FFPE DNA extraction protocol using the Bioruptor® The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, provid... | Download |
FFPE DNA extraction protocol using the Bioruptor® The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, provid... | Download |
FFPE DNA extraction kit manual - Bioruptor® Pico MANUAL The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions... | Download |
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Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples |
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Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p> <table style="width: 925px;"> <tbody> <tr valign="middle"> <td style="width: 213px;"></td> <td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td> <td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td> <td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td> <td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>SDS concentration</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">< 0.1%</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">0.2%</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">1%</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">0.5%</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Nuclei isolation</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">No</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">Yes</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">up to 25 g of tissue</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p> <p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p> <p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p> </td> <td style="text-align: center; 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These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s </span><span>FFPE DNA Extraction kit</span><span> is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><sup><span>®</span></sup><span> Pico. </span></p> </div> </div> </div> </div>', 'image_id' => null, 'type' => 'Manual', 'url' => 'files/products/kits/FFPE_DNA_extraction_kit_manual.pdf', 'slug' => 'ffpe-dna-extraction-kit-manual', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2015-07-27 14:43:15', 'created' => '2015-07-07 11:47:43', 'ProductsDocument' => array( [maximum depth reached] ) ) ), 'Feature' => array(), 'Image' => array(), 'Promotion' => array(), 'Protocol' => array( (int) 0 => array( 'id' => '10', 'name' => 'FFPE DNA extraction protocol using the Bioruptor®', 'description' => '<p><span>The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, providing an invaluable repository of information for genetic analysis. These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s FFPE DNA Extraction kit is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><span>®</span><span>. </span></p>', 'image_id' => '204', 'type' => 'Protocol', 'url' => 'files/protocols/FFPE_DNA_extraction_protocol.pdf', 'slug' => 'ffpe-dna-extraction-protocol', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2016-04-29 17:42:46', 'created' => '2015-07-20 10:35:07', 'ProductsProtocol' => array( [maximum depth reached] ) ) ), 'Publication' => array( (int) 0 => array( 'id' => '3108', 'name' => 'Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples', 'authors' => 'Bak S.T. et al.', 'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>', 'date' => '2016-12-19', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571', 'doi' => '', 'modified' => '2017-01-04 10:19:32', 'created' => '2017-01-04 10:19:32', 'ProductsPublication' => array( [maximum depth reached] ) ) ), 'Testimonial' => array(), 'Area' => array(), 'SafetySheet' => array() ) $country = 'US' $countries_allowed = array( (int) 0 => 'CA', (int) 1 => 'US', (int) 2 => 'IE', (int) 3 => 'GB', (int) 4 => 'DK', (int) 5 => 'NO', (int) 6 => 'SE', (int) 7 => 'FI', (int) 8 => 'NL', (int) 9 => 'BE', (int) 10 => 'LU', (int) 11 => 'FR', (int) 12 => 'DE', (int) 13 => 'CH', (int) 14 => 'AT', (int) 15 => 'ES', (int) 16 => 'IT', (int) 17 => 'PT' ) $outsource = false $other_formats = array() $edit = '' $testimonials = '' $featured_testimonials = '' $related_products = '<li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/bioruptor-pico-sonication-device"><img src="/img/product/shearing_technologies/bioruptor_pico.jpg" alt="Bioruptor pico next gen sequencing " 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="">B01060010</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> </div> </div> <div class="small-12 columns" > <h6 style="height:60px">Bioruptor® Pico sonication device</h6> </div> </div> </li> ' $related = array( 'id' => '1787', 'antibody_id' => null, 'name' => 'Bioruptor<sup>®</sup> Pico sonication device', 'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p> <p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p> <center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center> <p></p> <p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p> <p> <script>// <![CDATA[ (function(){var 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data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div>', 'label2' => 