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<div class="small-12 medium-12 large-12 columns"><br /><br />
<p><span>The Bioruptor® uses a unique system to uniformely process multiple samples in sealed tubes of 0.5 ml to 50 ml capacity. The built-in cooling system (water cooler and Single Cycle Valve) ensures high precision temperature control resulting in higher quality samples. An excellent device for shearing chromatin, cell and tissue disruption and many other applications (see below).</span></p>
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<p></p>
<p><span></span></p>
<div class="page" title="Page 9">
<div class="section">
<div class="layoutArea">
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'label1' => 'Which Bioruptor® Plus configuration is right for you?',
'info1' => '<p><strong>B01020001</strong> - Bioruptor Plus<sup>®</sup> device with 1.5 ml (6 samples) tube holder <span>& temperature controlled system (water cooler + single cycle valve) </span><em>for recommended sample volume 100 µl - 300 µl</em></p>
<p><strong>B01020002</strong> - Bioruptor Plus<sup>®</sup> device with 1.5 ml (6 samples) and 15 ml tube holders <span>& temperature controlled system (water cooler + single cycle valve)</span> <em>for recommended sample volume 100 µl - 2 ml</em></p>
<p><strong>B01020003</strong> - Bioruptor Plus<sup>®</sup> device with 0.5 ml (12 samples) tube holder <span>& temperature controlled system (water cooler + single cycle valve)</span> <em>for recommended sample volume 50 µl - 100 µl </em></p>',
'label2' => 'Available chromatin shearing kits',
'info2' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. 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>
<tbody>
<tr valign="middle">
<td></td>
<td style="text-align: center;"><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;"><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;"><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;"><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>
<p style="text-align: left;"><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">< 0.1%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">0.2%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">1%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">0.5%</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">No</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">up to 25 g of tissue</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<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;">
<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;">
<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;">
<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>
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'info3' => '<h3>Shearing Accessories</h3>
<table style="width: 641px;">
<thead>
<tr style="background-color: #dddddd; height: 37px;">
<td style="width: 300px; height: 37px;"><strong>Name</strong></td>
<td style="width: 171px; text-align: center; height: 37px;">Catalog number</td>
<td style="width: 160px; text-align: center; height: 37px;">Throughput</td>
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<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/0-5-0-65-ml-tube-holder-for-bioruptor-standard-plus-pico-1-pack">0.5/0.65 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200043</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">12 samples</span></td>
</tr>
<tr style="height: 38px;">
<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/1-5-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">1.5 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200011</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 38px;">
<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/10-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">10 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200012</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-sonication-accessories-for-bioruptor-standard-plus-pico-1-pack">15 ml sonication accessories</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200016</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">15 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200013</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">6 samples</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/50-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">50 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200014</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">3 samples</span></td>
</tr>
</tbody>
</table>
<h3>Shearing Consumables</h3>
<table style="width: 646px;">
<thead>
<tr style="background-color: #dddddd; height: 37px;">
<td style="width: 286px; height: 37px;"><strong>Name</strong></td>
<td style="width: 76px; height: 37px; text-align: center;">Catalog Number</td>
</tr>
</thead>
<tbody>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/0-5-ml-bioruptor-microtubes-500-tubes">0.5 ml Bioruptor Plus Microtubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010013</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/1-5-ml-tpx-microtubes-300-pc">1.5 ml Bioruptor Plus TPX microtubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010010</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/10-ml-tubes-100-tubes">10 ml Bioruptor Plus tubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010012</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-tpx-tubes-50-pc">15 ml Bioruptor Plus TPX tubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010009</span></td>
