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<center><img src="https://www.diagenode.com/img/product/data-mining-long.png" /></center>
<p></p>
<div id="paper" style="text-align: center;">
<h4><a href="https://www.youtube.com/watch?v=KXjnSHz3Jk8">Watch the webinar to gain insights on how data mining can be applied for epigenetics applications</a></h4>
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<div class="small-12 medium-12 large-12 columns">
<blockquote style="padding-bottom: 0;"><span class="label-green" style="margin-bottom: 16px; margin-left: -22px; font-size: 22px;">WHITE PAPERS</span>
<div id="portal" class="main-portal">
<div class="portal-inner"><nav class="portal-nav" style="text-align: left;">
<ul data-tab="" class="tips-menu">
<li><a href="#panel1" class="tips portal button">Smokers vs non-smokers </a></li>
<li><a href="#panel2" class="tips portal button">Breast cancer</a></li>
</ul>
</nav></div>
</div>
<div class="tabs-content">
<div class="content active" id="panel1">
<h3 style="margin-top: 0;">Powerful new insights with epigenetic data mining.<br /> A study to distinguish smokers from non-smokers using just one droplet of blood</h3>
<p>Next generation sequencing in combination with sophisticated bioinformatics technologies for genomic, transcriptomic and epigeneomic analyses have enormous potential to establish new biomarkers for disease diagnostics, enabling true precision medicine. Analyses of liquid biopsies to measure thousands of different data points simultaneously in easily accessible body fluids (e.g. blood, urine, and saliva) are extremely promising for such biomarker studies.<br />(...)</p>
<a href="https://www.diagenode.com/en/pages/form-bioinfo" class="alert small button" target="_blank">Read more</a></div>
<div class="content" id="panel2">
<h3 style="margin-top: 0;">Data mining on DNA methylation data in cancer samples<br />Distinguishing normal from breast cancer tissue</h3>
<p>Breast cancer is the most commonly occurring cancer in women and the second most common cancer overall.</p>
<p>One important aspect of cancer tissues it that they differ from normal tissues in their epigenetic make up, especially in the DNA methylation pattern. In normal cells methylation assures the proper regulation of gene expression and stable gene silencing. DNA methylation is associated with histone modifications, and the interplay of these epigenetic modifications is crucial to regulate the functioning of the genome by changing chromatin architecture.<br />(...)</p>
<a href="https://www.diagenode.com/en/pages/form-bioinfo?app_note=23" class="alert small button" target="_blank">Read more</a></div>
</div>
</blockquote>
</div>
</div>
<p>Diagenode's new data mining service utilizes methods at the frontier of machine learning, statistics, and database systems. This enhanced service supports new discoveries that were previously not possible by analyzing patterns in large data sets to give informative new insights.</p>
<p>If you have data from patient cohorts, single cell analyses or any other heterogeneous scenarios, our service team provides enhanced support with optimal data analysis using our latest data mining capabilities. Specifically, our team applies machine learning technologies to find previously undiscovered or unobvious relationships within and across datasets. This advanced technology allows discovery of informative features from mass data, essentially “finding a needle in a haystack.”</p>
<p>Diagenode utilizes multiple algorithms to achieve advanced data mining and uses the most optimal combination of algorithms specific to your data. Our goal is to build strong classifiers that separate data into two or more classes or groups depending on associated data.</p>
<p class="extra-spaced">Different and multiple -omics data classes can be mined simultaneously. Integration with phenotypic and/or clinical data is also possible. We offer data mining services for several data classes including:</p>
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<tbody>
<tr>
<td><strong>Epigenetic data</strong></td>
<td><strong>Transcriptomic data</strong></td>
</tr>
<tr>
<td>
<p>DNA Methylation (RRBS, WGBS, EPIC arrays)</p>
<p>ChIP-sequencing</p>
<p>ATAC-seq</p>
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<td>
<p>mRNA-sequencing</p>
<p>Small and long non coding RNA</p>
<p>Single-cell RNA-sequencing</p>
</td>
</tr>
</tbody>
</table>
<p></p>
<p><strong>Biological Interpretation</strong></p>
<p class="extra-spaced">Machine learning classifiers also mirror the underlying biological differences between classes and are used to uncover the molecular processes at work. In order to achieve this, we offer biological interpretation services and pathway mining analyses for your data.</p>
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<li>Initial feasibility report</li>
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<p></p>
<ol start="2">
<li><strong>Data Mining</strong></li>
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<p> </p>
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<p><a href="https://www.diagenode.com/en/categories/Services">Read about our wetlab services</a></p>
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'description' => '<p><strong>mRNA-seq</strong> is the method of choice to efficiently detect and precisely quantify coding RNAs present in a biological sample under specific circumstances. Accurate estimation of transcript abundance allows for differential expression analysis as well as the study of alternative splicing and discovery of new transcript isoforms.</p>