'Recommended settings for DNA shearing with Bioruptor® Pico', 'info2' => '<p>Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor® Pico</a></p> <p></p> <p> <script>// <![CDATA[ (function(){var qs,js,q,s,d=document,gi=d.getElementById,ce=d.createElement,gt=d.getElementsByTagName,id='typef_orm',b='https://s3-eu-west-1.amazonaws.com/share.typeform.com/';if(!gi.call(d,id)){js=ce.call(d,'script');js.id=id;js.src=b+'share.js';q=gt.call(d,'script')[0];q.parentNode.insertBefore(js,q)}id=id+'_';if(!gi.call(d,id)){qs=ce.call(d,'link');qs.rel='stylesheet';qs.id=id;qs.href=b+'share-button.css';s=gt.call(d,'head')[0];s.appendChild(qs,s)}})() // ]]></script> </p> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div 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Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p> <table style="width: 925px;"> <tbody> <tr valign="middle"> <td style="width: 213px;"></td> <td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td> <td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td> <td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td> <td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>SDS concentration</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">< 0.1%</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">0.2%</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">1%</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">0.5%</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Nuclei isolation</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">No</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">Yes</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">up to 25 g of tissue</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p> <p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p> <p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p> </td> </tr> </tbody> </table> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div 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11:01:33', 'created' => '2018-03-06 11:01:33', 'ProductsImage' => array( [maximum depth reached] ) ) ) ) $rrbs_service = array( (int) 0 => (int) 1894, (int) 1 => (int) 1895 ) $chipseq_service = array( (int) 0 => (int) 2683, (int) 1 => (int) 1835, (int) 2 => (int) 1836, (int) 3 => (int) 2684, (int) 4 => (int) 1838, (int) 5 => (int) 1839, (int) 6 => (int) 1856 ) $labelize = object(Closure) { } $old_catalog_number = '' $label = '<img src="/img/banners/banner-customizer-back.png" alt=""/>' $protocol = array( 'id' => '10', 'name' => 'FFPE DNA extraction protocol using the Bioruptor®', 'description' => '<p><span>The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, providing an invaluable repository of information for genetic analysis. These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s FFPE DNA Extraction kit is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><span>®</span><span>. </span></p>', 'image_id' => '204', 'type' => 'Protocol', 'url' => 'files/protocols/FFPE_DNA_extraction_protocol.pdf', 'slug' => 'ffpe-dna-extraction-protocol', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2016-04-29 17:42:46', 'created' => '2015-07-20 10:35:07', 'ProductsProtocol' => array( 'id' => '49', 'product_id' => '2619', 'protocol_id' => '10' ) ) $document = array( 'id' => '98', 'name' => 'FFPE DNA extraction kit manual - Bioruptor® Pico', 'description' => '<div class="page" title="Page 4"> <div class="section"> <div class="layoutArea"> <div class="column"> <p><span>The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, providing an invaluable repository of information for genetic analysis. These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s </span><span>FFPE DNA Extraction kit</span><span> is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><sup><span>®</span></sup><span> Pico. </span></p> </div> </div> </div> </div>', 'image_id' => null, 'type' => 'Manual', 'url' => 'files/products/kits/FFPE_DNA_extraction_kit_manual.pdf', 'slug' => 'ffpe-dna-extraction-kit-manual', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2015-07-27 14:43:15', 'created' => '2015-07-07 11:47:43', 'ProductsDocument' => array( 'id' => '290', 'product_id' => '2619', 'document_id' => '98' ) ) $publication = array( 'id' => '3108', 'name' => 'Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples', 'authors' => 'Bak S.T. et al.', 'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>', 'date' => '2016-12-19', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571', 'doi' => '', 'modified' => '2017-01-04 10:19:32', 'created' => '2017-01-04 10:19:32', 'ProductsPublication' => array( 'id' => '1820', 'product_id' => '2619', 'publication_id' => '3108' ) ) $externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/27995571" target="_blank"><i class="fa fa-external-link"></i></a>'include - APP/View/Products/view.ctp, line 755 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 ProductsController::slug() - APP/Controller/ProductsController.php, line 1052 ReflectionMethod::invokeArgs() - [internal], line ?? 