</tr>
</tbody>
</table>
<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor_accessories/TDS-BioruptorTubes.pdf">Find datasheet for Diagenode tubes here</a></p>
<p><a href="../documents/bioruptor-organigram-tubes">Which tubes for which Bioruptor®?</a></p>',
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'description' => '<div class="row">
<div class="small-12 medium-12 large-12 columns">The most important steps for a successful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, <strong>Diagenode's Bioruptor</strong><sup>®</sup> uses state-of-the-art ultrasound <strong>ACT</strong> (<strong>A</strong>daptive <strong>C</strong>avitation <strong>T</strong>echnology) to efficiently shear chromatin. ACT enables the highest chromatin quality for high IP efficiency and sensitivity for ChIP experiments with gentle yet highly effective shearing forces. Additionally, the Bioruptor<sup>®</sup> provides a precisely controlled temperature environment that preserves chromatin from heat degradation such that protein-DNA complexes are well-preserved for sensitive, unbiased, and accurate ChIP.<br /><br /> <strong>Diagenode's Bioruptor</strong><sup>®</sup> is the instrument of choice for chromatin shearing used for a number of downstream applications such as qPCR and ChIP-seq that require optimally sheared, unbiased chromatin.</div>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/applications/pico_dna_shearing_fig2.png" /></div>
<div class="small-10 medium-10 large-10 columns end small-offset-1"><small> <br /><strong>Panel A, 10 µl volume:</strong> Chromatin samples are sheared for 10, 20 and 30 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.1 ml Bioruptor® Microtubes (Cat. No. B01200041). <strong>Panel B, 100 µl volume:</strong> Chromatin samples are sheared for 10 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.65 ml Bioruptor® Microtubes (Cat. No. WA-005-0500). <strong>Panel C, 300 µl volume:</strong> Chromatin samples are sheared for 5, 10 and 15 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using using 1.5 ml Bioruptor microtubes (Cat. No. C30010016). Prior to de-crosslinking, samples are treated with RNase cocktail mixture at 37°C during 1 hour. The sheared chromatin is then de-crosslinked overnight and phenol/chloroform purified as described in the kit manual. 10 µl of DNA (equivalent of 500, 000 cells) are analyzed on a 2% agarose gel (MW corresponds to the 100 bp DNA molecular weight marker).</small></div>
<div class="small-12 medium-12 large-12 columns"><br /><br /></div>
<div class="small-12 medium-12 large-12 columns">
<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. 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>
</div>
<div class="small-12 medium-12 large-12 columns">
<div class="page" title="Page 7">
<table>
<tbody>
<tr valign="middle">
<td></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histone)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/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;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-medium-sds-100-million-cells">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p>< 0.1%</p>
</td>
<td style="text-align: center;">
<p>0.2%</p>
</td>
<td style="text-align: center;">
<p>1%</p>
</td>
<td style="text-align: center;">
<p>0.5%</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>No</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>up to 25 g of tissue</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
</table>
<p><em><span style="font-weight: 400;">Table comes from our </span><a href="https://www.diagenode.com/protocols/bioruptor-pico-chromatin-preparation-guide"><span style="font-weight: 400;">Guide for successful chromatin preparation using the Bioruptor® Pico</span></a></em></p>
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<div class="large-12 columns">Diagenode's high yields FFPE DNA extraction using Bioruptor<sup><span>®</span></sup> is a superior method for extracting DNA for Next-Gen Sequencing. Our FFPE DNA Extraction kit contains optimized reagents that are added directly to the FFPE samples to remove paraffin with no toxic reagents, digest tissues, and purify DNA with high yields and low sample degradation. The DNA can then be analyzed by traditional methods or can be sheared with the Bioruptor<sup>®</sup> Pico ultrasonicator for downstream NGS library prep using the MicroPlex Library Preparation Kit.</div>
<div class="small-12 medium-12 large-12 columns text-center"><img src="https://www.diagenode.com/img/applications/ffpe_workflow.png" /></div>
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<div class="small-6 medium-6 large-6 columns text-center end small-offset-3"><small><strong>Efficient extraction of pure RNA with high RIN. </strong><br /><span>Total RNA profiles from mouse brain. Tissue was disrupted with Bioruptor<sup>®</sup> Plus as described in the protocol and analyzed on BioAnalyzer (Agilent). Note that small RNAs are present in all profiles indicating that the RNA is largely intact.</span></small></div>