<p>Our Epigenomics Profiling Services assure a fully integrated service-workflow for generation of mRNA-seq libraries, multiplexed sequencing and data analysis. Serviced library preparation is based on specific poly A selection to produce Illumina compatible libraries enriched in mRNAs.</p>
<h2>High performance mRNA-seq</h2>
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<p><span><i class="fa fa-arrow-circle-right"></i> </span><a href="https://www.diagenode.com/en/categories/rna-seq-category">See our other RNA-seq Profiling Services</a></p>',
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<h2>What do we provide with the analysis?</h2>
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<h3 class="diacol" style="font-weight: 100;">Standard Analysis</h3>
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<div><center><img src="https://www.diagenode.com/img/product/services/RNA-theorie.png" /></center></div>
<p><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04544-3">MGcount</a>: Diagenode has developed a bioinformatics software for counting whole-transcriptome RNA-seq reads from one or more input alignment files. It is specially designed to incorporate multi-mapping and multi-overlapping reads in the quantification using a flexible methodology that is compatible with any biotype. At the end of its execution, it produces a count matrix, compatible with any downstream analysis.</p>
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<p>Our Epigenomics Profiling Services assure the sample preparation expertise and quality data that you seek. We provide epigenome-wide analyses for understanding epigenetic mechanisms, epigenetics-related drug discovery, transgenerational epigenetics studies, epigenetic biomarker identification (including epigenomic cancer biomarkers), and functional epigenomics. Diagenode offers expert epigenomics services that you can trust for chromatin, DNA, and RNA analysis. </p>
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<div class="small-12 medium-2 large-2 columns text-left"><img src="https://www.diagenode.com/img/logo-scientist-registered-supplier.png" /></div>
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<h3><span class="green">Chromatin</span> analysis</h3>
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<li>ChIP-seq analysis Histone modification</li>
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<li>Enhancer analysis</li>
<li>ChIP-seq analysis Transcription factor </li>
<li>(sc)ATAC-seq Chromatin accessibility</li>
<li>ChIP-seq Cas9 off-target</li>
<li>Customized NGS service</li>
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<p><i class="fa fa-arrow-circle-right"></i> <a href="../categories/chip-seq-service">Learn more</a></p>
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</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #474546;">
<h3><span class="darkgrey">DNA methylation</span> analysis</h3>
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<li>Reduced representation bisulfite sequencing (RRBS)</li>
<li>Whole genome bisulfite sequencing (WGBS)</li>
<li>Targeted methylation</li>
<li>MeDIP-seq/hMeDIP-seq</li>
<li>Infinium MethylationEPIC array </li>
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<p></p>
<p><i class="fa fa-arrow-circle-right"></i> <a href="../categories/dna-methylation-profiling-services">Learn more</a></p>
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<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #b11e33;">
<h3><span class="diacol"><g class="gr_ gr_44 gr-alert gr_spell gr_inline_cards gr_disable_anim_appear ContextualSpelling ins-del multiReplace" id="44" data-gr-id="44">RNA-seq</g></span> analysis</h3>
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<li><span style="display: inline !important; float: none; background-color: #f8f8f8; color: #333333; font-family: Helvetica,Arial,sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; -webkit-text-stroke-width: 0px; white-space: normal; word-spacing: 0px;">Gene expression profiling</span></li>
<li>mRNA<span style="display: inline !important; float: none; background-color: #f8f8f8; color: #333333; font-family: Helvetica,Arial,sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; -webkit-text-stroke-width: 0px; white-space: normal; word-spacing: 0px;"> analysis</span></li>
<li>Small non-coding RNA analysis</li>
<li><b></b>Whole transcriptome analysis<br /><br /><br /><br /><br /></li>
</ul>
<p><i class="fa fa-arrow-circle-right"></i> <a href="../categories/rna-seq-category">Learn more</a></p>
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<h2 style="text-align: center;"><a class="details radius small button" href="https://www.diagenode.com/en/documents/services-flyer">DOWNLOAD OUR FLYER</a></h2>
<h2>Why Diagenode</h2>
<ul>
<li><strong>Expertise and trust</strong>: Recognized epigenetics leader, official partner of <a href="http://www.blueprint-epigenome.eu/"><g class="gr_ gr_45 gr-alert gr_spell gr_inline_cards gr_disable_anim_appear ContextualSpelling ins-del multiReplace" id="45" data-gr-id="45">BLUEPRINT</g></a>, <a href="http://ihec-epigenomes.org/">IHEC</a> <g class="gr_ gr_46 gr-alert gr_gramm gr_inline_cards gr_disable_anim_appear Punctuation only-ins replaceWithoutSep" id="46" data-gr-id="46">and</g> <a href="https://www.faang.org/">FAANG</a></li>
<li><strong>Innovative technology</strong>: Utilization of the signature Bioruptor<sup>®</sup> sonication device for optimal chromatin and DNA shearing and the IP-Star<sup>®</sup> Automation device give reproducible and reliable optimization and results</li>
<li><strong>Quality</strong>: Multiple QC steps in all workflows and validated antibodies plus reagents deliver superior data</li>
<li><strong>Flexibility</strong>: Extensive range of sample species and sample origins</li>