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Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p> <table style="width: 925px;"> <tbody> <tr valign="middle"> <td style="width: 213px;"></td> <td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td> <td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td> <td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td> <td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>SDS concentration</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">< 0.1%</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">0.2%</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">1%</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">0.5%</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Nuclei isolation</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">No</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">Yes</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">up to 25 g of tissue</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p> <p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p> <p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p> </td> </tr> </tbody> </table> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div>', 'format' => '1 unit', 'catalog_number' => 'B01060010', 'old_catalog_number' => '', 'sf_code' => 'B01060010-', 'type' => 'ACC', 'search_order' => '00-Machine', 'price_EUR' => '22700', 'price_USD' => '26250', 'price_GBP' => '20150', 'price_JPY' => '3291500', 'price_CNY' => 'Discontinued', 'price_AUD' => '65625', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => true, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '0000-00-00', 'slug' => 'bioruptor-pico-sonication-device', 'meta_title' => 'Bioruptor® Pico sonication device for RNA,Chromatin and DNA shearing for Next-Generation-Sequencing | Diagenode', 'meta_keywords' => 'Bioruptor, sonication, Next-Generation-Sequencing,DNA shearing,Protein extraction', 'meta_description' => 'An all-in-one shearing system Ideal for DNA shearing for Next-Generation-Sequencing,Chromatin shearing,RNA shearing,Protein extraction from tissues and cells and FFPE DNA extraction', 'modified' => '2021-07-14 13:47:33', 'created' => '2015-06-29 14:08:20', 'ProductsRelated' => array( [maximum depth reached] ), 'Image' => array( [maximum depth reached] ) ) ), 'Application' => array(), 'Category' => array( (int) 0 => array( 'id' => '79', 'position' => '3', 'parent_id' => '14', 'name' => 'FFPE DNA Extraction', 'description' => '', 'no_promo' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'FFPE-DNA-Extraction', 'cookies_tag_id' => null, 'meta_keywords' => 'FFPE DNA Extraction, Bioruptor® sonication device ,Diagenode', 'meta_description' => 'Diagenode introduces FFPE DNA Extraction kit using Bioruptor® sonication device ', 'meta_title' => 'FFPE DNA Extraction | Diagenode', 'modified' => '2016-01-21 14:21:39', 'created' => '2015-09-16 22:14:30', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ) ), 'Document' => array( (int) 0 => array( 'id' => '98', 'name' => 'FFPE DNA extraction kit manual - Bioruptor® Pico', 'description' => '<div class="page" title="Page 4"> <div class="section"> <div class="layoutArea"> <div class="column"> <p><span>The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, providing an invaluable repository of information for genetic analysis. These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s </span><span>FFPE DNA Extraction kit</span><span> is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><sup><span>®</span></sup><span> Pico. </span></p> </div> </div> </div> </div>', 'image_id' => null, 'type' => 'Manual', 'url' => 'files/products/kits/FFPE_DNA_extraction_kit_manual.pdf', 'slug' => 'ffpe-dna-extraction-kit-manual', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2015-07-27 14:43:15', 'created' => '2015-07-07 11:47:43', 'ProductsDocument' => array( [maximum depth reached] ) ) ), 'Feature' => array(), 'Image' => array(), 'Promotion' => array(), 'Protocol' => array( (int) 0 => array( 'id' => '10', 'name' => 'FFPE DNA extraction protocol using the Bioruptor®', 'description' => '<p><span>The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, providing an invaluable repository of information for genetic analysis. These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s FFPE DNA Extraction kit is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><span>®</span><span>. </span></p>', 'image_id' => '204', 'type' => 'Protocol', 'url' => 'files/protocols/FFPE_DNA_extraction_protocol.pdf', 'slug' => 'ffpe-dna-extraction-protocol', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2016-04-29 17:42:46', 'created' => '2015-07-20 10:35:07', 'ProductsProtocol' => array( [maximum depth reached] ) ) ), 'Publication' => array( (int) 0 => array( 'id' => '3108', 'name' => 'Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples', 'authors' => 'Bak S.T. et al.', 'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>', 'date' => '2016-12-19', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571', 'doi' => '', 'modified' => '2017-01-04 10:19:32', 'created' => '2017-01-04 10:19:32', 'ProductsPublication' => array( [maximum depth reached] ) ) ), 