| Datasheet DNA hydroxymethylation control package DATASHEET | Download |
The DNA hydroxymethylation control package includes one hydroxymethylated spike-in control and its corresponding qPCR primer set that can be added to the DNA sample of interest for any hydroxymethylation profiling experiment (e.g. with Diagenode's hMeDIP Kit).
CAUTION: The hydroxymethylated spike-in control is produced from a genomic sequence from Arabidopsis thaliana and may therefore interfere with plant samples. However, it does not show significant homology with other samples species (e.g. human, mouse or rat).
 How to properly cite this product in your workDiagenode strongly recommends using this: DNA hydroxymethylation control package (Diagenode Cat# C02040018). Click here to copy to clipboard. Using our products in your publication? Let us know! |
5-Hydroxymethylation highlights the heterogeneity in keratinization andcell junctions in head and neck cancers. |
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However, it does not show significant homology with other samples species (e.g. human, mouse or rat).</em></p>', 'label1' => '', 'info1' => '', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '48 rxns', 'catalog_number' => 'C02040018', 'old_catalog_number' => '', 'sf_code' => 'C02040018-', 'type' => 'FRE', 'search_order' => '04-undefined', 'price_EUR' => '115', 'price_USD' => '150', 'price_GBP' => '105', 'price_JPY' => '18015', 'price_CNY' => '', 'price_AUD' => '375', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '', 'slug' => 'dna-hydroxymethylation-control-package-48-rxns', 'meta_title' => '', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-07-07 11:59:21', 'created' => '2020-12-03 12:35:34', 'locale' => 'eng' ), 'Antibody' => array( 'host' => '*****', 'id' => null, 'name' => null, 'description' => null, 'clonality' => null, 'isotype' => null, 'lot' => null, 'concentration' => null, 'reactivity' => null, 'type' => null, 'purity' => null, 'classification' => null, 'application_table' => null, 'storage_conditions' => null, 'storage_buffer' => null, 'precautions' => null, 'uniprot_acc' => null, 'slug' => null, 'meta_keywords' => null, 'meta_description' => null, 'modified' => null, 'created' => null, 'select_label' => null ), 'Slave' => array(), 'Group' => array(), 'Related' => array( (int) 0 => array( 'id' => '1882', 'antibody_id' => null, 'name' => 'hMeDIP kit x16 (monoclonal mouse antibody)', 'description' => '<p><a href="https://www.diagenode.com/files/products/kits/hMeDIP_kit_manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p> <p><span>The hMeDIP kit is designed for enrichment of hydroxymethylated DNA from fragmented genomic DNA<span><span> </span>samples for use in genome-wide methylation analysis. It features</span></span><span> a highly specific monoclonal antibody against </span>5-hydroxymethylcytosine (5-hmC) for the immunoprecipitation of hydroxymethylated DNA<span>. It includes control DNA and primers to assess the effiency of the assay. </span>Performing hydroxymethylation profiling with the hMeDIP kit is fast, reliable and highly specific.</p> <p><em>Looking for hMeDIP-seq protocol? <a href="https://go.diagenode.com/l/928883/2022-01-07/2m1ht" target="_blank" title="Contact us">Contact us</a></em></p> <p><span></span></p> <p><span></span></p>', 'label1' => 'Characteristics', 'info1' => '<ul style="list-style-type: disc;"> <li><span>Robust enrichment & immunoprecipitation of hydroxymethylated DNA</span></li> <li>Highly specific monoclonal antibody against 5-hmC<span> for reliable, reproducible results</span></li> <li>Including control DNA and primers to <span>monitor the efficiency of the assay</span> <ul style="list-style-type: circle;"> <li>hmeDNA and unmethylated DNA sequences and primer pairs</li> <li>Mouse primer pairs against Sfi1 targeting hydroxymethylated gene in mouse</li> </ul> </li> <li>Improved single-tube, magnetic bead-based protocol</li> </ul>', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '16 rxns', 'catalog_number' => 'C02010031', 'old_catalog_number' => 'AF-110-0016', 'sf_code' => 'C02010031-', 'type' => 'RFR', 'search_order' => '04-undefined', 'price_EUR' => '630', 'price_USD' => '690', 'price_GBP' => '580', 'price_JPY' => '98690', 'price_CNY' => '', 'price_AUD' => '1725', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => true, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '0000-00-00', 'slug' => 'hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns', 'meta_title' => 'hMeDIP kit x16 (monoclonal mouse antibody)', 'meta_keywords' => '', 'meta_description' => 'hMeDIP kit x16 (monoclonal mouse antibody)', 'modified' => '2023-04-20 16:12:48', 'created' => '2015-06-29 14:08:20', 'ProductsRelated' => array( [maximum depth reached] ), 'Image' => array( [maximum depth reached] ) ), (int) 1 => array( 'id' => '2595', 'antibody_id' => null, 'name' => 'Mouse GAPDH promoter primer pair', 'description' => '<p><span>The primer pair Cat. 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The primers are optimized to be used in quantitative polymerase chain reaction (qPCR).</p>', 'label1' => '', 'info1' => '', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '50 µl', 'catalog_number' => 'C17021046-50', 'old_catalog_number' => '', 'sf_code' => 'C17021046-D001-000014', 'type' => 'FRE', 'search_order' => '', 'price_EUR' => '60', 'price_USD' => '35', 'price_GBP' => '60', 'price_JPY' => '9400', 'price_CNY' => '', 'price_AUD' => '88', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '', 'slug' => 'mouse-sfi-promoter-primer-pair-50-ul', 'meta_title' => 'Mouse SFI1 promoter primer pair', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-01-25 09:15:42', 'created' => '2020-12-07 14:23:55', 'ProductsRelated' => array( [maximum depth reached] ), 'Image' => array([maximum depth reached]) ) ), 'Application' => array( (int) 0 => array( 'id' => '1', 'position' => '9', 'parent_id' => null, 'name' => 'DNA Methylation', 'description' => '<div class="row"> <div class="large-12 columns"> <div style="text-align: justify;" class="small-12 medium-8 large-8 columns"> <h2>Complete solutions for DNA methylation studies</h2> <p>Whether you are experienced or new to the field of DNA methylation, Diagenode has everything you need to make your assay as easy and convenient as possible while ensuring consistent data between samples and experiments. Diagenode offers sonication instruments, reagent kits, high quality antibodies, and high-throughput automation capability to address all of your specific DNA methylation analysis requirements.</p> </div> <div class="small-12 medium-4 large-4 columns text-center"><a href="../landing-pages/dna-methylation-grant-applications"><img src="https://www.diagenode.com/img/banners/banner-dna-grant.png" alt="" /></a></div> <div style="text-align: justify;" class="small-12 medium-12 large-12 columns"> <p>DNA methylation was the first discovered epigenetic mark and is the most widely studied topic in epigenetics. <em>In vivo</em>, DNA is methylated following DNA replication and is involved in a number of biological processes including the regulation of imprinted genes, X chromosome inactivation. and tumor suppressor gene silencing in cancer cells. Methylation often occurs in cytosine-guanine rich regions of DNA (CpG islands), which are commonly upstream of promoter regions.</p> </div> <div class="small-12 medium-12 large-12 columns"><br /><br /> <ul class="accordion" data-accordion=""> <li class="accordion-navigation"><a href="#dnamethyl"><i class="fa fa-caret-right"></i> Learn more</a> <div id="dnamethyl" class="content">5-methylcytosine (5-mC) has been known for a long time as the only modification of DNA for epigenetic regulation. In 2009, however, Kriaucionis discovered a second methylated cytosine, 5-hydroxymethylcytosine (5-hmC). The so-called 6th base, is generated by enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine by the TET family of oxygenases. Early reports suggested that 5-hmC may represent an intermediate of active demethylation in a new pathway which demethylates DNA, converting 5-mC to cytosine. Recent evidence fuel this hypothesis suggesting that further oxidation of the hydroxymethyl group leads to a formyl or carboxyl group followed by either deformylation or decarboxylation. The formyl and carboxyl groups of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) could be enzymatically removed without excision of the base. <p class="text-center"><img src="https://www.diagenode.com/img/categories/kits_dna/dna_methylation_variants.jpg" /></p> </div> </li> </ul> <br /> <h2>Main DNA methylation technologies</h2> <p style="text-align: justify;">Overview of the <span style="font-weight: 400;">three main approaches for studying DNA methylation.</span></p> <div class="row"> <ol> <li style="font-weight: 400;"><span style="font-weight: 400;">Chemical modification with bisulfite – Bisulfite conversion</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Enrichment of methylated DNA (including MeDIP and MBD)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Treatment with methylation-sensitive or dependent restriction enzymes</span></li> </ol> <p><span style="font-weight: 400;"> </span></p> <div class="row"> <table> <thead> <tr> <th></th> <th>Description</th> <th width="350">Features</th> </tr> </thead> <tbody> <tr> <td><strong>Bisulfite conversion</strong></td> <td><span style="font-weight: 400;">Chemical conversion of unmethylated cytosine to uracil. Methylated cytosines are protected from this conversion allowing to determine DNA methylation at single nucleotide resolution.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Single nucleotide resolution</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Quantitative analysis - methylation rate (%)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Gold standard and well studied</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li> </ul> </td> </tr> <tr> <td><b>Methylated DNA enrichment</b></td> <td><span style="font-weight: 400;">(Hydroxy-)Methylated DNA is enriched by using specific antibodies (hMeDIP or MeDIP) or proteins (MBD) that specifically bind methylated CpG sites in fragmented genomic DNA.