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<div class="small-12 medium-12 large-12 columns">In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniques for optimal sample preparation and genomic library construction. One of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size (depending on the sequencing platform) to enable sensitive and reliable NGS results. The <strong>Bioruptor</strong><sup>®</sup> <strong>Pico</strong> and the <strong>Megaruptor</strong><sup>®</sup> provide superior sample yields, fragment size, and consistency, which are essential for Next-Generation Sequencing workflows. 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<sup>®</sup></a>.</div>
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<p></p>
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<div class="small-7 medium-7 large-7 columns text-center"><img src="https://www.diagenode.com/img/applications/true-flexibility-with-br-ngs.jpg" /></div>
<div class="small-5 medium-5 large-5 columns"><small><strong>Programmable DNA size distribution and high reproducibility with Bioruptor<sup>®</sup> Pico using 0.65 (panel A) or 0.1 ml (panel B) microtubes</strong>. <b>Panel A:</b> 200 bp after 13 cycles (13 sec ON/OFF) using 100 µl volume. Average size: 204; CV%:1.89%). <b>Panel B:</b> 200 bp after 20 cycles (30 sec ON/OFF) using 10 µl volume. (Average size: 215 bp; CV%: 6.6%). <b>Panel A & B:</b> peak electropherogram view. <b>Panel C & D:</b> virtual gel view.</small></div>
</div>
<p><br /><br /></p>
<div class="row">
<div class="small-10 medium-10 large-10 columns text-center end small-offset-1"><img src="https://www.diagenode.com/img/applications/megaruptor-short-frag.jpg" /></div>
<div class="small-12 medium-12 large-12 columns"><small><strong> Reproducible and narrow DNA size distribution with Megaruptor® using short fragment size Hydropores Validation using two different DNA sources and two different methods of analysis. A:</strong> Shearing of lambda phage genomic DNA (20 ng/μl; 150 μl/sample) sheared at different speed settings and analyzed on 1% agarose gel. <strong>B:</strong> Bioanalyzer profiles of human genomic DNA (20 ng/μl; 150 μl/sample) sheared at different software settings of 2 and 5 kb. Three independent experiments were run for each setting. (Agilent DNA 12000 kit was used for separation and fragment sizing).</small></div>
</div>
<p><br /><br /></p>
<div class="row">
<div class="small-4 medium-4 large-4 columns text-center"><img src="https://www.diagenode.com/img/applications/megaruptor-long-frag.jpg" /></div>
<div class="small-8 medium-8 large-8 columns"><small><strong> Demonstrated shearing to fragment sizes between 15 kb and 75 kb with Megaruptor® using long fragment size Hydropores. </strong>Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. DNA was analyzed by pulsed field gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software.<br /> * indicates unsheared DNA </small></div>
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'name' => 'Transcriptional programming drives Ibrutinib-resistance evolution in mantlecell lymphoma.',
'authors' => 'Zhao, Xiaohong et al.',
'description' => '<p>Ibrutinib, a bruton's tyrosine kinase (BTK) inhibitor, provokes robust clinical responses in aggressive mantle cell lymphoma (MCL), yet many patients relapse with lethal Ibrutinib-resistant (IR) disease. Here, using genomic, chemical proteomic, and drug screen profiling, we report that enhancer remodeling-mediated transcriptional activation and adaptive signaling changes drive the aggressive phenotypes of IR. Accordingly, IR MCL cells are vulnerable to inhibitors of the transcriptional machinery and especially so to inhibitors of cyclin-dependent kinase 9 (CDK9), the catalytic subunit of the positive transcription elongation factor b (P-TEFb) of RNA polymerase II (RNAPII). Further, CDK9 inhibition disables reprogrammed signaling circuits and prevents the emergence of IR in MCL. Finally, and importantly, we find that a robust and facile ex vivo image-based functional drug screening platform can predict clinical therapeutic responses of IR MCL and identify vulnerabilities that can be targeted to disable the evolution of IR.</p>',
'date' => '2021-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33730585',
'doi' => '10.1016/j.celrep.2021.108870',
'modified' => '2021-12-21 15:28:26',
'created' => '2021-12-06 15:53:19',
'ProductsPublication' => array(
[maximum depth reached]
)
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(int) 1 => array(
'id' => '3784',
'name' => 'Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes.',
'authors' => 'Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Hölting TLB, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hart',
