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<li>Including control DNA and primers to <span>monitor the efficiency of the assay</span>
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'name' => 'Auto True MicroChIP kit',
'description' => '<p>The Auto True MicroChIP kit in combination with the <a href="../p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> allows for performing ChIP-seq on as few as 10,000 cells. This microChIP-seq assay has been validated with the new generation <a href="../p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star<sup>®</sup> Compact Automated Workstation</a>. Furthermore Diagenode's high quality ChIP-seq grade antibodies have been used.</p>
<div class="row">
<div class="small-12 medium-5 large-6 columns"><small style="color: #666;">Video article</small>
<div class="flex-video"><iframe width="420" height="315" style="float: left; margin-right: 20px;" src="//www.youtube.com/embed/JZC9ARbLh_U?rel=0" frameborder="0" allowfullscreen="allowfullscreen"></iframe></div>
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<h3>Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells</h3>
<p><a href="https://www.youtube.com/watch?v=JZC9ARbLh_U"><img src="https://www.diagenode.com/img/jove_logo.png" alt="Jove logo" border="0" width="100" height="58" /></a></p>
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<li><strong>Revolutionary:</strong> Only 10.000 cells needed for complete ChIP-seq procedure</li>
<li><strong>Reliable and accurate</strong> sequencing library preparation from just picogram inputs</li>
<li><strong>Validated on</strong> studies for histone marks and with the IP-Star<sup>®</sup> Compact Automated Platform</li>
</ul>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-histone-results.png" alt="ChIP on 10,000 cells" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>High efficiency ChIP on 10,000 cells</strong><br />ChIP efficiency on 10 000 cells. ChIP was performed on human Hela cells using the Diagenode antibodies H3K4me3 (Cat. No. pAb-003-050), H3K27ac (pAb-174-050), H3K9me3 (pAb-056-050) and H3K27me3 (pAb-069-050). Sheared chromatin from 10 000 cells and 0.1 µg (H3K27ac), 0.25 µg (H3K4me3 and H3K27me3) or 0.5 µg (H3K9me3) of the antibody were used per IP. Corresponding amount of IgG was used as control. Quantitative PCR was performed with primers for corresponding positive and negative loci. Figure shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-reliable-A.png" alt="ChIP amplification" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-reliable-B.png" alt="Match between True MicroChIP peaks and the reference dataset" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Reliable detection of enrichments in ChIP-seq</strong><br />A: ChIP has been peformed with H3K4me3 antibody, amplification of 17 pg of DNA ChIP'd from 10.000 cells and amplification of 35 pg of DNA ChIP'd from 100.000 cells (control experiment). The IP'd DNA was amplified and transformed into a sequencing-ready preparation for the Illumina plateform with the MicroPlex Library Preparation kit. The library was then analysed on an Illumina<sup>®</sup> Genome Analyzer. Cluster generation and sequencing were performed according to the manufacturer's instructions.<br />B: We observed a perfect match between the top 40% of True MicroChIP peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-result.png" alt="Cell lysis" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Hela cells were fixed with 1% formaldehyde (for 10 minutes at RT)</strong><br /> Cell lysis was performed using the Lysis Buffer tL1 of the Diagenode True MicroChIP kit. Samples corresponding to 10 000 cells are sheared during 5 rounds of 5 cycles of 30 seconds “ON” / 30 seconds “OFF” with the Bioruptor<sup>®</sup> Plus combined with the Bioruptor<sup>®</sup> Water cooler (Cat No. BioAcc-cool) at HIGH power setting (position H). For optimal results, samples are vortexed before and after performing 5 sonication cycles, followed by a short centrifugation at 4°C. 10 μl of DNA (equivalent to 60 000 cells) are analysed on a 1.5% agarose gel.</p>',
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'description' => '<p><strong>This product must be used with the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star Compact Automated System</a>.</strong></p>
<p>The DNA recovery after ChIP or MeDIP might be an issue for specific downstream applications (e.g. Next generation sequencing). Diagenode's IPure kit is the only DNA purification kit that is specifically optimized for extracting very low amounts of DNA after ChIP & MeDIP.</p>',
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'meta_title' => 'Auto IPure kit v2 x100',
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'meta_description' => 'Auto IPure kit v2 x100',
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'description' => '<p>The Auto MethylCap kit allows to specifically capture DNA fragments containing methylated CpGs. The assay is based on the affinity purification of methylated DNA using methyl-CpG-binding domain (MBD) of human MeCP2 protein. This procedure has been optimized to perform automated immunoprecipitation of chromatin using the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star® Compact Automated System</a> enabling highly reproducible results and allowing for high throughput.</p>',
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<li><strong>Fast & sensitive capture</strong> of methylated DNA</li>
<li><strong>High capture efficiency</strong></li>
<li><strong>Differential fractionation</strong> of methylated DNA by CpG density (3 eluted fractions)</li>
<li><strong>Automation compatibility</strong><strong></strong>
<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>F</strong><strong>igure 1.</strong><span> </span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
</li>
</ul>',
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'search_order' => '04-undefined',
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'slug' => 'auto-methylcap-kit-x48-48-rxns',
'meta_title' => 'Auto MethylCap kit x48',
'meta_keywords' => '',
'meta_description' => 'Auto MethylCap kit x48',
'modified' => '2020-09-17 13:33:12',
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'name' => 'Auto Premium Bisulfite kit',
'description' => '<p>Diagenode's Premium Bisulfite Kit rapidly converts DNA through bisulfite treatment. Our conversion reagent is added directly to DNA, requires no intermediate steps, and results in high yields of DNA ready for downstream analysis methods including PCR and Next-Generation Sequencing.</p>',
'label1' => 'Characteristics',
'info1' => '<p><strong>Bisulfite Conversion efficiency in TERTBS1 and CTS56 genomic regions.</strong></p>
<p>The figure shows the conversion efficiency in TERTBS1 and CTS56 genomic regions when using 1 μg, 500ng and 100 ng of genomic DNA. Between 1 and 5 clones were analyzed for the different amounts of genomic DNA</p>
<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
'label2' => '',
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'format' => '40 rxns',
'catalog_number' => 'C02030031',
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'sf_code' => 'C02030031-',
'type' => 'REF',
'search_order' => '04-undefined',
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'price_GBP' => '230',
'price_JPY' => '39945',
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'price_AUD' => '600',
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'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>
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</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>
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<div class="small-12 medium-3 large-3 columns"><center><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank"><img src="https://www.diagenode.com/img/banners/banner-nature-publication-580.png" /></a></center></div>
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<h3>Sensitive tumour detection and classification using plasma cell-free DNA methylomes<br /><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank">Read the publication</a></h3>
<h3 class="c-article-title u-h1" data-test="article-title" itemprop="name headline">Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA<br /><a href="https://www.nature.com/articles/s41596-019-0202-2" target="_blank" title="cfMeDIP-seq Nature Method">Read the method</a></h3>
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<div class="large-12 columns"><span>The Methylated DNA Immunoprecipitation is based on the affinity purification of methylated and hydroxymethylated DNA using, respectively, an antibody directed against 5-methylcytosine (5-mC) in the case of MeDIP or 5-hydroxymethylcytosine (5-hmC) in the case of hMeDIP.</span><br />