<li><strong>Experience</strong> in epigenomics profiling for a wide range of applications and fields of interest</li>
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<div class="block-distri"><span class="label-green" style="margin-bottom: 16px; margin-left: -3px;">HUMAN</span><center><img width="260" height="259" alt="services chip-seq - human" src="https://www.diagenode.com/img/categories/services/services-humans.png" caption="false" /></center></div>
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<div class="block-distri"><span class="label-green" style="margin-bottom: 16px; margin-left: -3px;">ANIMALS</span><center><img width="260" height="259" alt="services chip-seq - animals" src="https://www.diagenode.com/img/categories/services/services-animals.png" caption="false" /></center></div>
</li>
<li>
<div class="block-distri"><span class="label-green" style="margin-bottom: 16px; margin-left: -3px;">PLANTS</span><center><img width="260" height="259" alt="services methylation-plant" src="https://www.diagenode.com/img/categories/services/services-plants.png" caption="false" /></center></div>
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<h2>12 years of expertise and trust in epigenetics</h2>
<ul>
<li><strong>End-to-end</strong> epigenetic service</li>
<li><strong>Collaborative</strong> and customized project design</li>
<li>Dedicated <strong>in-house expert</strong> for your project</li>
<li><strong>Integrative</strong> data analysis</li>
<li>Presentation-<strong>quality data</strong> and graphs</li>
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<p><br />RNA-seqは、ディープシーケンス技術をを用いて、RNAの全細胞含有量であるトランスクリプトームを検査する革新的な技術です。トランスクリプトームに関するデータを取得することで、ゲノム上の情報をその機能的なタンパク質発現と結び付けることができます。細胞の発達メカニズムと疾患に関連する修飾に優れた洞察を提供します。</p>
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<center><img src="https://www.diagenode.com/img/logo-scientist-registered-supplier.png" /></center></div>
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<p>当社Diagenodeのエピゲノミクスプロファイリングサービスは、次世代シーケンシング（NGS）を使用し、完全なトランスクリプトミクスプロファイリング解析に役立ちます。 トランスクリプトミクスプロファイリング解析の究極目標を目指す経験豊富な科学者チームにより設計されたRNA-seq実験では細心の注意を払いサンプル処理し、RNAライブラリー調製、高品質のデータを提供するお手伝いをします。 お客様との緊密なコミュニケーションをとりながら、当社のバイオインフォマティクス専門家が、標準およびカスタマイズされた解析、包括的なサービスを提供します。</p>
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<li><a href="https://www.diagenode.com/jp/pages/dplex">D-Plexテクノロジーの活用</a></li>
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<h3 class="text-left"><a href="https://www.diagenode.com/jp/p/rna-seq-services">長鎖ノンコーディングRNA解析を含む全トランスクリプトーム</a></h3>
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<h6 style="height:60px">Bioinformatics Data Mining Service</h6>
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<span class="success label" style="">G02120000</span>
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<h3>Get a quote</h3><p class="lead">You are about to request a quote for <strong>mRNA-seq Service</strong>. Fill out the form below and we will be in touch with you very soon.</p><p><small>All <span style="font-size:16px;color:red;">*</span> fields are mandatory</small></p>
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<h2>Your project</h2>
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<h4>Which services are you interested in?</h4>
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<span class="prefix">Sample species</span>
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<div class="small-12 medium-12 large-9 columns">
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<span class="prefix">Total number of samples (including replicates)</span>
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</div>
</div>
<div class="small-12 columns" >
<h6 style="height:60px">mRNA-seq Service</h6>
</div>
</div>
</li>
<li>
<div class="row">
<div class="small-12 columns">
<a href="/cn/p/small-rna-seq-services"><img src="/img/grey-logo.jpg" alt="default alt" class="th"/></a> </div>
<div class="small-12 columns">
<div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px">
<span class="success label" style="">G02130000</span>
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<div class="small-12 medium-12 large-12 columns">
<h3>Get a quote</h3><p class="lead">You are about to request a quote for <strong>Small RNA-seq Services</strong>. Fill out the form below and we will be in touch with you very soon.</p><p><small>All <span style="font-size:16px;color:red;">*</span> fields are mandatory</small></p>
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<option value="GD">Grenada</option>
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<option value="GT">Guatemala</option>
<option value="GG">Guernsey</option>
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</div>
</div>
<div class="small-12 columns" >
<h6 style="height:60px">Small RNA-seq Services</h6>
</div>
</div>
</li>
<li>
<div class="row">
<div class="small-12 columns">
<a href="/cn/p/rna-data-analysis"><img src="/img/grey-logo.jpg" alt="default alt" class="th"/></a> </div>
<div class="small-12 columns">
<div class="small-6 columns" style="padding-left:0px;padding-right:0px;margin-top:-6px;margin-left:-1px">
<span class="success label" style="">G02030005</span>
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<div class="small-12 medium-12 large-12 columns">
<h3>Get a quote</h3><p class="lead">You are about to request a quote for <strong>RNA Data Analysis</strong>. Fill out the form below and we will be in touch with you very soon.</p><p><small>All <span style="font-size:16px;color:red;">*</span> fields are mandatory</small></p>
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</div>
</div>
<div class="small-12 columns" >
