of MeDIP or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP.</p>
<h2>How it works</h2>
<p>In brief, Methyl DNA IP is performed as follows: Genomic DNA from cultured cells or tissues is prepared, sheared, and then denatured. Then, immunoselection and immunoprecipitation can take place using the antibody directed against 5 methylcytosine and antibody binding beads. After isolation and purification is performed, the IP&rsquo;d methylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or next generation sequencing.</p>
<h2>Applications</h2>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> qPCR analysis</a></div>
<div align="center"><a href="https://www.diagenode.com/en/p/magmedip-kit-x48-48-rxns" class="center alert radius button"> NGS analysis </a></div>
<h2>Advantages</h2>
<ul style="font-size: 19px;" class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <strong>Unaffected</strong> DNA</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>High enrichment</strong> yield</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>Robust</strong> &amp; <strong>reproducible</strong> techniques</li>
<li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li>
</ul>
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			'description' => '<p><span>A step toward identifying subtle epigenetic variation in cancer and other complex disease </span></p>',
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			'name' => 'MagMeDIP qPCR Kit - User Manual v2',
			'description' => '<div class="page" title="Page 4">
<div class="section">
<div class="layoutArea">
<div class="column">
<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #15 and&nbsp;before;</strong></li>
<li><strong>MagMeDIP x10 batch #7 and&nbsp;before</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP). </span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</div>
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<div class="section">
<div class="layoutArea">
<div class="column">
<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #16 and after;</strong></li>
<li><strong>MagMeDIP x10 batch #7A and after.</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP).</span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
<p><span><span>MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</span></span></p>
<p><span></span></p>
<p><span></span></p>
</div>
</div>
</div>
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			'id' => '3783',
			'name' => 'Human mitochondrial DNA is extensively methylated in a non-CpG context',
			'authors' => 'Patil Vibha, Cuenin Cyrille, Chung Felicia, Aguilera Jesus R Rodriguez, Fernandez-Jimenez Nora, Romero-Garmendia Irati, Bilbao Jose Ramon, Cahais Vincent, Rothwell Joseph, Herceg Zdenko',
			'description' => '<p>Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global and site-specific methylation of the mitochondrial genome has been described. Investigation of any functional consequences however remains unclear and debated due to insufficient evidence of the quantitative degree and frequency of mitochondrial DNA (mtDNA) methylation. This study uses WGBS to provide the first quantitative report of mtDNA methylation at single base pair resolution. The data show that mitochondrial genomes are extensively methylated predominantly at non-CpG sites. Importantly, these methylation patterns display notable differences between normal and cancer cells. Furthermore, knockdown of DNA methyltransferase enzymes resulted in a marked global reduction of mtDNA methylation levels, indicating these enzymes may be associated with the establishment and/or maintenance of mtDNA methylation. DNMT3B knockdown cells displayed a comparatively pronounced global reduction in mtDNA methylation with concomitant increases in gene expression, suggesting a potential functional link between methylation and gene expression. Together these results demonstrate reproducible, non-random methylation patterns of mtDNA and challenge the notion that mtDNA is lowlymethylated. This study discusses key differences in methodology that suggest future investigations must allow for techniques that assess both CpG and non-CpG methylation.</p>',
			'date' => '2019-08-23',
			'pmid' => 'https://academic.oup.com/nar/article/47/19/10072/5563943?login=false',
			'doi' => '10.1093/nar/gkz762',
			'modified' => '2022-05-18 19:29:08',
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			'id' => '3661',
			'name' => 'Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues.',
			'authors' => 'Amorim BR, Dos Santos PAC, de Lima CL, Andia DC, Mazzeu JF, Acevedo AC',
			'description' => '<p>This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification methods are detailed. In addition, protocols for cell culture establishment and characterization from patients with inherited dental anomalies are described.</p>',
			'date' => '2019-01-01',
			'pmid' => 'http://www.pubmed.gov/30838595',
			'doi' => '10.1007/978-1-4939-9012-2_37,',
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			'name' => 'Molecular Signatures of Regression of the Canine Transmissible Venereal Tumor.',
			'authors' => 'Frampton D, Schwenzer H, Marino G, Butcher LM, Pollara G, Kriston-Vizi J, Venturini C, Austin R, de Castro KF, Ketteler R, Chain B, Goldstein RA, Weiss RA, Beck S, Fassati A',