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Resolution depends on the fragment size of the enriched methylated DNA (300 bp)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Qualitative analysis</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li> </ul> </td> </tr> <tr> <td><strong>Restriction enzyme-based digestion</strong></td> <td><span style="font-weight: 400;">Use of (hydroxy)methylation-sensitive or (hydroxy)methylation-dependent restriction enzymes for DNA methylation analysis at specific sites.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Determination of methylation status is limited by the enzyme recognition site</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Easy to use</span></li> </ul> </td> </tr> </tbody> </table> </div> </div> <div class="row"></div> </div> </div> <div class="large-12 columns"></div> </div>', 'in_footer' => true, 'in_menu' => true, 'online' => true, 'tabular' => true, 'slug' => 'epigenetics-dna-methylation', 'meta_keywords' => 'Epigenetics, DNA Methylation,5-hmC monoclonal antibody,hMeDIP,Bisulfite conversion,Methylated DNA immunoprecipitation', 'meta_description' => 'Complete, optimized solutions for analyzing DNA methylation manually or on our automated system.', 'meta_title' => 'DNA Methylation - Bisulfite sequencing - Epigenetics | Diagenode', 'modified' => '2019-03-25 10:07:27', 'created' => '2015-05-03 13:47:53', 'ProductsApplication' => array( [maximum depth reached] ) ), (int) 1 => 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’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> & <strong>reproducible</strong> techniques</li> <li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li> </ul> <h2></h2> </div> </div> <div id="gtx-trans" style="position: absolute; left: 17px; top: 652.938px;"> <div class="gtx-trans-icon"></div> </div>', 'in_footer' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'slug' => 'methylated-dna-immunoprecipitation', 'meta_keywords' => 'Methylated DNA immunoprecipitation,Epigenetic,DNA Methylation,qPCR,5 methylcytosine (5-mC)', 'meta_description' => 'Methylated DNA immunoprecipitation method is based on the affinity purification of methylated DNA using an antibody directed against 5 methylcytosine (5-mC). ', 'meta_title' => 'Methylated DNA immunoprecipitation(MeDIP) - Dna methylation | Diagenode', 'modified' => '2021-08-19 12:08:03', 'created' => '2014-09-14 05:33:34', 'ProductsApplication' => array( [maximum depth reached] ) ) ), 'Category' => array( (int) 0 => array( 'id' => '55', 'position' => '5', 'parent_id' => '12', 'name' => 'DNA methylation standard', 'description' => '', 'no_promo' => false, 'in_menu' => false, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'dna-methylation-standard', 'cookies_tag_id' => null, 'meta_keywords' => 'DNA methylation standard,hydroxymethylated ,5-hmC,5-mC.', 'meta_description' => 'Diagenode Offers Unmethylated, Methylated and Hydroxymethylated Standards for Monitoring of DNA Methylation Assays.', 'meta_title' => 'DNA Methylation Standard | Diagenode', 'modified' => '2019-07-03 10:43:22', 'created' => '2015-07-08 09:53:00', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ), (int) 1 => array( 'id' => '51', 'position' => '11', 'parent_id' => '12', 'name' => 'Hydroxymethylated DNA immunoprecipitation', 'description' => '<p></p> <div class="row"> <div class="large-12 columns">The hydroxymethylated DNA IP (hMeDIP) is based on the affinity purification of methylated DNA using an antibody directed against 5-hydroxymethylcytosine (5-hmC). <h3>How it works</h3> In brief, hydroxymethyl DNA IP is performed as follows: starting from sheared genomic DNA from cultured cells or tissues, the immunoselection and immunoprecipitation can take place using the antibody directed against 5-hydroxymethylcytosine and antibody binding beads. After isolation and purification is performed, the IP’d hydroxymethylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or Next Generation Sequencing. <h3>Overview</h3> <p class="text-center"><img src="https://www.diagenode.com/img/applications/magnetic_medip_overview.jpg" caption="false" width="726" height="916" /></p> </div> </div>', 'no_promo' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'hydroxymethylated-dna-immunoprecipitation', 'cookies_tag_id' => null, 'meta_keywords' => 'Hydroxymethylated DNA Immunoprecipitation,DNA methylation', 'meta_description' => 'Diagenode Offers Antibody-Based Isolation of Hydroxymethylated DNA for DNA Methylation Studies', 'meta_title' => 'Hydroxymethylated DNA Immunoprecipitation for DNA Methylation Studies | Diagenode', 'modified' => '2022-10-06 15:25:37', 'created' => '2015-07-08 09:24:17', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ) ), 'Document' => array( (int) 0 => array( 'id' => '1125', 'name' => 'Datasheet DNA hydroxymethylation control package', 'description' => '', 'image_id' => null, 'type' => 'Datasheet', 'url' => 'files/products/kits/Datasheet_DNA-hydroxymethylation-control-package.pdf', 'slug' => 'datasheet-dna-hydroxymethylation-control-package', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-01-18 16:08:24', 'created' => '2021-01-18 16:08:24', 'ProductsDocument' => array( [maximum depth reached] ) ) ), 'Feature' => array(), 'Image' => array( (int) 0 => array( 'id' => '1778', 'name' => 'product/kits/methyl-kit-icon.png', 'alt' => 'Methylation kit icon', 'modified' => '2019-04-23 15:17:01', 'created' => '2018-03-15 15:52:12', 'ProductsImage' => array( [maximum depth reached] ) ) ), 'Promotion' => array(), 'Protocol' => array(), 'Publication' => array( (int) 0 => array( 'id' => '4055', 'name' => '5-Hydroxymethylation highlights the heterogeneity in keratinization andcell junctions in head and neck cancers.', 'authors' => 'Liu, Siyu and de Medeiros, Marcell Costa and Fernandez, Evan M and Zarins,Katie R and Cavalcante, Raymond G and Qin, Tingting and Wolf, Gregory T andFigueroa, Maria E and D'Silva, Nisha J and Rozek, Laura S and Sartor,Maureen A', 'description' => '<p>BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, with human papillomavirus (HPV)-related HNSCC rising to concerning levels. Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS: We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION: Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.</p>', 'date' => '2020-11-01', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33203436', 'doi' => '10.1186/s13148-020-00965-8', 'modified' => '2021-02-19 17:15:37', 'created' => '2021-02-18 10:21:53', 'ProductsPublication' => array( [maximum depth reached] ) ) ), 'Testimonial' => array(), 'Area' => array(), 'SafetySheet' => array() ) $country = 'US' $countries_allowed = array( (int) 0 => 'CA', (int) 1 => 'US', (int) 2 => 'IE', (int) 3 => 'GB', (int) 4 => 'DK', (int) 5 => 'NO', (int) 6 => 'SE', (int) 7 => 'FI', (int) 8 => 'NL', (int) 9 => 'BE', (int) 10 => 'LU', (int) 11 => 'FR', (int) 12 => 'DE', (int) 13 => 'CH', (int) 14 => 'AT', (int) 15 => 'ES', (int) 16 => 'IT', (int) 17 => 'PT' ) $outsource = false $other_formats = array() $edit = '' $testimonials = '' $featured_testimonials = '' $related_products = '<li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns"><img src="/img/product/kits/methyl-kit-icon.png" alt="Methylation kit icon" class="th"/></a> </div> <div class="small-12 columns"> <div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px"> <span class="success label" style="">C02010031</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> <!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-1882" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog"> <form action="/en/carts/add/1882" id="CartAdd/1882Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="1882" id="CartProductId"/> <div class="row"> <div class="small-12 medium-12 large-12 columns"> <p>Add <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> hMeDIP kit x16 (monoclonal mouse antibody)</strong> to my shopping cart.</p> <div class="row"> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('hMeDIP kit x16 (monoclonal mouse antibody)', 'C02010031', '690', $('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">Checkout</button> </div> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('hMeDIP kit x16 (monoclonal mouse antibody)', 'C02010031', '690', $('#CartQuantity').val());" name="keepshop" id="keepshop" type="submit">Keep shopping</button> </div> </div> </div> </div> </form><a class="close-reveal-modal" aria-label="Close">×</a></div><!-- END: ADD TO CART MODAL --><a href="#" id="hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns" data-reveal-id="cartModal-1882" class="" style="color:#B21329"><i class="fa fa-cart-plus"></i></a> </div> </div> <div class="small-12 columns" > <h6 style="height:60px">hMeDIP kit x16 (monoclonal mouse antibody)</h6> </div> </div> </li> <li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/mouse-gapdh-promoter-primer-pair-50-ul"><img src="/img/grey-logo.jpg" alt="default alt" 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="">C17021045-50</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--> <!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-2595" class="reveal-modal 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Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS: We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION: Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.</p>', 'date' => '2020-11-01', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33203436', 'doi' => '10.1186/s13148-020-00965-8', 'modified' => '2021-02-19 17:15:37', 'created' => '2021-02-18 10:21:53', 'ProductsPublication' => array( 'id' => '4968', 'product_id' => '3154', 'publication_id' => '4055' ) ) $externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/33203436" 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 ?? 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However, it does not show significant homology with other samples species (e.g. human, mouse or rat).