<h2></h2>
<h2>How it works</h2>
<p>In brief, Methyl DNA IP is performed as follows: Genomic DNA from cultured cells or tissues is prepared, sheared, and then denatured. Then, immunoselection and immunoprecipitation can take place using the antibody directed against 5 methylcytosine and antibody binding beads. After isolation and purification is performed, the IP’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>
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<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>
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<p><span>The Auto hMeDIP kits allow you to perform DNA hydroxymethylation analysis of your sample together with optimized internal IP control. Performing hydroxymethylation profiling with the Auto hMeDIP kit is FAST, RELIABLE and HIGHLY SPECIFIC. </span></p>
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'name' => 'Exclusive Highly Specific Kits Antibodies for DNA HydroxyMethylation Studies',
'description' => '<p>Cytosine hydroxymethylation was recently discovered as an important epigenetic mechanism. This cytosine base modification results from the enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC) by the TET family of oxygenases. Though the precise role of 5-hmC is the subject of intense research and debate, early studies strongly indicate that it is also involved in gene regulation and in numerous important biological processes including embryonic development, cellular differentiation, stem cell reprogramming and carcinogenesis.</p>
<p>The study of 5-hmC has long been limited due to the lack of high quality, validated tools and technologies that discriminate hydroxymethylation from methylation in regulating gene expression. The use of highly specific antibodies against 5-hmC for the immunoprecipitation of hydroxymethylated DNA offers a reliable solution for hydroxymethylation profiling.</p>
<p></p>',
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'name' => 'Epigenetic remodelling of enhancers in response to estrogen deprivationand re-stimulation.',
'authors' => 'Sklias Athena et al.',
'description' => '<p>Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterize the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression, and more specifically of TET2 demethylase that may be involved in the DNA hypermethylation following short-term E2 deprivation. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER connection mainly with two partner TF families, AP-1 and FOX. These interactions take place in the proximity of E2 deprivation-mediated differentially methylated and histone acetylated enhancers. Finally, while most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation, DNA hypermethylation and H3K27 deacetylation at certain enhancers were partially retained. Overall, these results show that inactivation of ER mediates rapid and mostly reversible epigenetic changes at enhancers, and bring new insight into early events, which may ultimately lead to endocrine resistance.</p>',
'date' => '2021-09-01',
'pmid' => 'https://doi.org/10.1093%2Fnar%2Fgkab697',
'doi' => '10.1093/nar/gkab697',
'modified' => '2022-06-22 09:25:09',
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'name' => 'Involvement of Epigenetic Modifications of GABAergic Interneurons in Basolateral Amygdala in Anxiety-like Phenotype of Prenatally Stressed Mice.',
'authors' => 'Zhu C, Liang M, Li Y, Feng X, Hong J, Zhou R',
'description' => '<p>Background: Prenatal stress is considered a risk factor for anxiety disorder. Downregulation in the expression of GABAergic gene, that is, glutamic acid decarboxylase 67, associated with DNA methyltransferase overexpression in GABAergic neurons has been regarded as a characteristic component of anxiety disorder. Prenatal stress has an adverse effect on the development of the basolateral amygdala, which is a key region in anxiety regulation. The aim of this study is to analyze the possibility of epigenetic alterations of GABAergic neurons in the basolateral amygdala participating in prenatal stress-induced anxiety. Methods: Behavioral tests were used to explore the prenatal stress-induced anxiety behaviors of female adult mice. Real-time RT-PCR, western blot, chromatin immunoprecipitation, and electrophysiological analysis were employed to detect epigenetic changes of GABAergic system in the basolateral amygdala. Results: Prenatal stress mice developed an anxiety-like phenotype accompanied by a significant increase of DNA methyltransferase 1 and a reduced expression of glutamic acid decarboxylase 67 in the basolateral amygdala. Prenatal stress mice also showed the increased binding of DNA methyltransferase 1 and methyl CpG binding protein 2 to glutamic acid decarboxylase 67 promoter region. The decrease of glutamic acid decarboxylase 67 transcript was paralleled by an enrichment of 5-methylcytosine in glutamic acid decarboxylase 67 promoter regions. Electrophysiological study revealed the increase of postsynaptic neuronal excitability in the cortical-basolateral amygdala synaptic transmission of prenatal stress mice. 5-Aza-deoxycytidine treatment restored the increased synaptic transmission and anxiety-like behaviors in prenatal stress mice via improving GABAergic system. Conclusion: The above results suggest that DNA epigenetic modifications of GABAergic interneurons in the basolateral amygdala participate in the etiology of anxiety-like phenotype in prenatal stress mice.</p>',
'date' => '2018-06-01',
'pmid' => 'http://www.pubmed.gov/29471396',
'doi' => '10.1093/ijnp/pyy006',
'modified' => '2019-02-15 20:59:33',
'created' => '2019-02-14 15:01:22',
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'name' => 'TET-Catalyzed 5-Hydroxymethylation Precedes HNF4A Promoter Choice during Differentiation of Bipotent Liver Progenitors',
'authors' => 'Ancey P.B. et al.',
'description' => '<p>Understanding the processes that govern liver progenitor cell differentiation has important implications for the design of strategies targeting chronic liver diseases, whereby regeneration of liver tissue is critical. Although DNA methylation (5mC) and hydroxymethylation (5hmC) are highly dynamic during early embryonic development, less is known about their roles at later stages of differentiation. Using an in vitro model of hepatocyte differentiation, we show here that 5hmC precedes the expression of promoter 1 (P1)-dependent isoforms of HNF4A, a master transcription factor of hepatocyte identity. 5hmC and HNF4A expression from P1 are dependent on ten-eleven translocation (TET) dioxygenases. In turn, the liver pioneer factor FOXA2 is necessary for TET1 binding to the P1 locus. Both FOXA2 and TETs are required for the 5hmC-related switch in HNF4A expression. The epigenetic event identified here may be a key step for the establishment of the hepatocyte program by HNF4A.</p>',
'date' => '2017-07-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28648900',
'doi' => '',
'modified' => '2017-08-28 10:24:16',
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'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
'date' => '2017-06-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/',
'doi' => '',
'modified' => '2018-02-15 10:35:55',
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<p>将 <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> Auto Premium Bisulfite kit</strong> 添加至我的购物车。</p>
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<h6 style="height:60px">Auto Premium Bisulfite kit</h6>
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'description' => '<p>Cytosine hydroxymethylation was recently discovered as an important epigenetic mechanism. This cytosine base modification results from the enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC) by the TET family of oxygenases. Though the precise role of 5-hmC is the subject of intense research and debate, early studies strongly indicate that it is also involved in gene regulation and in numerous important biological processes including embryonic development, cellular differentiation, stem cell reprogramming and carcinogenesis.</p>
<p>The study of 5-hmC has long been limited due to the lack of high quality, validated tools and technologies that discriminate hydroxymethylation from methylation in regulating gene expression. The use of highly specific antibodies against 5-hmC for the immunoprecipitation of hydroxymethylated DNA offers a reliable solution for hydroxymethylation profiling.</p>
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<div class="small-12 medium-5 large-6 columns"><small style="color: #666;">Video article</small>
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<h3>Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells</h3>