<h6 style="height:60px">RNA Data Analysis</h6>
</div>
</div>
</li>
'
$related = array(
'id' => '3062',
'antibody_id' => null,
'name' => 'RNA Data Analysis',
'description' => '<p>Total RNA sequencing (RNA-Seq) detects both coding and noncoding RNAs and is typically used to measure gene and transcript abundance as well as to identify novel components of the transcriptome. Messenger RNA-Seq focuses on the quantification of gene expression, the identification of unknown transcripts, the discovery of alternative splicing and gene fusion events. And finally, small non-coding RNA sequencing (sncRNA-Seq) will detect small (<100 nucleotides long) RNAs that operate as key regulators in cellular processes.</p>
<div class="extra-spaced">
<h2>What do we provide with the analysis?</h2>
<p>This analysis provides information for either genes or isoforms with their expression levels.</p>
<h3 class="diacol" style="font-weight: 100;">Standard Analysis</h3>
<ul style="list-style-type: circle;">
<li>Summary statistics (total sequenced reads, total mapping reads, uniquely aligned reads, PCR duplicates, number of genes detected, average read density per gene, number of highly expressed genes, etc.)</li>
<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome or transcriptome (indexed bam files and bigwig files included)</li>
<li>Matrix with expression abundance obtained with specialized quantification tool MGCount (<a href="https://doi.org/10.1186/s12859-021-04544-3">software developed by Diagenode</a>). A table of MG communities linking each original feature in the GTF file with the resultant count matrix and metadata feature identifiers.</li>
</ul>
<h3 class="diacol" style="font-weight: 100;">Advanced Analysis</h3>
<ul style="list-style-type: circle;">
<li>Comparative analysis (also called differential analysis) aimed at finding differentially expressed genes (DEGs) between two groups of samples</li>
<li>Functional gene annotation</li>
<li>Gene ontology enrichment analysis on DEGs</li>
<li>Pathway enrichment analysis on DEGs (KEGG or DOSE for human samples)</li>
<li>Alternative splicing analysis</li>
<li>Gene fusion analysis</li>
<li>Novel transcript identification</li>
</ul>
<h3 class="diacol" style="font-weight: 100;">Customized Analysis</h3>
<p class="text-left">If you require a type of analysis that is not in the previous list, <a href="#" data-reveal-id="quoteModal-3062">please consult with our expert bioinformatics team</a>.</p>
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<div><center><img src="https://www.diagenode.com/img/product/services/RNA-theorie.png" /></center></div>
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<center><img src="https://www.diagenode.com/img/product/data-mining-long.png" /></center>
<p></p>
<div id="paper" style="text-align: center;">
<h4><a href="https://www.youtube.com/watch?v=KXjnSHz3Jk8">Watch the webinar to gain insights on how data mining can be applied for epigenetics applications</a></h4>
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<div class="small-12 medium-12 large-12 columns">
<blockquote style="padding-bottom: 0;"><span class="label-green" style="margin-bottom: 16px; margin-left: -22px; font-size: 22px;">WHITE PAPERS</span>
<div id="portal" class="main-portal">
<div class="portal-inner"><nav class="portal-nav" style="text-align: left;">
<ul data-tab="" class="tips-menu">
<li><a href="#panel1" class="tips portal button">Smokers vs non-smokers </a></li>
<li><a href="#panel2" class="tips portal button">Breast cancer</a></li>
</ul>
</nav></div>
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<div class="tabs-content">
<div class="content active" id="panel1">
<h3 style="margin-top: 0;">Powerful new insights with epigenetic data mining.<br /> A study to distinguish smokers from non-smokers using just one droplet of blood</h3>
<p>Next generation sequencing in combination with sophisticated bioinformatics technologies for genomic, transcriptomic and epigeneomic analyses have enormous potential to establish new biomarkers for disease diagnostics, enabling true precision medicine. Analyses of liquid biopsies to measure thousands of different data points simultaneously in easily accessible body fluids (e.g. blood, urine, and saliva) are extremely promising for such biomarker studies.<br />(...)</p>
<a href="https://www.diagenode.com/en/pages/form-bioinfo" class="alert small button" target="_blank">Read more</a></div>
<div class="content" id="panel2">
<h3 style="margin-top: 0;">Data mining on DNA methylation data in cancer samples<br />Distinguishing normal from breast cancer tissue</h3>
<p>Breast cancer is the most commonly occurring cancer in women and the second most common cancer overall.</p>
<p>One important aspect of cancer tissues it that they differ from normal tissues in their epigenetic make up, especially in the DNA methylation pattern. In normal cells methylation assures the proper regulation of gene expression and stable gene silencing. DNA methylation is associated with histone modifications, and the interplay of these epigenetic modifications is crucial to regulate the functioning of the genome by changing chromatin architecture.<br />(...)</p>
<a href="https://www.diagenode.com/en/pages/form-bioinfo?app_note=23" class="alert small button" target="_blank">Read more</a></div>
</div>
</blockquote>
</div>
</div>
<p>Diagenode's new data mining service utilizes methods at the frontier of machine learning, statistics, and database systems. This enhanced service supports new discoveries that were previously not possible by analyzing patterns in large data sets to give informative new insights.</p>