</em></p>', 'label1' => '', 'info1' => '', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '48 rxns', 'catalog_number' => 'C02040018', 'old_catalog_number' => '', 'sf_code' => 'C02040018-', 'type' => 'FRE', 'search_order' => '04-undefined', 'price_EUR' => '115', 'price_USD' => '150', 'price_GBP' => '105', 'price_JPY' => '18015', 'price_CNY' => '', 'price_AUD' => '375', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '', 'slug' => 'dna-hydroxymethylation-control-package-48-rxns', 'meta_title' => '', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-07-07 11:59:21', 'created' => '2020-12-03 12:35:34', 'locale' => 'eng' ), 'Antibody' => array( 'host' => '*****', 'id' => null, 'name' => null, 'description' => null, 'clonality' => null, 'isotype' => null, 'lot' => null, 'concentration' => null, 'reactivity' => null, 'type' => null, 'purity' => null, 'classification' => null, 'application_table' => null, 'storage_conditions' => null, 'storage_buffer' => null, 'precautions' => null, 'uniprot_acc' => null, 'slug' => null, 'meta_keywords' => null, 'meta_description' => null, 'modified' => null, 'created' => null, 'select_label' => null ), 'Slave' => array(), 'Group' => array(), 'Related' => array( (int) 0 => array( 'id' => '1882', 'antibody_id' => null, 'name' => 'hMeDIP kit x16 (monoclonal mouse antibody)', 'description' => '<p><a href="https://www.diagenode.com/files/products/kits/hMeDIP_kit_manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p> <p><span>The hMeDIP kit is designed for enrichment of hydroxymethylated DNA from fragmented genomic DNA<span><span> </span>samples for use in genome-wide methylation analysis. 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It includes control DNA and primers to assess the effiency of the assay. </span>Performing hydroxymethylation profiling with the hMeDIP kit is fast, reliable and highly specific.</p> <p><em>Looking for hMeDIP-seq protocol? <a href="https://go.diagenode.com/l/928883/2022-01-07/2m1ht" target="_blank" title="Contact us">Contact us</a></em></p> <p><span></span></p> <p><span></span></p>', 'label1' => 'Characteristics', 'info1' => '<ul style="list-style-type: disc;"> <li><span>Robust enrichment & immunoprecipitation of hydroxymethylated DNA</span></li> <li>Highly specific monoclonal antibody against 5-hmC<span> for reliable, reproducible results</span></li> <li>Including control DNA and primers to <span>monitor the efficiency of the assay</span> <ul style="list-style-type: circle;"> <li>hmeDNA and unmethylated DNA sequences and primer pairs</li> <li>Mouse primer pairs against Sfi1 targeting hydroxymethylated gene in mouse</li> </ul> </li> <li>Improved single-tube, magnetic bead-based protocol</li> </ul>', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '16 rxns', 'catalog_number' => 'C02010031', 'old_catalog_number' => 'AF-110-0016', 'sf_code' => 'C02010031-', 'type' => 'RFR', 'search_order' => '04-undefined', 'price_EUR' => '630', 'price_USD' => '690', 'price_GBP' => '580', 'price_JPY' => '98690', 'price_CNY' => '', 'price_AUD' => '1725', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => true, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '0000-00-00', 'slug' => 'hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns', 'meta_title' => 'hMeDIP kit x16 (monoclonal mouse antibody)', 'meta_keywords' => '', 'meta_description' => 'hMeDIP kit x16 (monoclonal mouse antibody)', 'modified' => '2023-04-20 16:12:48', 'created' => '2015-06-29 14:08:20', 'ProductsRelated' => array( [maximum depth reached] ), 'Image' => array( [maximum depth reached] ) ), (int) 1 => array( 'id' => '2595', 'antibody_id' => null, 'name' => 'Mouse GAPDH promoter primer pair', 'description' => '<p><span>The primer pair Cat. 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No. C17021046 is specific to SFI1 Centrin Binding Protein from mouse. SFI1 is a protein coding gene that has been identified as being hydroxymethylated using DNA immunoprecipitation assays (hMeDIP). The primers are optimized to be used in quantitative polymerase chain reaction (qPCR).</p>', 'label1' => '', 'info1' => '', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '50 µl', 'catalog_number' => 'C17021046-50', 'old_catalog_number' => '', 'sf_code' => 'C17021046-D001-000014', 'type' => 'FRE', 'search_order' => '', 'price_EUR' => '60', 'price_USD' => '35', 'price_GBP' => '60', 'price_JPY' => '9400', 'price_CNY' => '', 'price_AUD' => '88', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '', 'slug' => 'mouse-sfi-promoter-primer-pair-50-ul', 'meta_title' => 'Mouse SFI1 promoter primer pair', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-01-25 09:15:42', 'created' => '2020-12-07 14:23:55', 'ProductsRelated' => array( [maximum depth reached] ), 'Image' => array([maximum depth reached]) ) ), 'Application' => array( (int) 0 => array( 'id' => '1', 'position' => '9', 'parent_id' => null, 'name' => 'DNA Methylation', 'description' => '<div class="row"> <div class="large-12 columns"> <div style="text-align: justify;" class="small-12 medium-8 large-8 columns"> <h2>Complete solutions for DNA methylation studies</h2> <p>Whether you are experienced or new to the field of DNA methylation, Diagenode has everything you need to make your assay as easy and convenient as possible while ensuring consistent data between samples and experiments. Diagenode offers sonication instruments, reagent kits, high quality antibodies, and high-throughput automation capability to address all of your specific DNA methylation analysis requirements.</p> </div> <div class="small-12 medium-4 large-4 columns text-center"><a href="../landing-pages/dna-methylation-grant-applications"><img src="https://www.diagenode.com/img/banners/banner-dna-grant.png" alt="" /></a></div> <div style="text-align: justify;" class="small-12 medium-12 large-12 columns"> <p>DNA methylation was the first discovered epigenetic mark and is the most widely studied topic in epigenetics. <em>In vivo</em>, DNA is methylated following DNA replication and is involved in a number of biological processes including the regulation of imprinted genes, X chromosome inactivation. and tumor suppressor gene silencing in cancer cells. Methylation often occurs in cytosine-guanine rich regions of DNA (CpG islands), which are commonly upstream of promoter regions.</p> </div> <div class="small-12 medium-12 large-12 columns"><br /><br /> <ul class="accordion" data-accordion=""> <li class="accordion-navigation"><a href="#dnamethyl"><i class="fa fa-caret-right"></i> Learn more</a> <div id="dnamethyl" class="content">5-methylcytosine (5-mC) has been known for a long time as the only modification of DNA for epigenetic regulation. In 2009, however, Kriaucionis discovered a second methylated cytosine, 5-hydroxymethylcytosine (5-hmC). The so-called 6th base, is generated by enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine by the TET family of oxygenases. Early reports suggested that 5-hmC may represent an intermediate of active demethylation in a new pathway which demethylates DNA, converting 5-mC to cytosine. Recent evidence fuel this hypothesis suggesting that further oxidation of the hydroxymethyl group leads to a formyl or carboxyl group followed by either deformylation or decarboxylation. The formyl and carboxyl groups of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) could be enzymatically removed without excision of the base. <p class="text-center"><img src="https://www.diagenode.com/img/categories/kits_dna/dna_methylation_variants.jpg" /></p> </div> </li> </ul> <br /> <h2>Main DNA methylation technologies</h2> <p style="text-align: justify;">Overview of the <span style="font-weight: 400;">three main approaches for studying DNA methylation.</span></p> <div class="row"> <ol> <li style="font-weight: 400;"><span style="font-weight: 400;">Chemical modification with bisulfite – Bisulfite conversion</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Enrichment of methylated DNA (including MeDIP and MBD)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Treatment with methylation-sensitive or dependent restriction enzymes</span></li> </ol> <p><span style="font-weight: 400;"> </span></p> <div class="row"> <table> <thead> <tr> <th></th> <th>Description</th> <th width="350">Features</th> </tr> </thead> <tbody> <tr> <td><strong>Bisulfite conversion</strong></td> <td><span style="font-weight: 400;">Chemical conversion of unmethylated cytosine to uracil. Methylated cytosines are protected from this conversion allowing to determine DNA methylation at single nucleotide resolution.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Single nucleotide resolution</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Quantitative analysis - methylation rate (%)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Gold standard and well studied</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li> </ul> </td> </tr> <tr> <td><b>Methylated DNA enrichment</b></td> <td><span style="font-weight: 400;">(Hydroxy-)Methylated DNA is enriched by using specific antibodies (hMeDIP or MeDIP) or proteins (MBD) that specifically bind methylated CpG sites in fragmented genomic DNA.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Resolution depends on the fragment size of the enriched methylated DNA (300 bp)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Qualitative analysis</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li> </ul> </td> </tr> <tr> <td><strong>Restriction enzyme-based digestion</strong></td> <td><span style="font-weight: 400;">Use of (hydroxy)methylation-sensitive or (hydroxy)methylation-dependent restriction enzymes for DNA methylation analysis at specific sites.