'Testimonial' => array(), 'Area' => array(), 'SafetySheet' => array() ) $country = 'US' $countries_allowed = array( (int) 0 => 'CA', (int) 1 => 'US', (int) 2 => 'IE', (int) 3 => 'GB', (int) 4 => 'DK', (int) 5 => 'NO', (int) 6 => 'SE', (int) 7 => 'FI', (int) 8 => 'NL', (int) 9 => 'BE', (int) 10 => 'LU', (int) 11 => 'FR', (int) 12 => 'DE', (int) 13 => 'CH', (int) 14 => 'AT', (int) 15 => 'ES', (int) 16 => 'IT', (int) 17 => 'PT' ) $outsource = false $other_formats = array() $edit = '' $testimonials = '' $featured_testimonials = '' $related_products = '<li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/bioruptor-pico-sonication-device"><img src="/img/product/shearing_technologies/bioruptor_pico.jpg" alt="Bioruptor pico next gen sequencing " 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="">B01060010</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> </div> </div> <div class="small-12 columns" > <h6 style="height:60px">Bioruptor® Pico sonication device</h6> </div> </div> </li> ' $related = array( 'id' => '1787', 'antibody_id' => null, 'name' => 'Bioruptor<sup>®</sup> Pico sonication device', 'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p> <p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p> <center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center> <p></p> <p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p> <p> <script>// <![CDATA[ (function(){var 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data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div>', 'label2' => 'Recommended settings for DNA shearing with Bioruptor® Pico', 'info2' => '<p>Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor® Pico</a></p> <p></p> <p> <script>// <![CDATA[ (function(){var qs,js,q,s,d=document,gi=d.getElementById,ce=d.createElement,gt=d.getElementsByTagName,id='typef_orm',b='https://s3-eu-west-1.amazonaws.com/share.typeform.com/';if(!gi.call(d,id)){js=ce.call(d,'script');js.id=id;js.src=b+'share.js';q=gt.call(d,'script')[0];q.parentNode.insertBefore(js,q)}id=id+'_';if(!gi.call(d,id)){qs=ce.call(d,'link');qs.rel='stylesheet';qs.id=id;qs.href=b+'share-button.css';s=gt.call(d,'head')[0];s.appendChild(qs,s)}})() // ]]></script> </p> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div 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Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p> <table style="width: 925px;"> <tbody> <tr valign="middle"> <td style="width: 213px;"></td> <td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td> <td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td> <td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td> <td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>SDS concentration</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">< 0.1%</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">0.2%</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">1%</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">0.5%</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Nuclei isolation</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">No</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">Yes</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">up to 25 g of tissue</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p> <p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p> <p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p> </td> </tr> </tbody> </table> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div 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In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. 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Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p> <table style="width: 925px;"> <tbody> <tr valign="middle"> <td style="width: 213px;"></td> <td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td> <td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td> <td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td> <td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>SDS concentration</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">< 0.1%</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">0.2%</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">1%</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">0.5%</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Nuclei isolation</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">No</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">Yes</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">up to 25 g of tissue</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p> <p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p> <p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p> </td> </tr> </tbody> </table> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div>', 'format' => '1 unit', 'catalog_number' => 'B01060010', 'old_catalog_number' => '', 'sf_code' => 'B01060010-', 'type' => 'ACC', 'search_order' => '00-Machine', 'price_EUR' => '22700', 'price_USD' => '26250', 'price_GBP' => '20150', 'price_JPY' => '3291500', 'price_CNY' => 'Discontinued', 'price_AUD' => '65625', 'country' => 