<p><a href="https://www.youtube.com/watch?v=JZC9ARbLh_U"><img src="https://www.diagenode.com/img/jove_logo.png" alt="Jove logo" border="0" width="100" height="58" /></a></p>
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<li><strong>Revolutionary:</strong> Only 10.000 cells needed for complete ChIP-seq procedure</li>
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<li><strong>Validated on</strong> studies for histone marks and with the IP-Star<sup>®</sup> Compact Automated Platform</li>
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<p><strong>High efficiency ChIP on 10,000 cells</strong><br />ChIP efficiency on 10 000 cells. ChIP was performed on human Hela cells using the Diagenode antibodies H3K4me3 (Cat. No. pAb-003-050), H3K27ac (pAb-174-050), H3K9me3 (pAb-056-050) and H3K27me3 (pAb-069-050). Sheared chromatin from 10 000 cells and 0.1 µg (H3K27ac), 0.25 µg (H3K4me3 and H3K27me3) or 0.5 µg (H3K9me3) of the antibody were used per IP. Corresponding amount of IgG was used as control. Quantitative PCR was performed with primers for corresponding positive and negative loci. Figure shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-reliable-A.png" alt="ChIP amplification" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-reliable-B.png" alt="Match between True MicroChIP peaks and the reference dataset" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Reliable detection of enrichments in ChIP-seq</strong><br />A: ChIP has been peformed with H3K4me3 antibody, amplification of 17 pg of DNA ChIP'd from 10.000 cells and amplification of 35 pg of DNA ChIP'd from 100.000 cells (control experiment). The IP'd DNA was amplified and transformed into a sequencing-ready preparation for the Illumina plateform with the MicroPlex Library Preparation kit. The library was then analysed on an Illumina<sup>®</sup> Genome Analyzer. Cluster generation and sequencing were performed according to the manufacturer's instructions.<br />B: We observed a perfect match between the top 40% of True MicroChIP peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-result.png" alt="Cell lysis" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Hela cells were fixed with 1% formaldehyde (for 10 minutes at RT)</strong><br /> Cell lysis was performed using the Lysis Buffer tL1 of the Diagenode True MicroChIP kit. Samples corresponding to 10 000 cells are sheared during 5 rounds of 5 cycles of 30 seconds “ON” / 30 seconds “OFF” with the Bioruptor<sup>®</sup> Plus combined with the Bioruptor<sup>®</sup> Water cooler (Cat No. BioAcc-cool) at HIGH power setting (position H). For optimal results, samples are vortexed before and after performing 5 sonication cycles, followed by a short centrifugation at 4°C. 10 μl of DNA (equivalent to 60 000 cells) are analysed on a 1.5% agarose gel.</p>',
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'name' => 'Auto MethylCap kit',
'description' => '<p>The Auto MethylCap kit allows to specifically capture DNA fragments containing methylated CpGs. The assay is based on the affinity purification of methylated DNA using methyl-CpG-binding domain (MBD) of human MeCP2 protein. This procedure has been optimized to perform automated immunoprecipitation of chromatin using the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star® Compact Automated System</a> enabling highly reproducible results and allowing for high throughput.</p>',
'label1' => ' Characteristics',
'info1' => '<ul>
<li><strong>Fast & sensitive capture</strong> of methylated DNA</li>
<li><strong>High capture efficiency</strong></li>
<li><strong>Differential fractionation</strong> of methylated DNA by CpG density (3 eluted fractions)</li>
<li><strong>Automation compatibility</strong><strong></strong>
<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>F</strong><strong>igure 1.</strong><span> </span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
</li>
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'type' => 'RFR',
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'meta_title' => 'Auto MethylCap kit x48',
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'meta_description' => 'Auto MethylCap kit x48',
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'description' => '<p>Diagenode's Premium Bisulfite Kit rapidly converts DNA through bisulfite treatment. Our conversion reagent is added directly to DNA, requires no intermediate steps, and results in high yields of DNA ready for downstream analysis methods including PCR and Next-Generation Sequencing.</p>',
'label1' => 'Characteristics',
'info1' => '<p><strong>Bisulfite Conversion efficiency in TERTBS1 and CTS56 genomic regions.</strong></p>
<p>The figure shows the conversion efficiency in TERTBS1 and CTS56 genomic regions when using 1 μg, 500ng and 100 ng of genomic DNA. Between 1 and 5 clones were analyzed for the different amounts of genomic DNA</p>
<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
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'meta_title' => 'Auto Premium Bisulfite kit',
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'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>
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'meta_description' => 'Complete, optimized solutions for analyzing DNA methylation manually or on our automated system.',
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'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>
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<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>
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<p><span>The Auto hMeDIP kits allow you to perform DNA hydroxymethylation analysis of your sample together with optimized internal IP control. Performing hydroxymethylation profiling with the Auto hMeDIP kit is FAST, RELIABLE and HIGHLY SPECIFIC. </span></p>
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'name' => 'Exclusive Highly Specific Kits Antibodies for DNA HydroxyMethylation Studies',
'description' => '<p>Cytosine hydroxymethylation was recently discovered as an important epigenetic mechanism. This cytosine base modification results from the enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC) by the TET family of oxygenases. Though the precise role of 5-hmC is the subject of intense research and debate, early studies strongly indicate that it is also involved in gene regulation and in numerous important biological processes including embryonic development, cellular differentiation, stem cell reprogramming and carcinogenesis.</p>
<p>The study of 5-hmC has long been limited due to the lack of high quality, validated tools and technologies that discriminate hydroxymethylation from methylation in regulating gene expression. The use of highly specific antibodies against 5-hmC for the immunoprecipitation of hydroxymethylated DNA offers a reliable solution for hydroxymethylation profiling.</p>
<p></p>',
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'name' => 'Epigenetic remodelling of enhancers in response to estrogen deprivationand re-stimulation.',
'authors' => 'Sklias Athena et al.',
'description' => '<p>Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterize the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression, and more specifically of TET2 demethylase that may be involved in the DNA hypermethylation following short-term E2 deprivation. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER connection mainly with two partner TF families, AP-1 and FOX. These interactions take place in the proximity of E2 deprivation-mediated differentially methylated and histone acetylated enhancers. Finally, while most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation, DNA hypermethylation and H3K27 deacetylation at certain enhancers were partially retained. Overall, these results show that inactivation of ER mediates rapid and mostly reversible epigenetic changes at enhancers, and bring new insight into early events, which may ultimately lead to endocrine resistance.</p>',
'date' => '2021-09-01',
'pmid' => 'https://doi.org/10.1093%2Fnar%2Fgkab697',
'doi' => '10.1093/nar/gkab697',
'modified' => '2022-06-22 09:25:09',
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'name' => 'Involvement of Epigenetic Modifications of GABAergic Interneurons in Basolateral Amygdala in Anxiety-like Phenotype of Prenatally Stressed Mice.',
'authors' => 'Zhu C, Liang M, Li Y, Feng X, Hong J, Zhou R',