			'description' => '<p>The canine transmissible venereal tumor (CTVT) is a clonally transmissible cancer that regresses spontaneously or after treatment with vincristine, but we know little about the regression mechanisms. We performed global transcriptional, methylation, and functional pathway analyses on serial biopsies of vincristine-treated CTVTs and found that regression occurs in sequential steps; activation of the innate immune system and host epithelial tissue remodeling followed by immune infiltration of the tumor, arrest in the cell cycle, and repair of tissue damage. We identified CCL5 as a possible driver of CTVT regression. Changes in gene expression are associated with methylation changes at specific intragenic sites. Our results underscore the critical role of host innate immunity in triggering cancer regression.</p>',
			'date' => '2018-04-09',
			'pmid' => 'http://www.pubmed.gov/29634949',
			'doi' => '10.1016/j.ccell.2018.03.003',
			'modified' => '2018-12-31 11:57:33',
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			'name' => 'Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing',
			'authors' => 'Staunstrup N.H. et al.',
			'description' => '<p><b></b>Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest in peripheral surrogate tissues. Whereas most work has been conducted on blood, saliva is now becoming recognized as an interesting alternative due to the simple and non-invasive manner of collection allowing for self-sampling. Results: In this study we have evaluated if saliva samples are suitable for DNA methylation studies using methylated DNA immunoprecipitation coupled to next-generation sequencing (MeDIP-seq). This was done by comparing the DNA methylation profile in saliva against the benchmark profile of peripheral blood from three individuals. We show that the output, quality, and depth of paired-end 50 bp sequencing reads are comparable between saliva and peripheral blood and, moreover, that the distribution of reads along genomic regions are similar and follow canonical methylation patterns. Conclusion: In summary, we show that high-quality MeDIP-seq data can be generated using saliva, thus supporting the future use of saliva in the generation of DNA methylation information at annotated genes, non-RefSeq genes, and repetitive elements relevant to human disease.</p>',
			'date' => '2017-10-19',
			'pmid' => 'http://www.mdpi.com/2075-4655/1/3/14',
			'doi' => '',
			'modified' => '2018-01-04 09:57:38',
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			'name' => 'Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples',
			'authors' => 'Bak S.T. et al.',
			'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>',
			'date' => '2016-12-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571',
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			'name' => 'Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots',
			'authors' => 'Nicklas H. Staunstrup et al.',
			'description' => '<p><strong>Background</strong> In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.</p>
<p><strong>Results</strong> Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.</p>
<p><strong>Conclusions</strong> In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.</p>',
			'date' => '2016-07-26',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27462375',
			'doi' => '10.1186/s13148-016-0242-1',
			'modified' => '2016-08-03 10:40:55',
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		(int) 6 => array(
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			'name' => 'Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection',
			'authors' => 'Sharma G et al.',
			'description' => '<p>A mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative conditions and cardiovascular diseases have been documented. Here we show genome-wide DNA methylation changes in macrophages infected with the pathogen <i>M. tuberculosis</i>. Majority of the affected genomic loci were hypermethylated in <i>M. tuberculosis</i> infected THP1 macrophages. Hotspots of differential DNA methylation were enriched in genes involved in immune response and chromatin reorganization. Importantly, DNA methylation changes were observed predominantly for cytosines present in non-CpG dinucleotide context. This observation was consistent with our previous finding that the mycobacterial DNA methyltransferase, Rv2966c, targets non-CpG dinucleotides in the host DNA during <i>M. tuberculosis</i> infection and reiterates the hypothesis that pathogenic bacteria use non-canonical epigenetic strategies during infection.</p>',
			'date' => '2016-04-26',
			'pmid' => 'http://www.nature.com/articles/srep25006',
			'doi' => '10.1038/srep25006',
			'modified' => '2016-05-13 15:17:18',
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		'name' => 'Auto MagMeDIP qPCR Kit - ordering reference: C02010020 ',
		'description' => '<p><span>The reference&nbsp;C02010013 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns">C02010020</a>.</span></p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
<p><em><strong>Figure 2. Automated MeDIP (9h).&nbsp;</strong>IP reaction was performed on the SX-8G IP-Star&reg; Automated System&nbsp;with the anti-5-mC antibody. Methylated and unmethylated DNA were used as internal controls. Unmethylated DNA region of GADPH and a methylated DNA region of AlphaX1 were used to test DNA sample-IP efficiency. DNA has been isolated by using DNA Isolation Buffer (DIB).</em></p>',
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<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a> enabling highly reproducible results and allowing for high throughput assays.</p>
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<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