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Determination of methylation status is limited by the enzyme recognition site</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Easy to use</span></li> </ul> </td> </tr> </tbody> </table> </div> </div> <div class="row"></div> </div> </div> <div class="large-12 columns"></div> </div>', 'in_footer' => true, 'in_menu' => true, 'online' => true, 'tabular' => true, 'slug' => 'epigenetics-dna-methylation', 'meta_keywords' => 'Epigenetics, DNA Methylation,5-hmC monoclonal antibody,hMeDIP,Bisulfite conversion,Methylated DNA immunoprecipitation', 'meta_description' => 'Complete, optimized solutions for analyzing DNA methylation manually or on our automated system.', 'meta_title' => 'DNA Methylation - Bisulfite sequencing - Epigenetics | Diagenode', 'modified' => '2019-03-25 10:07:27', 'created' => '2015-05-03 13:47:53', 'ProductsApplication' => array( [maximum depth reached] ) ), (int) 1 => 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’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> & <strong>reproducible</strong> techniques</li> <li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li> </ul> <h2></h2> </div> </div> <div id="gtx-trans" style="position: absolute; left: 17px; top: 652.938px;"> <div class="gtx-trans-icon"></div> </div>', 'in_footer' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'slug' => 'methylated-dna-immunoprecipitation', 'meta_keywords' => 'Methylated DNA immunoprecipitation,Epigenetic,DNA Methylation,qPCR,5 methylcytosine (5-mC)', 'meta_description' => 'Methylated DNA immunoprecipitation method is based on the affinity purification of methylated DNA using an antibody directed against 5 methylcytosine (5-mC). ', 'meta_title' => 'Methylated DNA immunoprecipitation(MeDIP) - Dna methylation | Diagenode', 'modified' => '2021-08-19 12:08:03', 'created' => '2014-09-14 05:33:34', 'ProductsApplication' => array( [maximum depth reached] ) ) ), 'Category' => array( (int) 0 => array( 'id' => '55', 'position' => '5', 'parent_id' => '12', 'name' => 'DNA methylation standard', 'description' => '', 'no_promo' => false, 'in_menu' => false, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'dna-methylation-standard', 'cookies_tag_id' => null, 'meta_keywords' => 'DNA methylation standard,hydroxymethylated ,5-hmC,5-mC.', 'meta_description' => 'Diagenode Offers Unmethylated, Methylated and Hydroxymethylated Standards for Monitoring of DNA Methylation Assays.', 'meta_title' => 'DNA Methylation Standard | Diagenode', 'modified' => '2019-07-03 10:43:22', 'created' => '2015-07-08 09:53:00', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ), (int) 1 => array( 'id' => '51', 'position' => '11', 'parent_id' => '12', 'name' => 'Hydroxymethylated DNA immunoprecipitation', 'description' => '<p></p> <div class="row"> <div class="large-12 columns">The hydroxymethylated DNA IP (hMeDIP) is based on the affinity purification of methylated DNA using an antibody directed against 5-hydroxymethylcytosine (5-hmC). <h3>How it works</h3> In brief, hydroxymethyl DNA IP is performed as follows: starting from sheared genomic DNA from cultured cells or tissues, the immunoselection and immunoprecipitation can take place using the antibody directed against 5-hydroxymethylcytosine and antibody binding beads. After isolation and purification is performed, the IP’d hydroxymethylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or Next Generation Sequencing. <h3>Overview</h3> <p class="text-center"><img src="https://www.diagenode.com/img/applications/magnetic_medip_overview.jpg" caption="false" width="726" height="916" /></p> </div> </div>', 'no_promo' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'hydroxymethylated-dna-immunoprecipitation', 'cookies_tag_id' => null, 'meta_keywords' => 'Hydroxymethylated DNA Immunoprecipitation,DNA methylation', 'meta_description' => 'Diagenode Offers Antibody-Based Isolation of Hydroxymethylated DNA for DNA Methylation Studies', 'meta_title' => 'Hydroxymethylated DNA Immunoprecipitation for DNA Methylation Studies | Diagenode', 'modified' => '2022-10-06 15:25:37', 'created' => '2015-07-08 09:24:17', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ) ), 'Document' => array( (int) 0 => array( 'id' => '1125', 'name' => 'Datasheet DNA hydroxymethylation control package', 'description' => '', 'image_id' => null, 'type' => 'Datasheet', 'url' => 'files/products/kits/Datasheet_DNA-hydroxymethylation-control-package.pdf', 'slug' => 'datasheet-dna-hydroxymethylation-control-package', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-01-18 16:08:24', 'created' => '2021-01-18 16:08:24', 'ProductsDocument' => array( [maximum depth reached] ) ) ), 'Feature' => array(), 'Image' => array( (int) 0 => array( 'id' => '1778', 'name' => 'product/kits/methyl-kit-icon.png', 'alt' => 'Methylation kit icon', 'modified' => '2019-04-23 15:17:01', 'created' => '2018-03-15 15:52:12', 'ProductsImage' => array( [maximum depth reached] ) ) ), 'Promotion' => array(), 'Protocol' => array(), 'Publication' => array( (int) 0 => array( 'id' => '4055', 'name' => '5-Hydroxymethylation highlights the heterogeneity in keratinization andcell junctions in head and neck cancers.', 'authors' => 'Liu, Siyu and de Medeiros, Marcell Costa and Fernandez, Evan M and Zarins,Katie R and Cavalcante, Raymond G and Qin, Tingting and Wolf, Gregory T andFigueroa, Maria E and D'Silva, Nisha J and Rozek, Laura S and Sartor,Maureen A', 'description' => '<p>BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, with human papillomavirus (HPV)-related HNSCC rising to concerning levels. Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS: We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION: Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.</p>', 'date' => '2020-11-01', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33203436', 'doi' => '10.1186/s13148-020-00965-8', 'modified' => '2021-02-19 17:15:37', 'created' => '2021-02-18 10:21:53', 'ProductsPublication' => array( [maximum depth reached] ) ) ), 'Testimonial' => array(), 'Area' => array(), 'SafetySheet' => array() ) $country = 'US' $countries_allowed = array( (int) 0 => 'CA', (int) 1 => 'US', (int) 2 => 'IE', (int) 3 => 'GB', (int) 4 => 'DK', (int) 5 => 'NO', (int) 6 => 'SE', (int) 7 => 'FI', (int) 8 => 'NL', (int) 9 => 'BE', (int) 10 => 'LU', (int) 11 => 'FR', (int) 12 => 'DE', (int) 13 => 'CH', (int) 14 => 'AT', (int) 15 => 'ES', (int) 16 => 'IT', (int) 17 => 'PT' ) $outsource = false $other_formats = array() $edit = '' $testimonials = '' $featured_testimonials = '' $related_products = '<li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns"><img src="/img/product/kits/methyl-kit-icon.png" alt="Methylation kit icon" class="th"/></a> </div> <div class="small-12 columns"> <div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px"> <span class="success label" style="">C02010031</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> <!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-1882" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog"> <form action="/en/carts/add/1882" id="CartAdd/1882Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="1882" id="CartProductId"/> <div class="row"> <div class="small-12 medium-12 large-12 columns"> <p>Add <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> hMeDIP kit x16 (monoclonal mouse antibody)</strong> to my shopping cart.</p> <div class="row"> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('hMeDIP kit x16 (monoclonal mouse antibody)', 'C02010031', '690', $('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">Checkout</button> </div> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('hMeDIP kit x16 (monoclonal mouse antibody)', 'C02010031', '690', $('#CartQuantity').val());" name="keepshop" id="keepshop" type="submit">Keep shopping</button> </div> </div> </div> </div> </form><a class="close-reveal-modal" aria-label="Close">×</a></div><!-- END: ADD TO CART MODAL --><a href="#" id="hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns" data-reveal-id="cartModal-1882" class="" style="color:#B21329"><i class="fa fa-cart-plus"></i></a> </div> </div> <div class="small-12 columns" > <h6 style="height:60px">hMeDIP kit x16 (monoclonal mouse antibody)</h6> </div> </div> </li> <li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/mouse-gapdh-promoter-primer-pair-50-ul"><img src="/img/grey-logo.jpg" alt="default alt" class="th"/></a> </div> <div class="small-12 columns"> <div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px"> <span class="success label" style="">C17021045-50</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> <!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-2595" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog"> <form action="/en/carts/add/2595" id="CartAdd/2595Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="2595" id="CartProductId"/> <div class="row"> <div class="small-12 medium-12 large-12 columns"> <p>Add <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> Mouse GAPDH promoter primer pair</strong> to my shopping cart.</p> <div class="row"> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('Mouse GAPDH promoter primer pair', 'C17021045-50', '35', $('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">Checkout</button> </div> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('Mouse GAPDH promoter primer pair', 'C17021045-50', '35', $('#CartQuantity').val());" name="keepshop" id="keepshop" type="submit">Keep shopping</button> </div> </div> </div> </div> </form><a class="close-reveal-modal" aria-label="Close">×</a></div><!-- END: ADD TO CART MODAL --><a href="#" id="mouse-gapdh-promoter-primer-pair-50-ul" data-reveal-id="cartModal-2595" class="" style="color:#B21329"><i class="fa fa-cart-plus"></i></a> </div> </div> <div class="small-12 columns" > <h6 style="height:60px">Mouse GAPDH promoter primer pair</h6> </div> </div> </li> <li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/mouse-sfi-promoter-primer-pair-50-ul"><img src="/img/grey-logo.jpg" alt="default alt" class="th"/></a> </div> <div class="small-12 columns"> <div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px"> <span class="success label" style="">C17021046-50</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> <!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-3156" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog"> <form action="/en/carts/add/3156" id="CartAdd/3156Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="3156" id="CartProductId"/> <div class="row"> <div class="small-12 medium-12 large-12 columns"> <p>Add <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> Mouse SFI1 promoter primer pair</strong> to my shopping cart.