'ALL', 'except_countries' => 'None', 'quote' => false, 'in_stock' => true, 'featured' => false, 'no_promo' => false, 'online' => true, 'master' => true, 'last_datasheet_update' => '0000-00-00', 'slug' => 'bioruptor-pico-sonication-device', 'meta_title' => 'Bioruptor® Pico sonication device for RNA,Chromatin and DNA shearing for Next-Generation-Sequencing | Diagenode', 'meta_keywords' => 'Bioruptor, sonication, Next-Generation-Sequencing,DNA shearing,Protein extraction', 'meta_description' => 'An all-in-one shearing system Ideal for DNA shearing for Next-Generation-Sequencing,Chromatin shearing,RNA shearing,Protein extraction from tissues and cells and FFPE DNA extraction', 'modified' => '2021-07-14 13:47:33', 'created' => '2015-06-29 14:08:20', 'ProductsRelated' => array( [maximum depth reached] ), 'Image' => array( [maximum depth reached] ) ) ), 'Application' => array(), 'Category' => array( (int) 0 => array( 'id' => '79', 'position' => '3', 'parent_id' => '14', 'name' => 'FFPE DNA Extraction', 'description' => '', 'no_promo' => false, 'in_menu' => true, 'online' => true, 'tabular' => true, 'hide' => false, 'all_format' => false, 'is_antibody' => false, 'slug' => 'FFPE-DNA-Extraction', 'cookies_tag_id' => null, 'meta_keywords' => 'FFPE DNA Extraction, Bioruptor® sonication device ,Diagenode', 'meta_description' => 'Diagenode introduces FFPE DNA Extraction kit using Bioruptor® sonication device ', 'meta_title' => 'FFPE DNA Extraction | Diagenode', 'modified' => '2016-01-21 14:21:39', 'created' => '2015-09-16 22:14:30', 'ProductsCategory' => array( [maximum depth reached] ), 'CookiesTag' => array([maximum depth reached]) ) ), 'Document' => array( (int) 0 => array( 'id' => '98', 'name' => 'FFPE DNA extraction kit manual - Bioruptor® Pico', 'description' => '<div class="page" title="Page 4"> <div class="section"> <div class="layoutArea"> <div class="column"> <p><span>The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, providing an invaluable repository of information for genetic analysis. These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s </span><span>FFPE DNA Extraction kit</span><span> is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><sup><span>®</span></sup><span> Pico. </span></p> </div> </div> </div> </div>', 'image_id' => null, 'type' => 'Manual', 'url' => 'files/products/kits/FFPE_DNA_extraction_kit_manual.pdf', 'slug' => 'ffpe-dna-extraction-kit-manual', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2015-07-27 14:43:15', 'created' => '2015-07-07 11:47:43', 'ProductsDocument' => array( [maximum depth reached] ) ) ), 'Feature' => array(), 'Image' => array(), 'Promotion' => array(), 'Protocol' => array( (int) 0 => array( 'id' => '10', 'name' => 'FFPE DNA extraction protocol using the Bioruptor®', 'description' => '<p><span>The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, providing an invaluable repository of information for genetic analysis. These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s FFPE DNA Extraction kit is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><span>®</span><span>. </span></p>', 'image_id' => '204', 'type' => 'Protocol', 'url' => 'files/protocols/FFPE_DNA_extraction_protocol.pdf', 'slug' => 'ffpe-dna-extraction-protocol', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2016-04-29 17:42:46', 'created' => '2015-07-20 10:35:07', 'ProductsProtocol' => array( [maximum depth reached] ) ) ), 'Publication' => array( (int) 0 => array( 'id' => '3108', 'name' => 'Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples', 'authors' => 'Bak S.T. et al.', 'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>', 'date' => '2016-12-19', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571', 'doi' => '', 'modified' => '2017-01-04 10:19:32', 'created' => '2017-01-04 10:19:32', 'ProductsPublication' => array( [maximum depth reached] ) ) ), 'Testimonial' => array(), 'Area' => array(), 'SafetySheet' => array() ) $country = 'US' $countries_allowed = array( (int) 0 => 'CA', (int) 1 => 'US', (int) 2 => 'IE', (int) 3 => 'GB', (int) 4 => 'DK', (int) 5 => 'NO', (int) 6 => 'SE', (int) 7 => 'FI', (int) 8 => 'NL', (int) 9 => 'BE', (int) 10 => 'LU', (int) 11 => 'FR', (int) 12 => 'DE', (int) 13 => 'CH', (int) 14 => 'AT', (int) 15 => 'ES', (int) 16 => 'IT', (int) 17 => 'PT' ) $outsource = false $other_formats = array() $edit = '' $testimonials = '' $featured_testimonials = '' $related_products = '<li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/bioruptor-pico-sonication-device"><img src="/img/product/shearing_technologies/bioruptor_pico.jpg" alt="Bioruptor pico next gen sequencing " 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="">B01060010</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> </div> </div> <div class="small-12 columns" > <h6 style="height:60px">Bioruptor® Pico sonication device</h6> </div> </div> </li> ' $related = array( 'id' => '1787', 'antibody_id' => null, 'name' => 'Bioruptor<sup>®</sup> Pico sonication device', 'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p> <p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p> <center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center> <p></p> <p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p> <p> <script>// <![CDATA[ (function(){var 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Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. 