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	'description' => '<p><span>The reference&nbsp;C02010013 has been replaced by <a href="https://www.diagenode.com/en/p/magmedip-kit-x10-10-rxns">C02010020</a>.</span></p>
<p><span>Perform&nbsp;</span><strong>MeDIP</strong><span><span>&nbsp;</span>(Methylated DNA Immunoprecipitation)<span>&nbsp;</span><span>on the&nbsp;<a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span></span>followed by<span>&nbsp;</span></span><strong>qPCR</strong><span><span>&nbsp;</span>to estimate DNA methylation status of your sample using&nbsp;</span><span>5-methylcytosine</span><span><span>&nbsp;</span>antibody. Our kit contains high quality reagents to get the h</span><span>ighest enrichment of methylated DNA with an optimized user-friendly protocol.</span></p>
<p>Diagenode&rsquo;s Auto MagMeDIP qPCR is available in two formats (10 and 48 IPs) and has been optimized on the<span>&nbsp;</span><a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit" target="_blank">SX-8G IP-Star&reg; Automated System</a><span>&nbsp;</span>enabling highly reproducible results and allowing for high throughput assays.</p>
<h3><span>Characteristics</span></h3>
<ul>
<li>Generate highly consistent results with internal controls in 24h</li>
<li>Minimize error with many reagents in 1 tube</li>
<li>Optimized purification (DIB - DNA isolation buffer)</li>
<li>Allows direct correlation between IP&rsquo;d material &amp; methylation status</li>
</ul>
<p style="text-align: center;"><img src="https://www.diagenode.com/img/product/kits/magmedip-kit-validated-using-bioruptor.jpg" alt="MagMeDIP kit validated using Bioruptor" /></p>
<p><strong><em>Figure 1.</em></strong><em><span>&nbsp;</span><strong>IP results obtained with Diagenode Auto MagMeDIP qPCR Kit.</strong><span>&nbsp;</span>MeDIP assays were performed manually using DNA from blood, Gm12878, Hela and U20S cells and the Auto MagMeDIP qPCR kit (Diagenode). The DNA was prepared with the XL GenDNA Extraction Module included. The IP was performed including the kit meDNA and unDNA spike-in controls, together with the human DNA sample controls. The DNA was isolated/purified using DIB. Afterwards, qPCR was performed using the primer pairs also included in this kit.</em></p>
<p style="text-align: center;"><em><img src="https://www.diagenode.com/img/product/kits/AutomatedMeDIP_9h.png" alt="" width="678" height="365" /></em></p>
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	'description' => '<div class="page" title="Page 4">
<div class="section">
<div class="layoutArea">
<div class="column">
<p><strong>This manual concerns:</strong></p>
<ul>
<li><strong>MagMeDIP x48 batch #16 and after;</strong></li>
<li><strong>MagMeDIP x10 batch #7A and after.</strong></li>
</ul>
<p><span>The Diagenode MagMeDIP kit is designed to immunoprecipitate methylated DNA (Methyl DNA IP).</span></p>
<p><span>In our Methyl DNA IP kits either MeDIP or MagMeDIP</span><span>, our antibody directed against 5-methylcytosine is provided as well as meDNA and unDNA internal IP controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody, buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls.</span></p>
<p><span><span>MagMeDIP kit is suitable for several downstream applications: qPCR and NGS. Please see our MagMeDIP-seq protocol in this manual before starting the MeDIP-seq workflow.</span></span></p>
<p><span></span></p>
<p><span></span></p>
</div>
</div>
</div>
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	'name' => 'Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection',
	'authors' => 'Sharma G et al.',
	'description' => '<p>A mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative conditions and cardiovascular diseases have been documented. Here we show genome-wide DNA methylation changes in macrophages infected with the pathogen <i>M. tuberculosis</i>. Majority of the affected genomic loci were hypermethylated in <i>M. tuberculosis</i> infected THP1 macrophages. Hotspots of differential DNA methylation were enriched in genes involved in immune response and chromatin reorganization. Importantly, DNA methylation changes were observed predominantly for cytosines present in non-CpG dinucleotide context. This observation was consistent with our previous finding that the mycobacterial DNA methyltransferase, Rv2966c, targets non-CpG dinucleotides in the host DNA during <i>M. tuberculosis</i> infection and reiterates the hypothesis that pathogenic bacteria use non-canonical epigenetic strategies during infection.</p>',
	'date' => '2016-04-26',
	'pmid' => 'http://www.nature.com/articles/srep25006',
	'doi' => '10.1038/srep25006',
	'modified' => '2016-05-13 15:17:18',
	'created' => '2016-05-13 14:03:23',
	'ProductsPublication' => array(
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$externalLink = ' <a href="http://www.nature.com/articles/srep25006" target="_blank"><i class="fa fa-external-link"></i></a>'
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View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118

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Automating Whole-Genome DNA Methylation Analyses POSTER A step toward identifying subtle epigenetic variation in cancer and other complex disease	Download
MagMeDIP qPCR Kit - User Manual v2 MANUAL This manual concerns: MagMeDIP x48 batch #15 and before; MagMeDIP x10 batch #7 a...	Download
MagMeDIP qPCR Kit - User Manual v4 MANUAL This manual concerns: MagMeDIP x48 batch #16 and after; MagMeDIP x10 batch #7A and af...	Download