</p> <div class="row"> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('Mouse SFI1 promoter primer pair', 'C17021046-50', '35', $('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">Checkout</button> </div> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('Mouse SFI1 promoter primer pair', 'C17021046-50', '35', $('#CartQuantity').val());" name="keepshop" id="keepshop" type="submit">Keep shopping</button> </div> </div> </div> </div> </form><a class="close-reveal-modal" aria-label="Close">×</a></div><!-- END: ADD TO CART MODAL --><a href="#" id="mouse-sfi-promoter-primer-pair-50-ul" data-reveal-id="cartModal-3156" class="" style="color:#B21329"><i class="fa fa-cart-plus"></i></a> </div> </div> <div class="small-12 columns" > <h6 style="height:60px">Mouse SFI1 promoter primer pair</h6> </div> </div> </li> ' $related = array( 'id' => '3156', 'antibody_id' => null, 'name' => 'Mouse SFI1 promoter primer pair', 'description' => '<p>The primer pair Cat. No. C17021046 is specific to SFI1 Centrin Binding Protein from mouse. SFI1 is a protein coding gene that has been identified as being hydroxymethylated using DNA immunoprecipitation assays (hMeDIP). 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Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS: We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION: Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.</p>', 'date' => '2020-11-01', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33203436', 'doi' => '10.1186/s13148-020-00965-8', 'modified' => '2021-02-19 17:15:37', 'created' => '2021-02-18 10:21:53', 'ProductsPublication' => array( 'id' => '4968', 'product_id' => '3154', 'publication_id' => '4055' ) ) $externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/33203436" 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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However, it does not show significant homology with other samples species (e.g. human, mouse or rat).</em></p>', 'label1' => '', 'info1' => '', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '48 rxns', 'catalog_number' => 'C02040018', 'old_catalog_number' => '', 'sf_code' => 'C02040018-', 'type' => 'FRE', 'search_order' => '04-undefined', 'price_EUR' => '115', 'price_USD' => '150', 'price_GBP' => '105', 'price_JPY' => '18015', 'price_CNY' => '', 'price_AUD' => '375', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '', 'slug' => 'dna-hydroxymethylation-control-package-48-rxns', 'meta_title' => '', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-07-07 11:59:21', 'created' => '2020-12-03 12:35:34', 'locale' => 'eng' ), 'Antibody' => array( 'host' => '*****', 'id' => null, 'name' => null, 'description' => null, 'clonality' => null, 'isotype' => null, 'lot' => null, 'concentration' => null, 'reactivity' => null, 'type' => null, 'purity' => null, 'classification' => null, 'application_table' => null, 'storage_conditions' => null, 'storage_buffer' => null, 'precautions' => null, 'uniprot_acc' => null, 'slug' => null, 'meta_keywords' => null, 'meta_description' => null, 'modified' => null, 'created' => null, 'select_label' => null ), 'Slave' => array(), 'Group' => array(), 'Related' => array( (int) 0 => array( [maximum depth reached] ), (int) 1 => array( [maximum depth reached] ), (int) 2 => array( [maximum depth reached] ) ), 'Application' => array( (int) 0 => array( [maximum depth reached] ), (int) 1 => array( [maximum depth reached] ) ), 'Category' => array( (int) 0 => array( [maximum depth reached] ), (int) 1 => array( [maximum depth reached] ) ), 'Document' => array( (int) 0 => array( [maximum depth reached] ) ), 'Feature' => array(), 'Image' => array( (int) 0 => array( [maximum depth reached] ) ), 'Promotion' => array(), 'Protocol' => array(), 'Publication' => array( (int) 0 => array( [maximum depth reached] ) ), 'Testimonial' => array(), 'Area' => array(), 'SafetySheet' => array() ) ) $language = 'en' $meta_keywords = '' $meta_description = '' $meta_title = '' $product = array( 'Product' => array( 'id' => '3154', 'antibody_id' => null, 'name' => 'DNA hydroxymethylation control package', 'description' => '<p>The DNA hydroxymethylation control package includes one hydroxymethylated spike-in control and its corresponding qPCR primer set that can be added to the DNA sample of interest for any hydroxymethylation profiling experiment (e.g. with Diagenode's <a href="https://www.diagenode.com/en/p/hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns">hMeDIP Kit</a>).</p> <p><em><strong>CAUTION:</strong> The hydroxymethylated spike-in control is produced from a genomic sequence from Arabidopsis thaliana and may therefore interfere with plant samples. However, it does not show significant homology with other samples species (e.g. human, mouse or rat).</em></p>', 'label1' => '', 'info1' => '', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '48 rxns', 'catalog_number' => 'C02040018', 'old_catalog_number' => '', 'sf_code' => 'C02040018-', 'type' => 'FRE', 'search_order' => '04-undefined', 'price_EUR' => '115', 'price_USD' => '150', 'price_GBP' => '105', 'price_JPY' => '18015', 'price_CNY' => '', 'price_AUD' => '375', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '', 'slug' => 'dna-hydroxymethylation-control-package-48-rxns', 'meta_title' => '', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-07-07 11:59:21', 'created' => '2020-12-03 12:35:34', 'locale' => 'eng' ), 'Antibody' => array( 'host' => '*****', 'id' => null, 'name' => null, 'description' => null, 'clonality' => null, 'isotype' => null, 'lot' => null, 'concentration' => null, 'reactivity' => null, 'type' => null, 'purity' => null, 'classification' => null, 'application_table' => null, 'storage_conditions' => null, 'storage_buffer' => null, 'precautions' => null, 'uniprot_acc' => null, 'slug' => null, 'meta_keywords' => null, 'meta_description' => null, 'modified' => null, 'created' => null, 'select_label' => null ), 'Slave' => array(), 'Group' => array(), 'Related' => array( (int) 0 => array( 'id' => '1882', 'antibody_id' => null, 'name' => 'hMeDIP kit x16 (monoclonal mouse antibody)', 'description' => '<p><a href="https://www.diagenode.com/files/products/kits/hMeDIP_kit_manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p> <p><span>The hMeDIP kit is designed for enrichment of hydroxymethylated DNA from fragmented genomic DNA<span><span> </span>samples for use in genome-wide methylation analysis. It features</span></span><span> a highly specific monoclonal antibody against </span>5-hydroxymethylcytosine (5-hmC) for the immunoprecipitation of hydroxymethylated DNA<span>. It includes control DNA and primers to assess the effiency of the assay. </span>Performing hydroxymethylation profiling with the hMeDIP kit is fast, reliable and highly specific.</p> <p><em>Looking for hMeDIP-seq protocol? <a href="https://go.diagenode.com/l/928883/2022-01-07/2m1ht" target="_blank" title="Contact us">Contact us</a></em></p> <p><span></span></p> <p><span></span></p>', 'label1' => 'Characteristics', 'info1' => '<ul style="list-style-type: disc;"> <li><span>Robust enrichment & immunoprecipitation of hydroxymethylated DNA</span></li> <li>Highly specific monoclonal antibody against 5-hmC<span> for reliable, reproducible results</span></li> <li>Including control DNA and primers to <span>monitor the efficiency of the assay</span> <ul style="list-style-type: circle;"> <li>hmeDNA and unmethylated DNA sequences and primer pairs</li> <li>Mouse primer pairs against Sfi1 targeting hydroxymethylated gene in mouse</li> </ul> </li> <li>Improved single-tube, magnetic bead-based protocol</li> </ul>', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '16 rxns', 'catalog_number' => 'C02010031', 'old_catalog_number' => 'AF-110-0016', 'sf_code' => 'C02010031-', 'type' => 'RFR', 'search_order' => '04-undefined', 'price_EUR' => '630', 'price_USD' => '690', 'price_GBP' => '580', 'price_JPY' => '98690', 'price_CNY' => '', 'price_AUD' => '1725', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => true, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '0000-00-00', 'slug' => 'hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns', 'meta_title' => 'hMeDIP kit x16 (monoclonal mouse antibody)', 'meta_keywords' => '', 'meta_description' => 'hMeDIP kit x16 (monoclonal mouse antibody)', 'modified' => '2023-04-20 16:12:48', 'created' => '2015-06-29 14:08:20', 'ProductsRelated' => array( [maximum depth reached] ), 'Image' => array( [maximum depth reached] ) ), (int) 1 => array( 'id' => '2595', 'antibody_id' => null, 'name' => 'Mouse GAPDH promoter primer pair', 'description' => '<p><span>The primer pair Cat. No. C17021045 is specific to a promoter region of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene from mouse. The primers are optimized to be used in quantitative polymerase chain reaction (qPCR).</span></p>', 'label1' => '', 'info1' => '', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '50 µl', 'catalog_number' => 'C17021045-50', 'old_catalog_number' => 'pp-1045-050', 'sf_code' => 'C17021045-D001-000014', 'type' => 'FRE', 'search_order' => '01-Accessory', 'price_EUR' => '60', 'price_USD' => '35', 'price_GBP' => '60', 'price_JPY' => '9400', 'price_CNY' => '', 'price_AUD' => '88', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '0000-00-00', 'slug' => 'mouse-gapdh-promoter-primer-pair-50-ul', 'meta_title' => 'Mouse GAPDH promoter primer pair', 'meta_keywords' => '', 'meta_description' => 'Mouse GAPDH promoter primer pair', 'modified' => '2021-01-18 10:00:33', 'created' => '2015-06-29 14:08:20', 'ProductsRelated' => array( [maximum depth reached] ), 'Image' => array([maximum depth reached]) ), (int) 2 => array( 'id' => '3156', 'antibody_id' => null, 'name' => 'Mouse SFI1 promoter primer pair', 'description' => '<p>The primer pair Cat. No. C17021046 is specific to SFI1 Centrin Binding Protein from mouse. SFI1 is a protein coding gene that has been identified as being hydroxymethylated using DNA immunoprecipitation assays (hMeDIP). The primers are optimized to be used in quantitative polymerase chain reaction (qPCR).