<p>If you have data from patient cohorts, single cell analyses or any other heterogeneous scenarios, our service team provides enhanced support with optimal data analysis using our latest data mining capabilities. Specifically, our team applies machine learning technologies to find previously undiscovered or unobvious relationships within and across datasets. This advanced technology allows discovery of informative features from mass data, essentially “finding a needle in a haystack.”</p>
<p>Diagenode utilizes multiple algorithms to achieve advanced data mining and uses the most optimal combination of algorithms specific to your data. Our goal is to build strong classifiers that separate data into two or more classes or groups depending on associated data.</p>
<p class="extra-spaced">Different and multiple -omics data classes can be mined simultaneously. Integration with phenotypic and/or clinical data is also possible. We offer data mining services for several data classes including:</p>
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<tbody>
<tr>
<td><strong>Epigenetic data</strong></td>
<td><strong>Transcriptomic data</strong></td>
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<tr>
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<p>DNA Methylation (RRBS, WGBS, EPIC arrays)</p>
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<p>ATAC-seq</p>
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<p>mRNA-sequencing</p>
<p>Small and long non coding RNA</p>
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</td>
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</tbody>
</table>
<p></p>
<p><strong>Biological Interpretation</strong></p>
<p class="extra-spaced">Machine learning classifiers also mirror the underlying biological differences between classes and are used to uncover the molecular processes at work. In order to achieve this, we offer biological interpretation services and pathway mining analyses for your data.</p>
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<p><a href="https://www.diagenode.com/en/categories/Services">Read about our wetlab services</a></p>
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'meta_title' => 'Bioinformatics Data Mining Service | Diagenode',
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'meta_description' => 'Diagenode Data Mining Services utilizes multiple algorithms to achieve advanced data mining and uses the most optimal combination of algorithms specific to your data.',
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'description' => '<p><strong>mRNA-seq</strong> is the method of choice to efficiently detect and precisely quantify coding RNAs present in a biological sample under specific circumstances. Accurate estimation of transcript abundance allows for differential expression analysis as well as the study of alternative splicing and discovery of new transcript isoforms.</p>
<p>Our Epigenomics Profiling Services assure a fully integrated service-workflow for generation of mRNA-seq libraries, multiplexed sequencing and data analysis. Serviced library preparation is based on specific poly A selection to produce Illumina compatible libraries enriched in mRNAs.</p>
<h2>High performance mRNA-seq</h2>
<ul class="square">
<li>Superior complexity and high transcript coverage</li>
<li>Accurate comparison of gene expression levels</li>
<li>Detection of novel transcripts and alternative splicing events</li>
<li>Suitable for a broad range of input amounts</li>
<li>Compatible with FFPE samples</li>
<li>Fast turnaround time (from 5 to 6 weeks)</li>
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<p><span><i class="fa fa-arrow-circle-right"></i> </span><a href="https://www.diagenode.com/en/categories/rna-seq-category">See our other RNA-seq Profiling Services</a></p>',
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<li><strong>Project size</strong>: minimum of 24 samples</li>
<li><strong>Sample type</strong>: total isolated RNA</li>
<li><strong>Required quantities</strong>: minimum 10 ng of total RNA</li>
<li><strong>Shipment conditions</strong>: shipped in 1.5 mL or 0.5 mL tubes on dry ice</li>
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<h3 class="green">What our service includes</h3>
<ol>
<li><strong>RNA quality control</strong></li>
<ul>
<li>Determination of RIN value (RNA integration number)</li>
<li>Measurement of RNA concentration</li>
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<li><strong>Library preparation</strong></li>
<ul>
<li>Poly-A selection</li>
<li>Stranded library construction</li>
<li>Quality control of libraries prior to sequencing</li>
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<li><strong>Sequencing on Illumina platforms</strong></li>
<ul>
<li>25-30 million raw reads per sample</li>
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<li><strong>Data analysis</strong> (optional for additional fee)</li>
<ul>
<li>Standard bioinformatic analysis</li>
<li>Advanced bioinformatic analysis</li>
<li>Data delivery of raw data and all generated files through fast and secure file transfer or hard drive upon request</li>
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'label3' => 'Bioinformatics Analysis',
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<h4 class="text-center"><strong>Standard bioinformatic analysis</strong><br /> (optional for additional fee)</h4>
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<td>
<h4 class="text-center"><strong>Advanced bioinformatic analysis</strong><br /> (optional for additional fee)</h4>
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<td style="vertical-align: top; padding-left: 20px;">
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<li>Demultiplexing, read quality control, trimming and filtering</li>