'description' => '<p>Pediatric malignancies including Ewing sarcoma (EwS) feature a paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here, we demonstrate in EwS how cooperation of dominant oncogenes and regulatory germline variants determine tumor growth, patient survival and drug response. Binding of the oncogenic EWSR1-FLI1 fusion transcription factor to a polymorphic enhancer-like DNA element controls expression of the transcription factor MYBL2 mediating these phenotypes. Whole-genome and RNA sequencing reveals that variability at this locus is inherited via the germline and is associated with variable inter-tumoral MYBL2 expression. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Collectively, we establish cooperation of somatic mutations and regulatory germline variants as a major determinant of tumor progression and highlight the importance of integrating the regulatory genome in precision medicine.</p>',
'date' => '2019-09-11',
'pmid' => 'http://www.pubmed.gov/31511524',
'doi' => '10.1038/s41467-019-12071-2',
'modified' => '2019-10-02 16:48:03',
'created' => '2019-10-02 16:16:55',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'id' => '3665',
'name' => 'BCL2 Amplicon Loss and Transcriptional Remodeling Drives ABT-199 Resistance in B Cell Lymphoma Models.',
'authors' => 'Zhao X, Ren Y, Lawlor M, Shah BD, Park PMC, Lwin T, Wang X, Liu K, Wang M, Gao J, Li T, Xu M, Silva AS, Lee K, Zhang T, Koomen JM, Jiang H, Sudalagunta PR, Meads MB, Cheng F, Bi C, Fu K, Fan H, Dalton WS, Moscinski LC, Shain KH, Sotomayor EM, Wang GG, Gra',
'description' => '<p>Drug-tolerant "persister" tumor cells underlie emergence of drug-resistant clones and contribute to relapse and disease progression. Here we report that resistance to the BCL-2 targeting drug ABT-199 in models of mantle cell lymphoma and double-hit lymphoma evolves from outgrowth of persister clones displaying loss of 18q21 amplicons that harbor BCL2. Further, persister status is generated via adaptive super-enhancer remodeling that reprograms transcription and offers opportunities for overcoming ABT-199 resistance. Notably, pharmacoproteomic and pharmacogenomic screens revealed that persisters are vulnerable to inhibition of the transcriptional machinery and especially to inhibition of cyclin-dependent kinase 7 (CDK7), which is essential for the transcriptional reprogramming that drives and sustains ABT-199 resistance. Thus, transcription-targeting agents offer new approaches to disable drug resistance in B-cell lymphomas.</p>',
'date' => '2019-05-13',
'pmid' => 'http://www.pubmed.gov/31085176',
'doi' => '10.1016/j.ccell.2019.04.005',
'modified' => '2019-07-01 11:37:51',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'id' => '3690',
'name' => 'P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.',
'authors' => 'Bugai A, Quaresma AJC, Friedel CC, Lenasi T, Düster R, Sibley CR, Fujinaga K, Kukanja P, Hennig T, Blasius M, Geyer M, Ule J, Dölken L, Barborič M',
'description' => '<p>DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain ill defined. Here, we show that following genotoxic stress, the RNA-binding motif protein 7 (RBM7) stimulates RNA polymerase II (Pol II) transcription and promotes cell viability by activating the positive transcription elongation factor b (P-TEFb) via its release from the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP). This is mediated by activation of p38, which triggers enhanced binding of RBM7 with core subunits of 7SK snRNP. In turn, P-TEFb relocates to chromatin to induce transcription of short units, including key DDR genes and multiple classes of non-coding RNAs. Critically, interfering with the axis of RBM7 and P-TEFb provokes cellular hypersensitivity to DNA-damage-inducing agents due to activation of apoptosis. Our work uncovers the importance of stress-dependent stimulation of Pol II pause release, which enables a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult.</p>',
'date' => '2019-04-18',
'pmid' => 'http://www.pubmed.gov/30824372',
'doi' => '10.1016/j.molcel.2019.01.033',
'modified' => '2019-06-28 13:53:03',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '3694',
'name' => 'A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation.',
'authors' => 'Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A',
'description' => '<p>Humoral immunity depends on efficient activation of B cells and their subsequent differentiation into antibody-secreting cells (ASCs). The transcription factor NFκB cRel is critical for B cell proliferation, but incorporating its known regulatory interactions into a mathematical model of the ASC differentiation circuit prevented ASC generation in simulations. Indeed, experimental ectopic cRel expression blocked ASC differentiation by inhibiting the transcription factor Blimp1, and in wild-type (WT) cells cRel was dynamically repressed during ASC differentiation by Blimp1 binding the Rel locus. Including this bi-stable circuit of mutual cRel-Blimp1 antagonism into a multi-scale model revealed that dynamic repression of cRel controls the switch from B cell proliferation to ASC generation phases and hence the respective cell population dynamics. Our studies provide a mechanistic explanation of how dysregulation of this bi-stable circuit might result in pathologic B cell population phenotypes and thus offer new avenues for diagnostic stratification and treatment.</p>',
'date' => '2019-03-19',
'pmid' => 'http://www.pubmed.gov/30850343',
'doi' => '10.1016/j.immuni.2019.02.004',