'description' => '<p>Background: Prenatal stress is considered a risk factor for anxiety disorder. Downregulation in the expression of GABAergic gene, that is, glutamic acid decarboxylase 67, associated with DNA methyltransferase overexpression in GABAergic neurons has been regarded as a characteristic component of anxiety disorder. Prenatal stress has an adverse effect on the development of the basolateral amygdala, which is a key region in anxiety regulation. The aim of this study is to analyze the possibility of epigenetic alterations of GABAergic neurons in the basolateral amygdala participating in prenatal stress-induced anxiety. Methods: Behavioral tests were used to explore the prenatal stress-induced anxiety behaviors of female adult mice. Real-time RT-PCR, western blot, chromatin immunoprecipitation, and electrophysiological analysis were employed to detect epigenetic changes of GABAergic system in the basolateral amygdala. Results: Prenatal stress mice developed an anxiety-like phenotype accompanied by a significant increase of DNA methyltransferase 1 and a reduced expression of glutamic acid decarboxylase 67 in the basolateral amygdala. Prenatal stress mice also showed the increased binding of DNA methyltransferase 1 and methyl CpG binding protein 2 to glutamic acid decarboxylase 67 promoter region. The decrease of glutamic acid decarboxylase 67 transcript was paralleled by an enrichment of 5-methylcytosine in glutamic acid decarboxylase 67 promoter regions. Electrophysiological study revealed the increase of postsynaptic neuronal excitability in the cortical-basolateral amygdala synaptic transmission of prenatal stress mice. 5-Aza-deoxycytidine treatment restored the increased synaptic transmission and anxiety-like behaviors in prenatal stress mice via improving GABAergic system. Conclusion: The above results suggest that DNA epigenetic modifications of GABAergic interneurons in the basolateral amygdala participate in the etiology of anxiety-like phenotype in prenatal stress mice.</p>',
'date' => '2018-06-01',
'pmid' => 'http://www.pubmed.gov/29471396',
'doi' => '10.1093/ijnp/pyy006',
'modified' => '2019-02-15 20:59:33',
'created' => '2019-02-14 15:01:22',
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'id' => '3236',
'name' => 'TET-Catalyzed 5-Hydroxymethylation Precedes HNF4A Promoter Choice during Differentiation of Bipotent Liver Progenitors',
'authors' => 'Ancey P.B. et al.',
'description' => '<p>Understanding the processes that govern liver progenitor cell differentiation has important implications for the design of strategies targeting chronic liver diseases, whereby regeneration of liver tissue is critical. Although DNA methylation (5mC) and hydroxymethylation (5hmC) are highly dynamic during early embryonic development, less is known about their roles at later stages of differentiation. Using an in vitro model of hepatocyte differentiation, we show here that 5hmC precedes the expression of promoter 1 (P1)-dependent isoforms of HNF4A, a master transcription factor of hepatocyte identity. 5hmC and HNF4A expression from P1 are dependent on ten-eleven translocation (TET) dioxygenases. In turn, the liver pioneer factor FOXA2 is necessary for TET1 binding to the P1 locus. Both FOXA2 and TETs are required for the 5hmC-related switch in HNF4A expression. The epigenetic event identified here may be a key step for the establishment of the hepatocyte program by HNF4A.</p>',
'date' => '2017-07-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28648900',
'doi' => '',
'modified' => '2017-08-28 10:24:16',
'created' => '2017-08-28 09:44:46',
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(int) 3 => array(
'id' => '3340',
'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
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'description' => '<p>This kit has been designed to perform Hydroxymethylated DNA Immunoprecipitation using an antibody against 5-hydroxymethylcytosine (5-hmC) on our Automated Systems. It includes control sequences (5-hmC, 5-mC and unmodified cytosine DNA standards) and control primer pairs (internal and external controls), to assess the efficiency of your immunoprecipitation.</p>',
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<li><span>Robust enrichment & immunoprecipitation of hydroxymethylated DNA</span></li>
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<li>Including control DNA and primers to <span>monitor the efficiency of the assay</span>
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<li>5-hmC, 5-mC and unmethylated DNA sequences and primer pairs</li>
<li>Mouse primer pairs against Sfi1 targeting hydroxymethylated gene in mouse</li>
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<li>Improved single-tube, magnetic bead-based protocol</li>
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'name' => 'Auto True MicroChIP kit',
'description' => '<p>The Auto True MicroChIP kit in combination with the <a href="../p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> allows for performing ChIP-seq on as few as 10,000 cells. This microChIP-seq assay has been validated with the new generation <a href="../p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star<sup>®</sup> Compact Automated Workstation</a>. Furthermore Diagenode's high quality ChIP-seq grade antibodies have been used.</p>
<div class="row">
<div class="small-12 medium-5 large-6 columns"><small style="color: #666;">Video article</small>
<div class="flex-video"><iframe width="420" height="315" style="float: left; margin-right: 20px;" src="//www.youtube.com/embed/JZC9ARbLh_U?rel=0" frameborder="0" allowfullscreen="allowfullscreen"></iframe></div>
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<div class="small-12 medium-7 large-6 columns">
<h3>Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells</h3>
<p><a href="https://www.youtube.com/watch?v=JZC9ARbLh_U"><img src="https://www.diagenode.com/img/jove_logo.png" alt="Jove logo" border="0" width="100" height="58" /></a></p>
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<li><strong>Revolutionary:</strong> Only 10.000 cells needed for complete ChIP-seq procedure</li>
<li><strong>Reliable and accurate</strong> sequencing library preparation from just picogram inputs</li>
<li><strong>Validated on</strong> studies for histone marks and with the IP-Star<sup>®</sup> Compact Automated Platform</li>
</ul>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-histone-results.png" alt="ChIP on 10,000 cells" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>High efficiency ChIP on 10,000 cells</strong><br />ChIP efficiency on 10 000 cells. ChIP was performed on human Hela cells using the Diagenode antibodies H3K4me3 (Cat. No. pAb-003-050), H3K27ac (pAb-174-050), H3K9me3 (pAb-056-050) and H3K27me3 (pAb-069-050). Sheared chromatin from 10 000 cells and 0.1 µg (H3K27ac), 0.25 µg (H3K4me3 and H3K27me3) or 0.5 µg (H3K9me3) of the antibody were used per IP. Corresponding amount of IgG was used as control. Quantitative PCR was performed with primers for corresponding positive and negative loci. Figure shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-reliable-A.png" alt="ChIP amplification" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-reliable-B.png" alt="Match between True MicroChIP peaks and the reference dataset" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Reliable detection of enrichments in ChIP-seq</strong><br />A: ChIP has been peformed with H3K4me3 antibody, amplification of 17 pg of DNA ChIP'd from 10.000 cells and amplification of 35 pg of DNA ChIP'd from 100.000 cells (control experiment). The IP'd DNA was amplified and transformed into a sequencing-ready preparation for the Illumina plateform with the MicroPlex Library Preparation kit. The library was then analysed on an Illumina<sup>®</sup> Genome Analyzer. Cluster generation and sequencing were performed according to the manufacturer's instructions.<br />B: We observed a perfect match between the top 40% of True MicroChIP peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-result.png" alt="Cell lysis" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Hela cells were fixed with 1% formaldehyde (for 10 minutes at RT)</strong><br /> Cell lysis was performed using the Lysis Buffer tL1 of the Diagenode True MicroChIP kit. Samples corresponding to 10 000 cells are sheared during 5 rounds of 5 cycles of 30 seconds “ON” / 30 seconds “OFF” with the Bioruptor<sup>®</sup> Plus combined with the Bioruptor<sup>®</sup> Water cooler (Cat No. BioAcc-cool) at HIGH power setting (position H). For optimal results, samples are vortexed before and after performing 5 sonication cycles, followed by a short centrifugation at 4°C. 10 μl of DNA (equivalent to 60 000 cells) are analysed on a 1.5% agarose gel.</p>',
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'meta_title' => 'Auto True MicroChIP kit',
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'name' => 'Auto IPure kit v2',