<li>Alignment to reference genome</li>
<li>Quantification of known transcripts</li>
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<br />
<p><em>Provided files:</em></p>
<ul>
<li>Report with sequencing statistics</li>
<li>Raw data in FASTQ format</li>
<li>FastQC report</li>
<li>Alignment in BAM format</li>
<li>Un-normalized read counts</li>
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<td style="vertical-align: top;">
<ul>
<li>Differential expression analysis</li>
<li>Gene ontology terms analysis</li>
<li>Pathway analysis</li>
<li>Alternative splicing analysis</li>
<li>Novel transcript identification</li>
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'meta_title' => 'mRNA-seq Service - Coding Transcriptome Analysis| Diagenode',
'meta_keywords' => '',
'meta_description' => 'mRNA-seq provides a complete view of the coding transcriptome. mRNA-Seq detects known and novel transcripts and measures transcript abundance for accurate, comprehensive analysis.',
'modified' => '2020-12-24 12:47:26',
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'name' => 'Small RNA-seq Service',
'description' => '<p><strong>Small RNA-seq</strong> is the method of choice to investigate the regulatory network of small non-coding RNAs (<200 nt length), including but not limited to miRNA transcripts. It utilizes the proprietary technology D-Plex which ensures realistic representation of diverse small non-coding RNA transcripts with minimized bias. This approach is optimal for finding biomarkers from known transcripts and discover new RNA features.</p>
<p>Our Epigenomics Profiling Services assure a fully integrated service-workflow for generation of small RNA-seq libraries, multiplexed sequencing and data analysis. Serviced library preparation is based on a template-switching technology to produce Illumina compatible libraries enriched with the large variety of small non-coding RNAs.</p>
<h2>High transcript diversity with small RNA-seq</h2>
<ul class="square">
<li>Realistic representation of all small non-coding RNAs</li>
<li>Detection of novel transcripts and differentially-expressed small RNAs</li>
<li>Investigation of post-transcriptional regulation of gene expression</li>
<li>Leveraging the <a href="https://www.diagenode.com/en/pages/dplex">D-Plex technology</a></li>
<li>Working with ultra-low RNA inputs</li>
<li>Compatible with biological fluids</li>
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<p><span><i class="fa fa-arrow-circle-right"></i> </span><a href="https://www.diagenode.com/en/categories/rna-seq-category">See our other RNA-seq Profiling Services</a></p>',
'label1' => 'Sample Requirements',
'info1' => '<div class="extra-spaced">
<ul>
<li><strong>Project size</strong>: no minimum</li>
<li><strong>Sample type</strong>: total isolated RNA or small enriched RNA</li>
<li><strong>Required quantities</strong>: minimum 100 pg of total RNA or 10 pg of small RNA</li>
<li><strong>Shipment conditions</strong>: shipped in 1.5 mL or 0.5 mL tubes on dry ice</li>
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'label2' => 'Services Workflow',
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<div class="extra-spaced">
<h3 class="green">What our service includes</h3>
<ol>
<li><strong>RNA quality control</strong></li>
<ul>
<li>Determination of RIN value (RNA integration number)</li>
<li>Measurement of RNA concentration</li>
</ul>
<li><strong>Library preparation</strong></li>
<ul>
<li>Capture and amplification by tailing and switching</li>
<li>Library construction</li>
<li>Quality control of libraries prior to sequencing</li>
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<li><strong>Sequencing on Illumina platforms</strong></li>
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<li>10-20 million raw reads per sample</li>
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<li><strong>Data analysis</strong> (optional for additional fee)</li>
<ul>
<li>Standard bioinformatic analysis</li>
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<li>Data delivery of raw data and all generated files through fast and secure file transfer or hard drive upon request</li>
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'label3' => 'Bioinformatics Analysis',
'info3' => '<table style="padding: 40px;">
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<td>
<h4 class="text-center"><strong>Standard bioinformatic analysis</strong><br /> (optional for additional fee)</h4>
</td>
<td>
<h4 class="text-center"><strong>Advanced bioinformatic analysis</strong><br /> (optional for additional fee)</h4>
</td>
</tr>
<tr>
<td style="vertical-align: top; padding-left: 20px;">
<ul>
<li>Demultiplexing, read quality control, trimming and filtering</li>
<li>Alignment to reference genome</li>
<li>Quantification of small RNA biotypes with specialized quantification tool MGCount (<a href="https://doi.org/10.1186/s12859-021-04544-3">software developed by Diagenode</a>)</li>
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<br />
<p><em>Provided files:</em></p>
<ul>
<li>Report with sequencing statistics</li>
<li>Raw data in FASTQ format</li>
<li>FastQC report</li>
<li>Alignment in BAM format</li>
<li>Un-normalized read counts</li>
</ul>
</td>
<td style="vertical-align: top;">
<ul>
<li>Differential expression analysis</li>
<li>Gene ontology terms analysis</li>
<li>Pathway analysis</li>
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</td>
</tr>
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'slug' => 'small-rna-seq-services',
'meta_title' => 'Small RNA-seq Service - Small RNA and miRNA profiling | Diagenode',
'meta_keywords' => '',