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valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>SDS concentration</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">< 0.1%</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">0.2%</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">1%</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">0.5%</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Nuclei isolation</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">No</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">Yes</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">up to 25 g of tissue</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p> <p style="text-align: 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We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>', 'date' => '2016-12-19', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571', 'doi' => '', 'modified' => '2017-01-04 10:19:32', 'created' => '2017-01-04 10:19:32', 'ProductsPublication' => array( 'id' => '1820', 'product_id' => '2619', 'publication_id' => '3108' ) ) $externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/27995571" target="_blank"><i class="fa fa-external-link"></i></a>'include - APP/View/Products/view.ctp, line 755 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 ProductsController::slug() - APP/Controller/ProductsController.php, line 1052 ReflectionMethod::invokeArgs() - [internal], line ?? 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Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p> <table style="width: 925px;"> <tbody> <tr valign="middle"> <td style="width: 213px;"></td> <td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td> <td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td> <td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td> <td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>SDS concentration</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">< 0.1%</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">0.2%</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">1%</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">0.5%</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Nuclei isolation</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">No</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">Yes</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">up to 25 g of tissue</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p> <p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p> <p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p> </td> <td style="text-align: center; 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These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s FFPE DNA Extraction kit is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><span>®</span><span>. </span></p>', 'image_id' => '204', 'type' => 'Protocol', 'url' => 'files/protocols/FFPE_DNA_extraction_protocol.pdf', 'slug' => 'ffpe-dna-extraction-protocol', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2016-04-29 17:42:46', 'created' => '2015-07-20 10:35:07', 'ProductsProtocol' => array( [maximum depth reached] ) ) ), 'Publication' => array( (int) 0 => array( 'id' => '3108', 'name' => 'Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples', 'authors' => 'Bak S.T. et al.', 'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>', 'date' => '2016-12-19', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571', 'doi' => '', 'modified' => '2017-01-04 10:19:32', 'created' => '2017-01-04 10:19:32', 'ProductsPublication' => array( [maximum depth reached] ) ) ), 'Testimonial' => array(), 'Area' => array(), 'SafetySheet' => array() ) $country = 'US' $countries_allowed = array( (int) 0 => 'CA', (int) 1 => 'US', (int) 2 => 'IE', (int) 3 => 'GB', (int) 4 => 'DK', (int) 5 => 'NO', (int) 6 => 'SE', (int) 7 => 'FI', (int) 8 => 'NL', (int) 9 => 'BE', (int) 10 => 'LU', (int) 11 => 'FR', (int) 12 => 'DE', (int) 13 => 'CH', (int) 14 => 'AT', (int) 15 => 'ES', (int) 16 => 'IT', (int) 17 => 'PT' ) $outsource = false $other_formats = array() $edit = '' $testimonials = '' $featured_testimonials = '' $related_products = '<li> <div class="row"> <div class="small-12 columns"> <a href="/en/p/bioruptor-pico-sonication-device"><img src="/img/product/shearing_technologies/bioruptor_pico.jpg" alt="Bioruptor pico next gen sequencing " 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="">B01060010</span> </div> <div class="small-6 columns text-right" style="padding-left:0px;padding-right:0px;margin-top:-6px"> <!