'description' => '<p><strong>This product must be used with the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star Compact Automated System</a>.</strong></p>
<p>The DNA recovery after ChIP or MeDIP might be an issue for specific downstream applications (e.g. Next generation sequencing). Diagenode's IPure kit is the only DNA purification kit that is specifically optimized for extracting very low amounts of DNA after ChIP & MeDIP.</p>',
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'sf_code' => 'C03010010-',
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'search_order' => '04-undefined',
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'slug' => 'auto-ipure-kit-v2-x100-100-rxns',
'meta_title' => 'Auto IPure kit v2 x100',
'meta_keywords' => '',
'meta_description' => 'Auto IPure kit v2 x100',
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'name' => 'Auto MethylCap kit',
'description' => '<p>The Auto MethylCap kit allows to specifically capture DNA fragments containing methylated CpGs. The assay is based on the affinity purification of methylated DNA using methyl-CpG-binding domain (MBD) of human MeCP2 protein. This procedure has been optimized to perform automated immunoprecipitation of chromatin using the <a href="https://www.diagenode.com/en/p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star® Compact Automated System</a> enabling highly reproducible results and allowing for high throughput.</p>',
'label1' => ' Characteristics',
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<li><strong>Fast & sensitive capture</strong> of methylated DNA</li>
<li><strong>High capture efficiency</strong></li>
<li><strong>Differential fractionation</strong> of methylated DNA by CpG density (3 eluted fractions)</li>
<li><strong>Automation compatibility</strong><strong></strong>
<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>F</strong><strong>igure 1.</strong><span> </span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
</li>
</ul>',
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'format' => '48 rxns',
'catalog_number' => 'C02020011',
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'price_EUR' => '740',
'price_USD' => '695',
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'slug' => 'auto-methylcap-kit-x48-48-rxns',
'meta_title' => 'Auto MethylCap kit x48',
'meta_keywords' => '',
'meta_description' => 'Auto MethylCap kit x48',
'modified' => '2020-09-17 13:33:12',
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'id' => '1893',
'antibody_id' => null,
'name' => 'Auto Premium Bisulfite kit',
'description' => '<p>Diagenode's Premium Bisulfite Kit rapidly converts DNA through bisulfite treatment. Our conversion reagent is added directly to DNA, requires no intermediate steps, and results in high yields of DNA ready for downstream analysis methods including PCR and Next-Generation Sequencing.</p>',
'label1' => 'Characteristics',
'info1' => '<p><strong>Bisulfite Conversion efficiency in TERTBS1 and CTS56 genomic regions.</strong></p>
<p>The figure shows the conversion efficiency in TERTBS1 and CTS56 genomic regions when using 1 μg, 500ng and 100 ng of genomic DNA. Between 1 and 5 clones were analyzed for the different amounts of genomic DNA</p>
<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
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'format' => '40 rxns',
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'price_USD' => '240',
'price_GBP' => '230',
'price_JPY' => '39945',
'price_CNY' => '',
'price_AUD' => '600',
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'slug' => 'auto-premium-bisulfite-kit-40-rxns',
'meta_title' => 'Auto Premium Bisulfite kit',
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'meta_description' => 'Auto Premium Bisulfite kit',
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'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>
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'meta_description' => 'Complete, optimized solutions for analyzing DNA methylation manually or on our automated system.',
'meta_title' => 'DNA Methylation - Bisulfite sequencing - Epigenetics | Diagenode',
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'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>
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'name' => 'Hydroxymethylated DNA immunoprecipitation',
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<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>
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'meta_description' => 'Diagenode Offers Antibody-Based Isolation of Hydroxymethylated DNA for DNA Methylation Studies',
'meta_title' => 'Hydroxymethylated DNA Immunoprecipitation for DNA Methylation Studies | Diagenode',
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<p><span>The Auto hMeDIP kits allow you to perform DNA hydroxymethylation analysis of your sample together with optimized internal IP control. Performing hydroxymethylation profiling with the Auto hMeDIP kit is FAST, RELIABLE and HIGHLY SPECIFIC. </span></p>
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'name' => 'Exclusive Highly Specific Kits Antibodies for DNA HydroxyMethylation Studies',
'description' => '<p>Cytosine hydroxymethylation was recently discovered as an important epigenetic mechanism. This cytosine base modification results from the enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC) by the TET family of oxygenases. Though the precise role of 5-hmC is the subject of intense research and debate, early studies strongly indicate that it is also involved in gene regulation and in numerous important biological processes including embryonic development, cellular differentiation, stem cell reprogramming and carcinogenesis.</p>
<p>The study of 5-hmC has long been limited due to the lack of high quality, validated tools and technologies that discriminate hydroxymethylation from methylation in regulating gene expression. The use of highly specific antibodies against 5-hmC for the immunoprecipitation of hydroxymethylated DNA offers a reliable solution for hydroxymethylation profiling.</p>
<p></p>',
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'name' => 'Epigenetic remodelling of enhancers in response to estrogen deprivationand re-stimulation.',
'authors' => 'Sklias Athena et al.',
'description' => '<p>Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterize the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression, and more specifically of TET2 demethylase that may be involved in the DNA hypermethylation following short-term E2 deprivation. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER connection mainly with two partner TF families, AP-1 and FOX. These interactions take place in the proximity of E2 deprivation-mediated differentially methylated and histone acetylated enhancers. Finally, while most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation, DNA hypermethylation and H3K27 deacetylation at certain enhancers were partially retained. Overall, these results show that inactivation of ER mediates rapid and mostly reversible epigenetic changes at enhancers, and bring new insight into early events, which may ultimately lead to endocrine resistance.</p>',
'date' => '2021-09-01',
'pmid' => 'https://doi.org/10.1093%2Fnar%2Fgkab697',
'doi' => '10.1093/nar/gkab697',
'modified' => '2022-06-22 09:25:09',
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'name' => 'Involvement of Epigenetic Modifications of GABAergic Interneurons in Basolateral Amygdala in Anxiety-like Phenotype of Prenatally Stressed Mice.',
'authors' => 'Zhu C, Liang M, Li Y, Feng X, Hong J, Zhou R',
'description' => '<p>Background: Prenatal stress is considered a risk factor for anxiety disorder. Downregulation in the expression of GABAergic gene, that is, glutamic acid decarboxylase 67, associated with DNA methyltransferase overexpression in GABAergic neurons has been regarded as a characteristic component of anxiety disorder. Prenatal stress has an adverse effect on the development of the basolateral amygdala, which is a key region in anxiety regulation. The aim of this study is to analyze the possibility of epigenetic alterations of GABAergic neurons in the basolateral amygdala participating in prenatal stress-induced anxiety. Methods: Behavioral tests were used to explore the prenatal stress-induced anxiety behaviors of female adult mice. Real-time RT-PCR, western blot, chromatin immunoprecipitation, and electrophysiological analysis were employed to detect epigenetic changes of GABAergic system in the basolateral amygdala. Results: Prenatal stress mice developed an anxiety-like phenotype accompanied by a significant increase of DNA methyltransferase 1 and a reduced expression of glutamic acid decarboxylase 67 in the basolateral amygdala. Prenatal stress mice also showed the increased binding of DNA methyltransferase 1 and methyl CpG binding protein 2 to glutamic acid decarboxylase 67 promoter region. The decrease of glutamic acid decarboxylase 67 transcript was paralleled by an enrichment of 5-methylcytosine in glutamic acid decarboxylase 67 promoter regions. Electrophysiological study revealed the increase of postsynaptic neuronal excitability in the cortical-basolateral amygdala synaptic transmission of prenatal stress mice. 5-Aza-deoxycytidine treatment restored the increased synaptic transmission and anxiety-like behaviors in prenatal stress mice via improving GABAergic system. Conclusion: The above results suggest that DNA epigenetic modifications of GABAergic interneurons in the basolateral amygdala participate in the etiology of anxiety-like phenotype in prenatal stress mice.</p>',