'meta_description' => 'Small RNA-seq enables small RNA discovery, mutation characterization, and expression profiling of small RNAs by leveraging of sequencing technologies and data analysis pipeline.',
'modified' => '2022-03-07 09:12:41',
'created' => '2020-07-13 11:09:54',
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'id' => '3062',
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'name' => 'RNA Data Analysis',
'description' => '<p>Total RNA sequencing (RNA-Seq) detects both coding and noncoding RNAs and is typically used to measure gene and transcript abundance as well as to identify novel components of the transcriptome. Messenger RNA-Seq focuses on the quantification of gene expression, the identification of unknown transcripts, the discovery of alternative splicing and gene fusion events. And finally, small non-coding RNA sequencing (sncRNA-Seq) will detect small (<100 nucleotides long) RNAs that operate as key regulators in cellular processes.</p>
<div class="extra-spaced">
<h2>What do we provide with the analysis?</h2>
<p>This analysis provides information for either genes or isoforms with their expression levels.</p>
<h3 class="diacol" style="font-weight: 100;">Standard Analysis</h3>
<ul style="list-style-type: circle;">
<li>Summary statistics (total sequenced reads, total mapping reads, uniquely aligned reads, PCR duplicates, number of genes detected, average read density per gene, number of highly expressed genes, etc.)</li>
<li>Trimmed and filtered reads in fastQ files after sequencing QC</li>
<li>BAM sorted files from alignment to reference genome or transcriptome (indexed bam files and bigwig files included)</li>
<li>Matrix with expression abundance obtained with specialized quantification tool MGCount (<a href="https://doi.org/10.1186/s12859-021-04544-3">software developed by Diagenode</a>). A table of MG communities linking each original feature in the GTF file with the resultant count matrix and metadata feature identifiers.</li>
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<h3 class="diacol" style="font-weight: 100;">Advanced Analysis</h3>
<ul style="list-style-type: circle;">
<li>Comparative analysis (also called differential analysis) aimed at finding differentially expressed genes (DEGs) between two groups of samples</li>
<li>Functional gene annotation</li>
<li>Gene ontology enrichment analysis on DEGs</li>
<li>Pathway enrichment analysis on DEGs (KEGG or DOSE for human samples)</li>
<li>Alternative splicing analysis</li>
<li>Gene fusion analysis</li>
<li>Novel transcript identification</li>
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<h3 class="diacol" style="font-weight: 100;">Customized Analysis</h3>
<p class="text-left">If you require a type of analysis that is not in the previous list, <a href="#" data-reveal-id="quoteModal-3062">please consult with our expert bioinformatics team</a>.</p>
</div>
<div><center><img src="https://www.diagenode.com/img/product/services/RNA-theorie.png" /></center></div>
<p><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04544-3">MGcount</a>: Diagenode has developed a bioinformatics software for counting whole-transcriptome RNA-seq reads from one or more input alignment files. It is specially designed to incorporate multi-mapping and multi-overlapping reads in the quantification using a flexible methodology that is compatible with any biotype. At the end of its execution, it produces a count matrix, compatible with any downstream analysis.</p>
<center><img src="https://www.diagenode.com/img/product/services/mGcount-img.png" width="600px" /></center>',
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'slug' => 'rna-data-analysis',
'meta_title' => 'RNA Data Analysis Services | Diagenode',
'meta_keywords' => '',
'meta_description' => 'RNA-seq data analysis service is made to extract information from a large variety of RNA-seq data (small RNA, mRNA and much more).',
'modified' => '2022-11-22 15:26:24',
'created' => '2020-03-26 10:04:58',
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(int) 0 => array(
'id' => '51',
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'name' => '小型RNAとmiRNA',
'description' => '<ul>
<li><span> </span>遺伝子発現の転写後調節</li>
<li><span> </span>新規転写物および差示的に発現される小RNA</li>
<li><span> </span>腫瘍抑制遺伝子発現の調節に関与するmiRNA</li>
<li><span> </span>差次的miRNA発現</li>
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'modified' => '2018-01-12 15:03:17',
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'description' => '<ul>
<li><span> </span>特異的ポリA選定で<span>タンパク質コーディング</span><span>RNA</span><span></span><span></span></li>
<li><span> </span>がん関連mRNAシグネチャー</li>
<li><span> </span>癌の病因における異常なmRNA転換</li>
<li><span> </span>遺伝子発現プロファイリングおよび示差的に発現される遺伝子の同定（DEG）</li>
<li><span> </span>遺伝子発現のエピジェネティックな機構（トランスクリプトーム+ H3K36me3およびH3K4me3標識）</li>
<li><span> </span>コーディング遺伝子の機能的アノテーション</li>
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'modified' => '2018-01-12 16:17:37',
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'description' => '<ul>
<li><span> </span>トランスクリプトーム配列決定：任意のrRNA<span>除去</span>を伴う200ntより大きい<span>RNA</span><span>および</span>全トランスクリプトーム<span></span><span></span>の分析</li>
<li><span> </span>クロマチンリモデリングおよび転写/転写後調節に関与する非タンパク質コードRNA</li>
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<p><span> </span></p>',
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'name' => 'Epigenomics Profiling Services',
'description' => '<div class="row">
<div class="small-12 medium-10 large-10 columns text-left">