</p>', 'label1' => '', 'info1' => '', 'label2' => '', 'info2' => '', 'label3' => '', 'info3' => '', 'format' => '50 µl', 'catalog_number' => 'C17021046-50', 'old_catalog_number' => '', 'sf_code' => 'C17021046-D001-000014', 'type' => 'FRE', 'search_order' => '', 'price_EUR' => '60', 'price_USD' => '35', 'price_GBP' => '60', 'price_JPY' => '9400', 'price_CNY' => '', 'price_AUD' => '88', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => false, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '', 'slug' => 'mouse-sfi-promoter-primer-pair-50-ul', 'meta_title' => 'Mouse SFI1 promoter primer pair', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-01-25 09:15:42', 'created' => '2020-12-07 14:23:55', 'ProductsRelated' => array( [maximum depth reached] ), 'Image' => array([maximum depth reached]) ) ), 'Application' => array( (int) 0 => array( 'id' => '1', 'position' => '9', 'parent_id' => null, 'name' => 'DNA Methylation', 'description' => '<div class="row"> <div class="large-12 columns"> <div style="text-align: justify;" class="small-12 medium-8 large-8 columns"> <h2>Complete solutions for DNA methylation studies</h2> <p>Whether you are experienced or new to the field of DNA methylation, Diagenode has everything you need to make your assay as easy and convenient as possible while ensuring consistent data between samples and experiments. Diagenode offers sonication instruments, reagent kits, high quality antibodies, and high-throughput automation capability to address all of your specific DNA methylation analysis requirements.</p> </div> <div class="small-12 medium-4 large-4 columns text-center"><a href="../landing-pages/dna-methylation-grant-applications"><img src="https://www.diagenode.com/img/banners/banner-dna-grant.png" alt="" /></a></div> <div style="text-align: justify;" class="small-12 medium-12 large-12 columns"> <p>DNA methylation was the first discovered epigenetic mark and is the most widely studied topic in epigenetics. <em>In vivo</em>, DNA is methylated following DNA replication and is involved in a number of biological processes including the regulation of imprinted genes, X chromosome inactivation. and tumor suppressor gene silencing in cancer cells. Methylation often occurs in cytosine-guanine rich regions of DNA (CpG islands), which are commonly upstream of promoter regions.</p> </div> <div class="small-12 medium-12 large-12 columns"><br /><br /> <ul class="accordion" data-accordion=""> <li class="accordion-navigation"><a href="#dnamethyl"><i class="fa fa-caret-right"></i> Learn more</a> <div id="dnamethyl" class="content">5-methylcytosine (5-mC) has been known for a long time as the only modification of DNA for epigenetic regulation. In 2009, however, Kriaucionis discovered a second methylated cytosine, 5-hydroxymethylcytosine (5-hmC). The so-called 6th base, is generated by enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine by the TET family of oxygenases. Early reports suggested that 5-hmC may represent an intermediate of active demethylation in a new pathway which demethylates DNA, converting 5-mC to cytosine. Recent evidence fuel this hypothesis suggesting that further oxidation of the hydroxymethyl group leads to a formyl or carboxyl group followed by either deformylation or decarboxylation. The formyl and carboxyl groups of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) could be enzymatically removed without excision of the base. <p class="text-center"><img src="https://www.diagenode.com/img/categories/kits_dna/dna_methylation_variants.jpg" /></p> </div> </li> </ul> <br /> <h2>Main DNA methylation technologies</h2> <p style="text-align: justify;">Overview of the <span style="font-weight: 400;">three main approaches for studying DNA methylation.</span></p> <div class="row"> <ol> <li style="font-weight: 400;"><span style="font-weight: 400;">Chemical modification with bisulfite – Bisulfite conversion</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Enrichment of methylated DNA (including MeDIP and MBD)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Treatment with methylation-sensitive or dependent restriction enzymes</span></li> </ol> <p><span style="font-weight: 400;"> </span></p> <div class="row"> <table> <thead> <tr> <th></th> <th>Description</th> <th width="350">Features</th> </tr> </thead> <tbody> <tr> <td><strong>Bisulfite conversion</strong></td> <td><span style="font-weight: 400;">Chemical conversion of unmethylated cytosine to uracil. Methylated cytosines are protected from this conversion allowing to determine DNA methylation at single nucleotide resolution.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Single nucleotide resolution</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Quantitative analysis - methylation rate (%)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Gold standard and well studied</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li> </ul> </td> </tr> <tr> <td><b>Methylated DNA enrichment</b></td> <td><span style="font-weight: 400;">(Hydroxy-)Methylated DNA is enriched by using specific antibodies (hMeDIP or MeDIP) or proteins (MBD) that specifically bind methylated CpG sites in fragmented genomic DNA.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Resolution depends on the fragment size of the enriched methylated DNA (300 bp)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Qualitative analysis</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li> </ul> </td> </tr> <tr> <td><strong>Restriction enzyme-based digestion</strong></td> <td><span style="font-weight: 400;">Use of (hydroxy)methylation-sensitive or (hydroxy)methylation-dependent restriction enzymes for DNA methylation analysis at specific sites.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Determination of methylation status is limited by the enzyme recognition site</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Easy to use</span></li> </ul> </td> </tr> </tbody> </table> </div> </div> <div class="row"></div> </div> </div> <div class="large-12 columns"></div> </div>', 'in_footer' => true, 'in_menu' => true, 'online' => true, 'tabular' => true, 'slug' => 'epigenetics-dna-methylation', 'meta_keywords' => 'Epigenetics, DNA Methylation,5-hmC monoclonal antibody,hMeDIP,Bisulfite conversion,Methylated DNA immunoprecipitation', 'meta_description' => 'Complete, optimized solutions for analyzing DNA methylation manually or on our automated system.', 'meta_title' => 'DNA Methylation - Bisulfite sequencing - Epigenetics | Diagenode', 'modified' => '2019-03-25 10:07:27', 'created' => '2015-05-03 13:47:53', 'ProductsApplication' => array( [maximum depth reached] ) ), (int) 1 => 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’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> & <strong>reproducible</strong> techniques</li> <li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li> </ul> <h2></h2> </div> </div> <div id="gtx-trans" style="position: absolute; left: 17px; top: 652.938px;"> <div class="gtx-trans-icon"></div> </div>', 'in_footer' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'slug' => 'methylated-dna-immunoprecipitation', 'meta_keywords' => 'Methylated DNA immunoprecipitation,Epigenetic,DNA Methylation,qPCR,5 methylcytosine (5-mC)', 'meta_description' => 'Methylated DNA immunoprecipitation method is based on the affinity purification of methylated DNA using an antibody directed against 5 methylcytosine (5-mC). ', 'meta_title' => 'Methylated DNA immunoprecipitation(MeDIP) - Dna methylation | Diagenode', 'modified' => '2021-08-19 12:08:03', 'created' => '2014-09-14 05:33:34', 'ProductsApplication' => array( [maximum depth reached] ) ) ), 'Category' => array( (int) 0 => array( 'id' => '55', 'position' => '5', 'parent_id' => '12', 'name' => 'DNA methylation standard', 'description' => '', 'no_promo' => false, 'in_menu' => false, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'dna-methylation-standard', 'cookies_tag_id' => null, 'meta_keywords' => 'DNA methylation standard,hydroxymethylated ,5-hmC,5-mC.', 'meta_description' => 'Diagenode Offers Unmethylated, Methylated and Hydroxymethylated Standards for Monitoring of DNA Methylation Assays.', 'meta_title' => 'DNA Methylation Standard | Diagenode', 'modified' => '2019-07-03 10:43:22', 'created' => '2015-07-08 09:53:00', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ), (int) 1 => array( 'id' => '51', 'position' => '11', 'parent_id' => '12', 'name' => 'Hydroxymethylated DNA immunoprecipitation', 'description' => '<p></p> <div class="row"> <div class="large-12 columns">The hydroxymethylated DNA IP (hMeDIP) is based on the affinity purification of methylated DNA using an antibody directed against 5-hydroxymethylcytosine (5-hmC). <h3>How it works</h3> In brief, hydroxymethyl DNA IP is performed as follows: starting from sheared genomic DNA from cultured cells or tissues, the immunoselection and immunoprecipitation can take place using the antibody directed against 5-hydroxymethylcytosine and antibody binding beads. After isolation and purification is performed, the IP’d hydroxymethylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or Next Generation Sequencing. <h3>Overview</h3> <p class="text-center"><img src="https://www.diagenode.com/img/applications/magnetic_medip_overview.jpg" caption="false" width="726" height="916" /></p> </div> </div>', 'no_promo' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'hydroxymethylated-dna-immunoprecipitation', 'cookies_tag_id' => null, 'meta_keywords' => 'Hydroxymethylated DNA Immunoprecipitation,DNA methylation', 'meta_description' => 'Diagenode Offers Antibody-Based Isolation of Hydroxymethylated DNA for DNA Methylation Studies', 'meta_title' => 'Hydroxymethylated DNA Immunoprecipitation for DNA Methylation Studies | Diagenode', 'modified' => '2022-10-06 15:25:37', 'created' => '2015-07-08 09:24:17', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ) ), 'Document' => array( (int) 0 => array( 'id' => '1125', 'name' => 'Datasheet DNA hydroxymethylation control package', 'description' => '', 'image_id' => null, 'type' => 'Datasheet', 'url' => 'files/products/kits/Datasheet_DNA-hydroxymethylation-control-package.pdf', 'slug' => 'datasheet-dna-hydroxymethylation-control-package', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-01-18 16:08:24', 'created' => '2021-01-18 16:08:24', 'ProductsDocument' => array( [maximum depth reached] ) ) ), 'Feature' => array(), 'Image' => array( (int) 0 => array( 'id' => '1778', 'name' => 'product/kits/methyl-kit-icon.png', 'alt' => 'Methylation kit icon', 'modified' => '2019-04-23 15:17:01', 'created' => '2018-03-15 15:52:12', 'ProductsImage' => array( [maximum depth reached] ) ) ), 'Promotion' => array(), 'Protocol' => array(), 'Publication' => array( (int) 0 => array( 'id' => '4055', 'name' => '5-Hydroxymethylation highlights the heterogeneity in keratinization andcell junctions in head and neck cancers.', 'authors' => 'Liu, Siyu and de Medeiros, Marcell Costa and Fernandez, Evan M and Zarins,Katie R and Cavalcante, Raymond G and Qin, Tingting and Wolf, Gregory T andFigueroa, Maria E and D'Silva, Nisha J and Rozek, Laura S and Sartor,Maureen A', 'description' => '<p>BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, with human papillomavirus (HPV)-related HNSCC rising to concerning levels. Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS: We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION: Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.</p>', 'date' => '2020-11-01', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33203436', 'doi' => '10.1186/s13148-020-00965-8', 'modified' => '2021-02-19 17:15:37', 'created' => '2021-02-18 10:21:53', 'ProductsPublication' => array( [maximum depth reached] ) ) ), 'Testimonial' => array(), 'Area' => array(), 'SafetySheet' => array() ) $country = 'US' $countries_allowed = array( (int) 0 => 'CA', (int) 1 => 'US', (int) 2 => 'IE', (int) 3 => 'GB', (int) 4 => 'DK', (int) 5 => 'NO', (int) 6 => 'SE', (int) 7 => 'FI', (int) 8 => 'NL', (int) 9 => 'BE', (int) 10 => 'LU', (int) 11 => 'FR', (int) 12 => 'DE', (int) 13 => 'CH', (int) 14 => 'AT', (int) 15 => 'ES', (int) 16 => 'IT', (int) 17 => 'PT' ) $outsource = false $other_formats = array() $edit = '' $testimonials = '' $featured_testimonials = '' $related_products = '<li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/hmedip-kit-x16-monoclonal-mouse-antibody-16-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="">C02010031</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--> <!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-1882" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog"> <form action="/en/carts/add/1882" id="CartAdd/1882Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="1882" id="CartProductId"/> <div 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style="">C17021046-50</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--> <!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-3156" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog"> <form action="/en/carts/add/3156" id="CartAdd/3156Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="3156" id="CartProductId"/> <div class="row"> <div class="small-12 medium-12 large-12 columns"> <p>Add <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> Mouse SFI1 promoter primer pair</strong> to my shopping cart.</p> <div class="row"> <div class="small-6 medium-6 large-6 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No. C17021046 is specific to SFI1 Centrin Binding Protein from mouse. SFI1 is a protein coding gene that has been identified as being hydroxymethylated using DNA immunoprecipitation assays (hMeDIP). 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Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS: We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION: Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.</p>', 'date' => '2020-11-01', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33203436', 'doi' => '10.1186/s13148-020-00965-8', 'modified' => '2021-02-19 17:15:37', 'created' => '2021-02-18 10:21:53', 'ProductsPublication' => array( 'id' => '4968', 'product_id' => '3154', 'publication_id' => '4055' ) ) $externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/33203436" 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 ?? 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Diagenode offers sonication instruments, reagent kits, high quality antibodies, and high-throughput automation capability to address all of your specific DNA methylation analysis requirements.</p> </div> <div class="small-12 medium-4 large-4 columns text-center"><a href="../landing-pages/dna-methylation-grant-applications"><img src="https://www.diagenode.com/img/banners/banner-dna-grant.png" alt="" /></a></div> <div style="text-align: justify;" class="small-12 medium-12 large-12 columns"> <p>DNA methylation was the first discovered epigenetic mark and is the most widely studied topic in epigenetics. <em>In vivo</em>, DNA is methylated following DNA replication and is involved in a number of biological processes including the regulation of imprinted genes, X chromosome inactivation. and tumor suppressor gene silencing in cancer cells. Methylation often occurs in cytosine-guanine rich regions of DNA (CpG islands), which are commonly upstream of promoter regions.</p> </div> <div class="small-12 medium-12 large-12 columns"><br /><br /> <ul class="accordion" data-accordion=""> <li class="accordion-navigation"><a href="#dnamethyl"><i class="fa fa-caret-right"></i> Learn more</a> <div id="dnamethyl" class="content">5-methylcytosine (5-mC) has been known for a long time as the only modification of DNA for epigenetic regulation. In 2009, however, Kriaucionis discovered a second methylated cytosine, 5-hydroxymethylcytosine (5-hmC). The so-called 6th base, is generated by enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine by the TET family of oxygenases. Early reports suggested that 5-hmC may represent an intermediate of active demethylation in a new pathway which demethylates DNA, converting 5-mC to cytosine. Recent evidence fuel this hypothesis suggesting that further oxidation of the hydroxymethyl group leads to a formyl or carboxyl group followed by either deformylation or decarboxylation. The formyl and carboxyl groups of 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC) could be enzymatically removed without excision of the base. <p class="text-center"><img src="https://www.diagenode.com/img/categories/kits_dna/dna_methylation_variants.jpg" /></p> </div> </li> </ul> <br /> <h2>Main DNA methylation technologies</h2> <p style="text-align: justify;">Overview of the <span style="font-weight: 400;">three main approaches for studying DNA methylation.</span></p> <div class="row"> <ol> <li style="font-weight: 400;"><span style="font-weight: 400;">Chemical modification with bisulfite – Bisulfite conversion</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Enrichment of methylated DNA (including MeDIP and MBD)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Treatment with methylation-sensitive or dependent restriction enzymes</span></li> </ol> <p><span style="font-weight: 400;"> </span></p> <div class="row"> <table> <thead> <tr> <th></th> <th>Description</th> <th width="350">Features</th> </tr> </thead> <tbody> <tr> <td><strong>Bisulfite conversion</strong></td> <td><span style="font-weight: 400;">Chemical conversion of unmethylated cytosine to uracil. Methylated cytosines are protected from this conversion allowing to determine DNA methylation at single nucleotide resolution.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Single nucleotide resolution</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Quantitative analysis - methylation rate (%)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Gold standard and well studied</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li> </ul> </td> </tr> <tr> <td><b>Methylated DNA enrichment</b></td> <td><span style="font-weight: 400;">(Hydroxy-)Methylated DNA is enriched by using specific antibodies (hMeDIP or MeDIP) or proteins (MBD) that specifically bind methylated CpG sites in fragmented genomic DNA.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Resolution depends on the fragment size of the enriched methylated DNA (300 bp)</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Qualitative analysis</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li> </ul> </td> </tr> <tr> <td><strong>Restriction enzyme-based digestion</strong></td> <td><span style="font-weight: 400;">Use of (hydroxy)methylation-sensitive or (hydroxy)methylation-dependent restriction enzymes for DNA methylation analysis at specific sites.</span></td> <td> <ul style="list-style-type: circle;"> <li style="font-weight: 400;"><span style="font-weight: 400;">Determination of methylation status is limited by the enzyme recognition site</span></li> <li style="font-weight: 400;"><span style="font-weight: 400;">Easy to use</span></li> </ul> </td> </tr> </tbody> </table> </div> </div> <div class="row"></div> </div> </div> <div class="large-12 columns"></div> </div>', 'in_footer' => true, 'in_menu' => true, 'online' => true, 'tabular' => true, 'slug' => 'epigenetics-dna-methylation', 'meta_keywords' => 'Epigenetics, DNA Methylation,5-hmC monoclonal antibody,hMeDIP,Bisulfite conversion,Methylated DNA immunoprecipitation', 'meta_description' => 'Complete, optimized solutions for analyzing DNA methylation manually or on our automated system.', 'meta_title' => 'DNA Methylation - Bisulfite sequencing - Epigenetics | Diagenode', 'modified' => '2019-03-25 10:07:27', 'created' => '2015-05-03 13:47:53', 'ProductsApplication' => array( [maximum depth reached] ) ), (int) 1 => 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’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> & <strong>reproducible</strong> techniques</li> <li><i class="fa fa-arrow-circle-right"></i> <strong>NGS</strong> compatible</li> </ul> <h2></h2> </div> </div> <div id="gtx-trans" style="position: absolute; left: 17px; top: 652.938px;"> <div class="gtx-trans-icon"></div> </div>', 'in_footer' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'slug' => 'methylated-dna-immunoprecipitation', 'meta_keywords' => 'Methylated DNA immunoprecipitation,Epigenetic,DNA Methylation,qPCR,5 methylcytosine (5-mC)', 'meta_description' => 'Methylated DNA immunoprecipitation method is based on the affinity purification of methylated DNA using an antibody directed against 5 methylcytosine (5-mC). ', 'meta_title' => 'Methylated DNA