'date' => '2018-06-01',
'pmid' => 'http://www.pubmed.gov/29471396',
'doi' => '10.1093/ijnp/pyy006',
'modified' => '2019-02-15 20:59:33',
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'name' => 'TET-Catalyzed 5-Hydroxymethylation Precedes HNF4A Promoter Choice during Differentiation of Bipotent Liver Progenitors',
'authors' => 'Ancey P.B. et al.',
'description' => '<p>Understanding the processes that govern liver progenitor cell differentiation has important implications for the design of strategies targeting chronic liver diseases, whereby regeneration of liver tissue is critical. Although DNA methylation (5mC) and hydroxymethylation (5hmC) are highly dynamic during early embryonic development, less is known about their roles at later stages of differentiation. Using an in vitro model of hepatocyte differentiation, we show here that 5hmC precedes the expression of promoter 1 (P1)-dependent isoforms of HNF4A, a master transcription factor of hepatocyte identity. 5hmC and HNF4A expression from P1 are dependent on ten-eleven translocation (TET) dioxygenases. In turn, the liver pioneer factor FOXA2 is necessary for TET1 binding to the P1 locus. Both FOXA2 and TETs are required for the 5hmC-related switch in HNF4A expression. The epigenetic event identified here may be a key step for the establishment of the hepatocyte program by HNF4A.</p>',
'date' => '2017-07-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28648900',
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'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
'date' => '2017-06-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/',
'doi' => '',
'modified' => '2018-02-15 10:35:55',
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'name' => 'Exclusive Highly Specific Kits Antibodies for DNA HydroxyMethylation Studies',
'description' => '<p>Cytosine hydroxymethylation was recently discovered as an important epigenetic mechanism. This cytosine base modification results from the enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC) by the TET family of oxygenases. Though the precise role of 5-hmC is the subject of intense research and debate, early studies strongly indicate that it is also involved in gene regulation and in numerous important biological processes including embryonic development, cellular differentiation, stem cell reprogramming and carcinogenesis.</p>
<p>The study of 5-hmC has long been limited due to the lack of high quality, validated tools and technologies that discriminate hydroxymethylation from methylation in regulating gene expression. The use of highly specific antibodies against 5-hmC for the immunoprecipitation of hydroxymethylated DNA offers a reliable solution for hydroxymethylation profiling.</p>
<p></p>',
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'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
'date' => '2017-06-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/',
'doi' => '',
'modified' => '2018-02-15 10:35:55',
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'description' => '<p>The Auto True MicroChIP kit in combination with the <a href="../p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> allows for performing ChIP-seq on as few as 10,000 cells. This microChIP-seq assay has been validated with the new generation <a href="../p/sx-8g-ip-star-compact-automated-system-1-unit">IP-Star<sup>®</sup> Compact Automated Workstation</a>. Furthermore Diagenode's high quality ChIP-seq grade antibodies have been used.</p>
<div class="row">
<div class="small-12 medium-5 large-6 columns"><small style="color: #666;">Video article</small>
<div class="flex-video"><iframe width="420" height="315" style="float: left; margin-right: 20px;" src="//www.youtube.com/embed/JZC9ARbLh_U?rel=0" frameborder="0" allowfullscreen="allowfullscreen"></iframe></div>
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<h3>Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells</h3>
<p><a href="https://www.youtube.com/watch?v=JZC9ARbLh_U"><img src="https://www.diagenode.com/img/jove_logo.png" alt="Jove logo" border="0" width="100" height="58" /></a></p>
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<li><strong>Revolutionary:</strong> Only 10.000 cells needed for complete ChIP-seq procedure</li>
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<li><strong>Validated on</strong> studies for histone marks and with the IP-Star<sup>®</sup> Compact Automated Platform</li>
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<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-histone-results.png" alt="ChIP on 10,000 cells" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>High efficiency ChIP on 10,000 cells</strong><br />ChIP efficiency on 10 000 cells. ChIP was performed on human Hela cells using the Diagenode antibodies H3K4me3 (Cat. No. pAb-003-050), H3K27ac (pAb-174-050), H3K9me3 (pAb-056-050) and H3K27me3 (pAb-069-050). Sheared chromatin from 10 000 cells and 0.1 µg (H3K27ac), 0.25 µg (H3K4me3 and H3K27me3) or 0.5 µg (H3K9me3) of the antibody were used per IP. Corresponding amount of IgG was used as control. Quantitative PCR was performed with primers for corresponding positive and negative loci. Figure shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-reliable-A.png" alt="ChIP amplification" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-reliable-B.png" alt="Match between True MicroChIP peaks and the reference dataset" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Reliable detection of enrichments in ChIP-seq</strong><br />A: ChIP has been peformed with H3K4me3 antibody, amplification of 17 pg of DNA ChIP'd from 10.000 cells and amplification of 35 pg of DNA ChIP'd from 100.000 cells (control experiment). The IP'd DNA was amplified and transformed into a sequencing-ready preparation for the Illumina plateform with the MicroPlex Library Preparation kit. The library was then analysed on an Illumina<sup>®</sup> Genome Analyzer. Cluster generation and sequencing were performed according to the manufacturer's instructions.<br />B: We observed a perfect match between the top 40% of True MicroChIP peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>
<p><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-result.png" alt="Cell lysis" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Hela cells were fixed with 1% formaldehyde (for 10 minutes at RT)</strong><br /> Cell lysis was performed using the Lysis Buffer tL1 of the Diagenode True MicroChIP kit. Samples corresponding to 10 000 cells are sheared during 5 rounds of 5 cycles of 30 seconds “ON” / 30 seconds “OFF” with the Bioruptor<sup>®</sup> Plus combined with the Bioruptor<sup>®</sup> Water cooler (Cat No. BioAcc-cool) at HIGH power setting (position H). For optimal results, samples are vortexed before and after performing 5 sonication cycles, followed by a short centrifugation at 4°C. 10 μl of DNA (equivalent to 60 000 cells) are analysed on a 1.5% agarose gel.</p>',
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<p>The DNA recovery after ChIP or MeDIP might be an issue for specific downstream applications (e.g. Next generation sequencing). Diagenode's IPure kit is the only DNA purification kit that is specifically optimized for extracting very low amounts of DNA after ChIP & MeDIP.</p>',
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<li><strong>Automation compatibility</strong><strong></strong>
<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>F</strong><strong>igure 1.</strong><span> </span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
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'label1' => 'Characteristics',
'info1' => '<p><strong>Bisulfite Conversion efficiency in TERTBS1 and CTS56 genomic regions.</strong></p>