'modified' => '2019-06-28 13:48:31',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '3717',
'name' => 'TF-ChIP Method for Tissue-Specific Gene Targets.',
'authors' => 'Perna A, Alberi LA',
'description' => '<p>Chromatin immunoprecipitation (ChIP) is an assay developed in order to define the dynamic nature of transcription processes. This method has been widely employed to identify methylated and acetylated DNA sequences in a variety of organs both in animals and humans. Nevertheless, this technique is significantly less employed to study transcriptional targets of specific nuclear signaling factors (TFs) and the data published so far have mainly used cell culture material and have been hardly reproduced in tissue. As nuclear signaling underlies important adaptive and maladaptive responses in chronic conditions such as cancer and neurodegeneration, there is a need for streamlining the upfront workflow of TF-ChIP for subsequent target sequencing. Based on the typical low concentration of the signaling transcriptional complex and the complexity/length of the ChIP Seq protocol, the field of cellular signaling has been confronted with a major roadblock in identifying clinically relevant targets of pathological and physiological signaling pathways. The present protocol offers a standardized procedure for detecting signaling targets in any whole tissue or specific dissected regions. The advantages of the protocol compared to the existing published methods are: (1) the small amount of starting material; appropriate for tissue subregions; (2) the optimization of DNA fragmentation from whole tissue; (3) suitability for sparsely populated tissues (i.e., brain); (4) the specificity of the TF-targeting readout; and (5) high DNA quality for sequencing or hybridization. The present protocol is highly detailed and can be reproduced using both fresh and fresh-frozen tissue. This is particularly relevant in the clinical setting, where specimen integrity is often the limiting step and where transcriptional target profiling is therapeutically relevant. The method is centered on Notch signaling but can be applied to a variety of nuclear signaling pathways as long as specific antibodies are available for pull down. Taken the superior yield/readout of this procedure, ChIP may finally provide relevant information about dynamic downstream gene changes for use in both basic research and clinical applications.</p>',
'date' => '2019-03-19',
'pmid' => 'http://www.pubmed.gov/30941015',
'doi' => '10.3389/fncel.2019.00095',
'modified' => '2019-07-05 13:11:18',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'id' => '3547',
'name' => 'A Lamina-Associated Domain Border Governs Nuclear Lamina Interactions, Transcription, and Recombination of the Tcrb Locus.',
'authors' => 'Chen S, Luperchio TR, Wong X, Doan EB, Byrd AT, Roy Choudhury K, Reddy KL, Krangel MS',
'description' => '<p>Tcrb locus V(D)J recombination is regulated by positioning at the nuclear periphery. Here, we used DamID to profile Tcrb locus interactions with the nuclear lamina at high resolution. We identified a lamina-associated domain (LAD) border composed of several CTCF-binding elements that segregates active non-LAD from inactive LAD regions of the locus. Deletion of the LAD border causes an enhancer-dependent spread of histone H3 lysine 27 acetylation from the active recombination center into recombination center-proximal LAD chromatin. This is associated with a disruption to nuclear lamina association, increased chromatin looping to the recombination center, and increased transcription and recombination of recombination center-proximal gene segments. Our results show that a LAD and LAD border are critical components of Tcrb locus gene regulation and suggest that LAD borders may generally function to constrain the activity of nearby enhancers.</p>',
'date' => '2018-11-13',
'pmid' => 'http://www.pubmed.gov/30428344',
'doi' => '10.1016/j.celrep.2018.10.052',
'modified' => '2019-02-27 15:40:26',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '3537',
'name' => 'spe-43 is required for sperm activation in C. elegans.',
'authors' => 'Krauchunas AR, Mendez E, Ni JZ, Druzhinina M, Mulia A, Parry J, Gu SG, Stanfield GM, Singson A',
'description' => '<p>Successful fertilization requires that sperm are activated prior to contacting an oocyte. In C. elegans, this activation process, called spermiogenesis, transforms round immobile spermatids into motile, fertilization-competent spermatozoa. We describe the phenotypic and genetic characterization of spe-43, a new component of the spe-8 pathway, which is required for spermiogenesis in hermaphrodites; spe-43 hermaphrodites are self-sterile, while spe-43 males show wild-type fertility. When exposed to Pronase to activate sperm in vitro, spe-43 spermatids form long rigid spikes radiating outward from the cell periphery instead of forming a motile pseudopod, indicating that spermiogenesis initiates but is not completed. Using a combination of recombinant and deletion mapping and whole genome sequencing, we identified F09E8.1 as spe-43. SPE-43 is predicted to exist in two isoforms; one isoform appears to be a single-pass transmembrane protein while the other is predicted to be a secreted protein. SPE-43 can bind to other known sperm proteins, including SPE-4 and SPE-29, which are known to impact spermiogenesis. In summary, we have identified a membrane protein that is present in C. elegans sperm and is required for sperm activation via the hermaphrodite activation signal.</p>',