immunoprecipitation(MeDIP) - Dna methylation | Diagenode', 'modified' => '2021-08-19 12:08:03', 'created' => '2014-09-14 05:33:34', 'ProductsApplication' => array( [maximum depth reached] ) ) ), 'Category' => array( (int) 0 => array( 'id' => '55', 'position' => '5', 'parent_id' => '12', 'name' => 'DNA methylation standard', 'description' => '', 'no_promo' => false, 'in_menu' => false, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'dna-methylation-standard', 'cookies_tag_id' => null, 'meta_keywords' => 'DNA methylation standard,hydroxymethylated ,5-hmC,5-mC.', 'meta_description' => 'Diagenode Offers Unmethylated, Methylated and Hydroxymethylated Standards for Monitoring of DNA Methylation Assays.', 'meta_title' => 'DNA Methylation Standard | Diagenode', 'modified' => '2019-07-03 10:43:22', 'created' => '2015-07-08 09:53:00', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ), (int) 1 => array( 'id' => '51', 'position' => '11', 'parent_id' => '12', 'name' => 'Hydroxymethylated DNA immunoprecipitation', 'description' => '<p></p> <div class="row"> <div class="large-12 columns">The hydroxymethylated DNA IP (hMeDIP) is based on the affinity purification of methylated DNA using an antibody directed against 5-hydroxymethylcytosine (5-hmC). <h3>How it works</h3> In brief, hydroxymethyl DNA IP is performed as follows: starting from sheared genomic DNA from cultured cells or tissues, the immunoselection and immunoprecipitation can take place using the antibody directed against 5-hydroxymethylcytosine and antibody binding beads. After isolation and purification is performed, the IP’d hydroxymethylated DNA is ready for any subsequent analysis as qPCR, amplification, hybridization on microarrays or Next Generation Sequencing. <h3>Overview</h3> <p class="text-center"><img src="https://www.diagenode.com/img/applications/magnetic_medip_overview.jpg" caption="false" width="726" height="916" /></p> </div> </div>', 'no_promo' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'hydroxymethylated-dna-immunoprecipitation', 'cookies_tag_id' => null, 'meta_keywords' => 'Hydroxymethylated DNA Immunoprecipitation,DNA methylation', 'meta_description' => 'Diagenode Offers Antibody-Based Isolation of Hydroxymethylated DNA for DNA Methylation Studies', 'meta_title' => 'Hydroxymethylated DNA Immunoprecipitation for DNA Methylation Studies | Diagenode', 'modified' => '2022-10-06 15:25:37', 'created' => '2015-07-08 09:24:17', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ) ), 'Document' => array( (int) 0 => array( 'id' => '1125', 'name' => 'Datasheet DNA hydroxymethylation control package', 'description' => '', 'image_id' => null, 'type' => 'Datasheet', 'url' => 'files/products/kits/Datasheet_DNA-hydroxymethylation-control-package.pdf', 'slug' => 'datasheet-dna-hydroxymethylation-control-package', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2021-01-18 16:08:24', 'created' => '2021-01-18 16:08:24', 'ProductsDocument' => array( [maximum depth reached] ) ) ), 'Feature' => array(), 'Image' => array( (int) 0 => array( 'id' => '1778', 'name' => 'product/kits/methyl-kit-icon.png', 'alt' => 'Methylation kit icon', 'modified' => '2019-04-23 15:17:01', 'created' => '2018-03-15 15:52:12', 'ProductsImage' => array( [maximum depth reached] ) ) ), 'Promotion' => array(), 'Protocol' => array(), 'Publication' => array( (int) 0 => array( 'id' => '4055', 'name' => '5-Hydroxymethylation highlights the heterogeneity in keratinization andcell junctions in head and neck cancers.', 'authors' => 'Liu, Siyu and de Medeiros, Marcell Costa and Fernandez, Evan M and Zarins,Katie R and Cavalcante, Raymond G and Qin, Tingting and Wolf, Gregory T andFigueroa, Maria E and D'Silva, Nisha J and Rozek, Laura S and Sartor,Maureen A', 'description' => '<p>BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, with human papillomavirus (HPV)-related HNSCC rising to concerning levels. Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS: We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION: Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.</p>', 'date' => '2020-11-01', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33203436', 'doi' => '10.1186/s13148-020-00965-8', 'modified' => '2021-02-19 17:15:37', 'created' => '2021-02-18 10:21:53', 'ProductsPublication' => array( [maximum depth reached] ) ) ), 'Testimonial' => array(), 'Area' => array(), 'SafetySheet' => array() ) $country = 'US' $countries_allowed = array( (int) 0 => 'CA', (int) 1 => 'US', (int) 2 => 'IE', (int) 3 => 'GB', (int) 4 => 'DK', (int) 5 => 'NO', (int) 6 => 'SE', (int) 7 => 'FI', (int) 8 => 'NL', (int) 9 => 'BE', (int) 10 => 'LU', (int) 11 => 'FR', (int) 12 => 'DE', (int) 13 => 'CH', (int) 14 => 'AT', (int) 15 => 'ES', (int) 16 => 'IT', (int) 17 => 'PT' ) $outsource = false $other_formats = array() $edit = '' $testimonials = '' $featured_testimonials = '' $related_products = '<li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns"><img src="/img/product/kits/methyl-kit-icon.png" alt="Methylation kit icon" class="th"/></a> </div> <div class="small-12 columns"> <div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px"> <span class="success label" style="">C02010031</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> <!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-1882" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog"> <form action="/en/carts/add/1882" id="CartAdd/1882Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="1882" id="CartProductId"/> <div class="row"> <div class="small-12 medium-12 large-12 columns"> <p>Add <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> hMeDIP kit x16 (monoclonal mouse antibody)</strong> to my shopping cart.</p> <div class="row"> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('hMeDIP kit x16 (monoclonal mouse antibody)', 'C02010031', '690', $('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">Checkout</button> </div> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('hMeDIP kit x16 (monoclonal mouse antibody)', 'C02010031', '690', $('#CartQuantity').val());" name="keepshop" id="keepshop" type="submit">Keep shopping</button> </div> </div> </div> </div> </form><a class="close-reveal-modal" aria-label="Close">×</a></div><!-- END: ADD TO CART MODAL --><a href="#" id="hmedip-kit-x16-monoclonal-mouse-antibody-16-rxns" data-reveal-id="cartModal-1882" class="" style="color:#B21329"><i class="fa fa-cart-plus"></i></a> </div> </div> <div class="small-12 columns" > <h6 style="height:60px">hMeDIP kit x16 (monoclonal mouse antibody)</h6> </div> </div> </li> <li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/mouse-gapdh-promoter-primer-pair-50-ul"><img src="/img/grey-logo.jpg" alt="default alt" class="th"/></a> </div> <div class="small-12 columns"> <div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px"> <span class="success label" style="">C17021045-50</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> <!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-2595" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog"> <form action="/en/carts/add/2595" id="CartAdd/2595Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="2595" id="CartProductId"/> <div class="row"> <div class="small-12 medium-12 large-12 columns"> <p>Add <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> Mouse GAPDH promoter primer pair</strong> to my shopping cart.</p> <div class="row"> <div class="small-6 medium-6 large-6 columns"> <button class="alert small button expand" onclick="$(this).addToCart('Mouse GAPDH promoter primer pair', 'C17021045-50', '35', $('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">Checkout</button> </div> <div class="small-6 medium-6 large-6 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SFI1 promoter primer pair', 'description' => '<p>The primer pair Cat. No. C17021046 is specific to SFI1 Centrin Binding Protein from mouse. SFI1 is a protein coding gene that has been identified as being hydroxymethylated using DNA immunoprecipitation assays (hMeDIP). 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Extensive clinical, genetic and epigenetic differences exist between HPV-associated HNSCC and HPV-negative HNSCC, which is often linked to tobacco use. However, 5-hydroxymethylation (5hmC), an oxidative derivative of DNA methylation and its heterogeneity among HNSCC subtypes, has not been studied. RESULTS: We characterized genome-wide 5hmC profiles in HNSCC by HPV status and subtype in 18 HPV(+) and 18 HPV(-) well-characterized tumors. Results showed significant genome-wide hyper-5hmC in HPV(-) tumors, with both promoter and enhancer 5hmC able to distinguish meaningful tumor subgroups. We identified specific genes whose differential expression by HPV status is driven by differential hydroxymethylation. CDKN2A (p16), used as a key biomarker for HPV status, exhibited the most extensive hyper-5hmC in HPV(+) tumors, while HPV(-) tumors showed hyper-5hmC in CDH13, TIMP2, MMP2 and other cancer-related genes. Among the previously reported two HPV(+) subtypes, IMU (stronger immune response) and KRT (more keratinization), the IMU subtype revealed hyper-5hmC and up-regulation of genes in cell migration, and hypo-5hmC with down-regulation in keratinization and cell junctions. We experimentally validated our key prediction of higher secreted and intracellular protein levels of the invasion gene MMP2 in HPV(-) oral cavity cell lines. CONCLUSION: Our results implicate 5hmC in driving differences in keratinization, cell junctions and other cancer-related processes among tumor subtypes. We conclude that 5hmC levels are critical for defining tumor characteristics and potentially used to define clinically meaningful cancer patient subgroups.</p>', 'date' => '2020-11-01', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33203436', 'doi' => '10.1186/s13148-020-00965-8', 'modified' => '2021-02-19 17:15:37', 'created' => '2021-02-18 10:21:53', 'ProductsPublication' => array( 'id' => '4968', 'product_id' => '3154', 'publication_id' => '4055' ) ) $externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/33203436" 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 ?? 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