--a href="#" style="color:#B21329"><i class="fa fa-info-circle"></i></a--> </div> </div> <div class="small-12 columns" > <h6 style="height:60px">Bioruptor® Pico sonication device</h6> </div> </div> </li> ' $related = array( 'id' => '1787', 'antibody_id' => null, 'name' => 'Bioruptor<sup>®</sup> Pico sonication device', 'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p> <p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p> <center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center> <p></p> <p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p> <p> <script>// <![CDATA[ (function(){var 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id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" 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Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p> <table style="width: 925px;"> <tbody> <tr valign="middle"> <td style="width: 213px;"></td> <td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td> <td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td> <td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td> <td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>SDS concentration</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">< 0.1%</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">0.2%</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">1%</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">0.5%</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Nuclei isolation</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">Yes</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">No</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">Yes</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;">100 million cells</p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;">up to 25 g of tissue</p> </td> </tr> <tr style="background-color: #fff;" valign="middle"> <td style="width: 213px;"> <p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p> </td> <td style="text-align: center; width: 208px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p> <p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p> </td> <td style="text-align: center; width: 180px;"> <p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p> <p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p> </td> <td style="text-align: center; width: 154px;"> <p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p> </td> <td style="text-align: center; width: 155px;"> <p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p> </td> </tr> </tbody> </table> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div id="ConnectiveDocSignExtentionInstalled" data-extension-version="1.0.4"></div> <div 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These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s FFPE DNA Extraction kit is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><span>®</span><span>. </span></p>', 'image_id' => '204', 'type' => 'Protocol', 'url' => 'files/protocols/FFPE_DNA_extraction_protocol.pdf', 'slug' => 'ffpe-dna-extraction-protocol', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2016-04-29 17:42:46', 'created' => '2015-07-20 10:35:07', 'ProductsProtocol' => array( 'id' => '49', 'product_id' => '2619', 'protocol_id' => '10' ) ) $document = array( 'id' => '98', 'name' => 'FFPE DNA extraction kit manual - Bioruptor® Pico', 'description' => '<div class="page" title="Page 4"> <div class="section"> <div class="layoutArea"> <div class="column"> <p><span>The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, providing an invaluable repository of information for genetic analysis. These samples can be analyzed for a wealth of applications including biomarker discovery, drug development, and cancer research. </span><span>Diagenode’s </span><span>FFPE DNA Extraction kit</span><span> is optimized for the extraction of DNA from FFPE tissue sections in conjunction with the Bioruptor</span><sup><span>®</span></sup><span> Pico. </span></p> </div> </div> </div> </div>', 'image_id' => null, 'type' => 'Manual', 'url' => 'files/products/kits/FFPE_DNA_extraction_kit_manual.pdf', 'slug' => 'ffpe-dna-extraction-kit-manual', 'meta_keywords' => '', 'meta_description' => '', 'modified' => '2015-07-27 14:43:15', 'created' => '2015-07-07 11:47:43', 'ProductsDocument' => array( 'id' => '290', 'product_id' => '2619', 'document_id' => '98' ) ) $publication = array( 'id' => '3108', 'name' => 'Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples', 'authors' => 'Bak S.T. et al.', 'description' => '<p>We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.</p>', 'date' => '2016-12-19', 'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27995571', 'doi' => '', 'modified' => '2017-01-04 10:19:32', 'created' => '2017-01-04 10:19:32', 'ProductsPublication' => array( 'id' => '1820', 'product_id' => '2619', 'publication_id' => '3108' ) ) $externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/27995571" target="_blank"><i class="fa fa-external-link"></i></a>'include - APP/View/Products/view.ctp, line 755 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::render() - CORE/Cake/View/View.php, line 473 Controller::render() - CORE/Cake/Controller/Controller.php, line 963 ProductsController::slug() - APP/Controller/ProductsController.php, line 1052 ReflectionMethod::invokeArgs() - [internal], line ?? 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