<p>The figure shows the conversion efficiency in TERTBS1 and CTS56 genomic regions when using 1 μg, 500ng and 100 ng of genomic DNA. Between 1 and 5 clones were analyzed for the different amounts of genomic DNA</p>
<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
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<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>
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<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>
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</li>
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<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>
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<td><strong>Bisulfite conversion</strong></td>
<td><span style="font-weight: 400;">Chemical conversion of unmethylated cytosine to uracil. Methylated cytosines are protected from this conversion allowing to determine DNA methylation at single nucleotide resolution.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Single nucleotide resolution</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Quantitative analysis - methylation rate (%)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Gold standard and well studied</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><b>Methylated DNA enrichment</b></td>
<td><span style="font-weight: 400;">(Hydroxy-)Methylated DNA is enriched by using specific antibodies (hMeDIP or MeDIP) or proteins (MBD) that specifically bind methylated CpG sites in fragmented genomic DNA.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Resolution depends on the fragment size of the enriched methylated DNA (300 bp)</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Qualitative analysis</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Compatible with automation</span></li>
</ul>
</td>
</tr>
<tr>
<td><strong>Restriction enzyme-based digestion</strong></td>
<td><span style="font-weight: 400;">Use of (hydroxy)methylation-sensitive or (hydroxy)methylation-dependent restriction enzymes for DNA methylation analysis at specific sites.</span></td>
<td>
<ul style="list-style-type: circle;">
<li style="font-weight: 400;"><span style="font-weight: 400;">Determination of methylation status is limited by the enzyme recognition site</span></li>
<li style="font-weight: 400;"><span style="font-weight: 400;">Easy to use</span></li>
</ul>
</td>
</tr>
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<div class="row"></div>
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<div class="small-12 medium-3 large-3 columns"><center><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank"><img src="https://www.diagenode.com/img/banners/banner-nature-publication-580.png" /></a></center></div>
<div class="small-12 medium-9 large-9 columns">
<h3>Sensitive tumour detection and classification using plasma cell-free DNA methylomes<br /><a href="https://www.ncbi.nlm.nih.gov/pubmed/30429608" target="_blank">Read the publication</a></h3>
<h3 class="c-article-title u-h1" data-test="article-title" itemprop="name headline">Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA<br /><a href="https://www.nature.com/articles/s41596-019-0202-2" target="_blank" title="cfMeDIP-seq Nature Method">Read the method</a></h3>
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<div class="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>
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<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>
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<p><span>The Auto hMeDIP kits allow you to perform DNA hydroxymethylation analysis of your sample together with optimized internal IP control. Performing hydroxymethylation profiling with the Auto hMeDIP kit is FAST, RELIABLE and HIGHLY SPECIFIC. </span></p>
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'description' => '<p>Cytosine hydroxymethylation was recently discovered as an important epigenetic mechanism. This cytosine base modification results from the enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC) by the TET family of oxygenases. Though the precise role of 5-hmC is the subject of intense research and debate, early studies strongly indicate that it is also involved in gene regulation and in numerous important biological processes including embryonic development, cellular differentiation, stem cell reprogramming and carcinogenesis.</p>
<p>The study of 5-hmC has long been limited due to the lack of high quality, validated tools and technologies that discriminate hydroxymethylation from methylation in regulating gene expression. The use of highly specific antibodies against 5-hmC for the immunoprecipitation of hydroxymethylated DNA offers a reliable solution for hydroxymethylation profiling.</p>
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'description' => '<p>Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER), the main nuclear factor mediating estrogen signaling, orchestrates a complex molecular circuitry that is not yet fully elucidated. Here, we investigated genome-wide DNA methylation, histone acetylation and transcription after estradiol (E2) deprivation and re-stimulation to better characterize the ability of ER to coordinate gene regulation. We found that E2 deprivation mostly resulted in DNA hypermethylation and histone deacetylation in enhancers. Transcriptome analysis revealed that E2 deprivation leads to a global down-regulation in gene expression, and more specifically of TET2 demethylase that may be involved in the DNA hypermethylation following short-term E2 deprivation. Further enrichment analysis of transcription factor (TF) binding and motif occurrence highlights the importance of ER connection mainly with two partner TF families, AP-1 and FOX. These interactions take place in the proximity of E2 deprivation-mediated differentially methylated and histone acetylated enhancers. Finally, while most deprivation-dependent epigenetic changes were reversed following E2 re-stimulation, DNA hypermethylation and H3K27 deacetylation at certain enhancers were partially retained. Overall, these results show that inactivation of ER mediates rapid and mostly reversible epigenetic changes at enhancers, and bring new insight into early events, which may ultimately lead to endocrine resistance.</p>',
'date' => '2021-09-01',
'pmid' => 'https://doi.org/10.1093%2Fnar%2Fgkab697',
'doi' => '10.1093/nar/gkab697',
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'name' => 'Involvement of Epigenetic Modifications of GABAergic Interneurons in Basolateral Amygdala in Anxiety-like Phenotype of Prenatally Stressed Mice.',
'authors' => 'Zhu C, Liang M, Li Y, Feng X, Hong J, Zhou R',
'description' => '<p>Background: Prenatal stress is considered a risk factor for anxiety disorder. Downregulation in the expression of GABAergic gene, that is, glutamic acid decarboxylase 67, associated with DNA methyltransferase overexpression in GABAergic neurons has been regarded as a characteristic component of anxiety disorder. Prenatal stress has an adverse effect on the development of the basolateral amygdala, which is a key region in anxiety regulation. The aim of this study is to analyze the possibility of epigenetic alterations of GABAergic neurons in the basolateral amygdala participating in prenatal stress-induced anxiety. Methods: Behavioral tests were used to explore the prenatal stress-induced anxiety behaviors of female adult mice. Real-time RT-PCR, western blot, chromatin immunoprecipitation, and electrophysiological analysis were employed to detect epigenetic changes of GABAergic system in the basolateral amygdala. Results: Prenatal stress mice developed an anxiety-like phenotype accompanied by a significant increase of DNA methyltransferase 1 and a reduced expression of glutamic acid decarboxylase 67 in the basolateral amygdala. Prenatal stress mice also showed the increased binding of DNA methyltransferase 1 and methyl CpG binding protein 2 to glutamic acid decarboxylase 67 promoter region. The decrease of glutamic acid decarboxylase 67 transcript was paralleled by an enrichment of 5-methylcytosine in glutamic acid decarboxylase 67 promoter regions. Electrophysiological study revealed the increase of postsynaptic neuronal excitability in the cortical-basolateral amygdala synaptic transmission of prenatal stress mice. 5-Aza-deoxycytidine treatment restored the increased synaptic transmission and anxiety-like behaviors in prenatal stress mice via improving GABAergic system. Conclusion: The above results suggest that DNA epigenetic modifications of GABAergic interneurons in the basolateral amygdala participate in the etiology of anxiety-like phenotype in prenatal stress mice.</p>',
'date' => '2018-06-01',
'pmid' => 'http://www.pubmed.gov/29471396',
'doi' => '10.1093/ijnp/pyy006',
'modified' => '2019-02-15 20:59:33',