<p>Our Epigenomics Profiling Services assure the sample preparation expertise and quality data that you seek. We provide epigenome-wide analyses for understanding epigenetic mechanisms, epigenetics-related drug discovery, transgenerational epigenetics studies, epigenetic biomarker identification (including epigenomic cancer biomarkers), and functional epigenomics. Diagenode offers expert epigenomics services that you can trust for chromatin, DNA, and RNA analysis. </p>
</div>
<div class="small-12 medium-2 large-2 columns text-left"><img src="https://www.diagenode.com/img/logo-scientist-registered-supplier.png" /></div>
</div>
<center><img alt="DNA-RNA-Chromatin-Diagenode" src="https://www.diagenode.com/img/categories/services/chromatin-dna-rna.png" /></center>
<div class="row">
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #099f92;">
<h3><span class="green">Chromatin</span> analysis</h3>
<ul>
<li>ChIP-seq analysis Histone modification</li>
<li>Promoter analysis</li>
<li>Enhancer analysis</li>
<li>ChIP-seq analysis Transcription factor </li>
<li>(sc)ATAC-seq Chromatin accessibility</li>
<li>ChIP-seq Cas9 off-target</li>
<li>Customized NGS service</li>
</ul>
<p><i class="fa fa-arrow-circle-right"></i> <a href="../categories/chip-seq-service">Learn more</a></p>
</div>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #474546;">
<h3><span class="darkgrey">DNA methylation</span> analysis</h3>
<ul>
<li>Reduced representation bisulfite sequencing (RRBS)</li>
<li>Whole genome bisulfite sequencing (WGBS)</li>
<li>Targeted methylation</li>
<li>MeDIP-seq/hMeDIP-seq</li>
<li>Infinium MethylationEPIC array </li>
</ul>
<p></p>
<p><i class="fa fa-arrow-circle-right"></i> <a href="../categories/dna-methylation-profiling-services">Learn more</a></p>
</div>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #b11e33;">
<h3><span class="diacol"><g class="gr_ gr_44 gr-alert gr_spell gr_inline_cards gr_disable_anim_appear ContextualSpelling ins-del multiReplace" id="44" data-gr-id="44">RNA-seq</g></span> analysis</h3>
<ul>
<li><span style="display: inline !important; float: none; background-color: #f8f8f8; color: #333333; font-family: Helvetica,Arial,sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; -webkit-text-stroke-width: 0px; white-space: normal; word-spacing: 0px;">Gene expression profiling</span></li>
<li>mRNA<span style="display: inline !important; float: none; background-color: #f8f8f8; color: #333333; font-family: Helvetica,Arial,sans-serif; font-size: 16px; font-style: normal; font-variant: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: left; text-decoration: none; text-indent: 0px; text-transform: none; -webkit-text-stroke-width: 0px; white-space: normal; word-spacing: 0px;"> analysis</span></li>
<li>Small non-coding RNA analysis</li>
<li><b></b>Whole transcriptome analysis<br /><br /><br /><br /><br /></li>
</ul>
<p><i class="fa fa-arrow-circle-right"></i> <a href="../categories/rna-seq-category">Learn more</a></p>
</div>
</div>
</div>
<h2 style="text-align: center;"><a class="details radius small button" href="https://www.diagenode.com/en/documents/services-flyer">DOWNLOAD OUR FLYER</a></h2>
<h2>Why Diagenode</h2>
<ul>
<li><strong>Expertise and trust</strong>: Recognized epigenetics leader, official partner of <a href="http://www.blueprint-epigenome.eu/"><g class="gr_ gr_45 gr-alert gr_spell gr_inline_cards gr_disable_anim_appear ContextualSpelling ins-del multiReplace" id="45" data-gr-id="45">BLUEPRINT</g></a>, <a href="http://ihec-epigenomes.org/">IHEC</a> <g class="gr_ gr_46 gr-alert gr_gramm gr_inline_cards gr_disable_anim_appear Punctuation only-ins replaceWithoutSep" id="46" data-gr-id="46">and</g> <a href="https://www.faang.org/">FAANG</a></li>
<li><strong>Innovative technology</strong>: Utilization of the signature Bioruptor<sup>®</sup> sonication device for optimal chromatin and DNA shearing and the IP-Star<sup>®</sup> Automation device give reproducible and reliable optimization and results</li>
<li><strong>Quality</strong>: Multiple QC steps in all workflows and validated antibodies plus reagents deliver superior data</li>
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<option value="TK">Tokelau</option>
<option value="TO">Tonga</option>
<option value="TT">Trinidad and Tobago</option>
<option value="TN">Tunisia</option>
<option value="TR">Turkey</option>
<option value="TM">Turkmenistan</option>
<option value="TC">Turks and Caicos Islands</option>
<option value="TV">Tuvalu</option>
<option value="UG">Uganda</option>
<option value="UA">Ukraine</option>
<option value="AE">United Arab Emirates</option>
<option value="GB">United Kingdom</option>
<option value="US" selected="selected">United States</option>
<option value="UM">United States Minor Outlying Islands</option>
<option value="UY">Uruguay</option>
<option value="UZ">Uzbekistan</option>
<option value="VU">Vanuatu</option>
<option value="VE">Venezuela</option>
<option value="VN">Viet Nam</option>
<option value="VG">Virgin Islands, British</option>
<option value="VI">Virgin Islands, U.S.</option>
<option value="WF">Wallis and Futuna</option>
<option value="EH">Western Sahara</option>
<option value="YE">Yemen</option>
<option value="ZM">Zambia</option>
<option value="ZW">Zimbabwe</option>
</select><script>
$('#country_selector_quote-3022').selectize();
</script><br />
</div>
</div>
<div class="row collapse">
<div class="small-3 large-2 columns">
<span class="prefix">State</span>
</div>
<div class="small-9 large-10 columns">
<input name="data[Quote][state]" id="state-3022" maxlength="3" type="text"/><br />
</div>
</div>
<div class="row collapse">
<div class="small-3 large-2 columns">
<span class="prefix">Email <sup style="font-size:16px;color:red;">*</sup></span>
</div>
<div class="small-9 large-10 columns">
<input name="data[Quote][email]" placeholder="email@address.com" maxlength="255" type="email" id="QuoteEmail" required="required"