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'name' => 'TET-Catalyzed 5-Hydroxymethylation Precedes HNF4A Promoter Choice during Differentiation of Bipotent Liver Progenitors',
'authors' => 'Ancey P.B. et al.',
'description' => '<p>Understanding the processes that govern liver progenitor cell differentiation has important implications for the design of strategies targeting chronic liver diseases, whereby regeneration of liver tissue is critical. Although DNA methylation (5mC) and hydroxymethylation (5hmC) are highly dynamic during early embryonic development, less is known about their roles at later stages of differentiation. Using an in vitro model of hepatocyte differentiation, we show here that 5hmC precedes the expression of promoter 1 (P1)-dependent isoforms of HNF4A, a master transcription factor of hepatocyte identity. 5hmC and HNF4A expression from P1 are dependent on ten-eleven translocation (TET) dioxygenases. In turn, the liver pioneer factor FOXA2 is necessary for TET1 binding to the P1 locus. Both FOXA2 and TETs are required for the 5hmC-related switch in HNF4A expression. The epigenetic event identified here may be a key step for the establishment of the hepatocyte program by HNF4A.</p>',
'date' => '2017-07-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28648900',
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'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
'date' => '2017-06-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/',
'doi' => '',
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<div class="small-6 medium-6 large-6 columns">
<button class="alert small button expand" onclick="$(this).addToCart('Auto IPure kit v2',
'C03010010',
'410',
$('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">结账</button> </div>
<div class="small-6 medium-6 large-6 columns">
<button class="alert small button expand" onclick="$(this).addToCart('Auto IPure kit v2',
'C03010010',
'410',
$('#CartQuantity').val());" name="keepshop" id="keepshop" type="submit">继续购物</button> </div>
</div>
</div>
</div>
</form><a class="close-reveal-modal" aria-label="Close">×</a></div><!-- END: ADD TO CART MODAL --><a href="#" id="auto-ipure-kit-v2-x100-100-rxns" data-reveal-id="cartModal-1899" class="" style="color:#B21329"><i class="fa fa-cart-plus"></i></a>
</div>
</div>
<div class="small-12 columns" >
<h6 style="height:60px">Auto IPure kit v2</h6>
</div>
</div>
</li>
<li>
<div class="row">
<div class="small-12 columns">
<a href="/cn/p/auto-methylcap-kit-x48-48-rxns"><img src="/img/product/kits/methyl-kit-icon.png" alt="Methylation kit icon" class="th"/></a> </div>
<div class="small-12 columns">
<div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px">
<span class="success label" style="">C02020011</span>
</div>
<div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px">
<!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a-->
<!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-1888" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<form action="/cn/carts/add/1888" id="CartAdd/1888Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="1888" id="CartProductId"/>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p>将 <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> Auto MethylCap kit</strong> 添加至我的购物车。</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns">
<button class="alert small button expand" onclick="$(this).addToCart('Auto MethylCap kit',
'C02020011',
'695',
$('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">结账</button> </div>
<div class="small-6 medium-6 large-6 columns">
<button class="alert small button expand" onclick="$(this).addToCart('Auto MethylCap kit',
'C02020011',
'695',
$('#CartQuantity').val());" name="keepshop" id="keepshop" type="submit">继续购物</button> </div>
</div>
</div>
</div>
</form><a class="close-reveal-modal" aria-label="Close">×</a></div><!-- END: ADD TO CART MODAL --><a href="#" id="auto-methylcap-kit-x48-48-rxns" data-reveal-id="cartModal-1888" class="" style="color:#B21329"><i class="fa fa-cart-plus"></i></a>
</div>
</div>
<div class="small-12 columns" >
<h6 style="height:60px">Auto MethylCap kit</h6>
</div>
</div>
</li>
<li>
<div class="row">
<div class="small-12 columns">
<a href="/cn/p/auto-premium-bisulfite-kit-40-rxns"><img src="/img/product/kits/methyl-kit-icon.png" alt="Methylation kit icon" class="th"/></a> </div>
<div class="small-12 columns">
<div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px">
<span class="success label" style="">C02030031</span>
</div>
<div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px">
<!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a-->
<!-- BEGIN: ADD TO CART MODAL --><div id="cartModal-1893" class="reveal-modal small" data-reveal aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<form action="/cn/carts/add/1893" id="CartAdd/1893Form" method="post" accept-charset="utf-8"><div style="display:none;"><input type="hidden" name="_method" value="POST"/></div><input type="hidden" name="data[Cart][product_id]" value="1893" id="CartProductId"/>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p>将 <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> Auto Premium Bisulfite kit</strong> 添加至我的购物车。</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns">
<button class="alert small button expand" onclick="$(this).addToCart('Auto Premium Bisulfite kit',
'C02030031',
'240',
$('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">结账</button> </div>
<div class="small-6 medium-6 large-6 columns">
<button class="alert small button expand" onclick="$(this).addToCart('Auto Premium Bisulfite kit',
'C02030031',
'240',
$('#CartQuantity').val());" name="keepshop" id="keepshop" type="submit">继续购物</button> </div>
</div>
</div>
</div>
</form><a class="close-reveal-modal" aria-label="Close">×</a></div><!-- END: ADD TO CART MODAL --><a href="#" id="auto-premium-bisulfite-kit-40-rxns" data-reveal-id="cartModal-1893" class="" style="color:#B21329"><i class="fa fa-cart-plus"></i></a>
</div>
</div>
<div class="small-12 columns" >
<h6 style="height:60px">Auto Premium Bisulfite kit</h6>
</div>
</div>
</li>
'
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'info1' => '<p><strong>Bisulfite Conversion efficiency in TERTBS1 and CTS56 genomic regions.</strong></p>
<p>The figure shows the conversion efficiency in TERTBS1 and CTS56 genomic regions when using 1 μg, 500ng and 100 ng of genomic DNA. Between 1 and 5 clones were analyzed for the different amounts of genomic DNA</p>
<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
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'meta_description' => 'Auto Premium Bisulfite kit',
'modified' => '2019-12-16 10:05:26',
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'created' => '2018-03-15 15:52:12',
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[maximum depth reached]
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'name' => 'Exclusive Highly Specific Kits Antibodies for DNA HydroxyMethylation Studies',
'description' => '<p>Cytosine hydroxymethylation was recently discovered as an important epigenetic mechanism. This cytosine base modification results from the enzymatic conversion of 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC) by the TET family of oxygenases. Though the precise role of 5-hmC is the subject of intense research and debate, early studies strongly indicate that it is also involved in gene regulation and in numerous important biological processes including embryonic development, cellular differentiation, stem cell reprogramming and carcinogenesis.</p>
<p>The study of 5-hmC has long been limited due to the lack of high quality, validated tools and technologies that discriminate hydroxymethylation from methylation in regulating gene expression. The use of highly specific antibodies against 5-hmC for the immunoprecipitation of hydroxymethylated DNA offers a reliable solution for hydroxymethylation profiling.</p>
<p></p>',
'image_id' => null,
'type' => 'Poster',
'url' => 'files/posters/Exclusive_Highly_Specific_Kits_Antibodies_for_DNA_HydroxyMethylation_Studies_Poster.pdf',
'slug' => 'exclusive-highly-specific-kits-antibodies-for-dna-hydroxymethylation-studies-poster',
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'modified' => '2020-11-23 17:39:14',
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'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
'date' => '2017-06-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/',
'doi' => '',
'modified' => '2018-02-15 10:35:55',
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$externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/" 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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