'date' => '2018-04-15',
'pmid' => 'http://www.pubmed.gov/29477340',
'doi' => '10.1016/j.ydbio.2018.02.013',
'modified' => '2019-02-28 10:40:50',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '3528',
'name' => 'Selenite and methylseleninic acid epigenetically affects distinct gene sets in myeloid leukemia: A genome wide epigenetic analysis.',
'authors' => 'Khalkar P, Ali HA, Codó P, Argelich ND, Martikainen A, Arzenani MK, Lehmann S, Walfridsson J, Ungerstedt J, Fernandes AP',
'description' => '<p>Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). Both selenite and MSA had major effects on histone marks but the effects of MSA were more pronounced. Gene ontology analysis revealed that selenite affected genes involved in response to oxygen and hypoxia, whereas MSA affected distinct gene sets associated with cell adhesion and glucocorticoid receptors, also apparent by global gene expression analysis using RNA sequencing. The correlation to adhesion was functionally confirmed by a significantly weakened ability of MSA treated cells to attach to fibronectin and linked to decreased expression of integrin beta 1. A striking loss of cellular adhesion was also confirmed in primary patient AML cells. Recent strategies to enhance the cytotoxicity of chemotherapeutic drugs by disrupting the interaction between leukemic and stromal cells in the bone marrow are of increasing interest; and organic selenium compounds like MSA might be promising candidates. In conclusion, these results provide new insight on the mechanism of action of selenium compounds, and will be of value for the understanding, usage, and development of new selenium compounds as anticancer agents.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29438720',
'doi' => '10.1016/j.freeradbiomed.2018.02.014',
'modified' => '2019-02-28 10:49:31',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
)
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'authors' => 'Khalkar P, Ali HA, Codó P, Argelich ND, Martikainen A, Arzenani MK, Lehmann S, Walfridsson J, Ungerstedt J, Fernandes AP',
'description' => '<p>Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). Both selenite and MSA had major effects on histone marks but the effects of MSA were more pronounced. Gene ontology analysis revealed that selenite affected genes involved in response to oxygen and hypoxia, whereas MSA affected distinct gene sets associated with cell adhesion and glucocorticoid receptors, also apparent by global gene expression analysis using RNA sequencing. The correlation to adhesion was functionally confirmed by a significantly weakened ability of MSA treated cells to attach to fibronectin and linked to decreased expression of integrin beta 1. A striking loss of cellular adhesion was also confirmed in primary patient AML cells. Recent strategies to enhance the cytotoxicity of chemotherapeutic drugs by disrupting the interaction between leukemic and stromal cells in the bone marrow are of increasing interest; and organic selenium compounds like MSA might be promising candidates. In conclusion, these results provide new insight on the mechanism of action of selenium compounds, and will be of value for the understanding, usage, and development of new selenium compounds as anticancer agents.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29438720',
'doi' => '10.1016/j.freeradbiomed.2018.02.014',
'modified' => '2019-02-28 10:49:31',
'created' => '2019-02-27 12:54:44',
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<p><span>The Bioruptor® uses a unique system to uniformely process multiple samples in sealed tubes of 0.5 ml to 50 ml capacity. The built-in cooling system (water cooler and Single Cycle Valve) ensures high precision temperature control resulting in higher quality samples. An excellent device for shearing chromatin, cell and tissue disruption and many other applications (see below).</span></p>
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<p></p>
<p><span></span></p>
<div class="page" title="Page 9">
<div class="section">
<div class="layoutArea">
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</div>
</div>
</div>',
'label1' => 'Which Bioruptor® Plus configuration is right for you?',
'info1' => '<p><strong>B01020001</strong> - Bioruptor Plus<sup>®</sup> device with 1.5 ml (6 samples) tube holder <span>& temperature controlled system (water cooler + single cycle valve) </span><em>for recommended sample volume 100 µl - 300 µl</em></p>
<p><strong>B01020002</strong> - Bioruptor Plus<sup>®</sup> device with 1.5 ml (6 samples) and 15 ml tube holders <span>& temperature controlled system (water cooler + single cycle valve)</span> <em>for recommended sample volume 100 µl - 2 ml</em></p>
<p><strong>B01020003</strong> - Bioruptor Plus<sup>®</sup> device with 0.5 ml (12 samples) tube holder <span>& temperature controlled system (water cooler + single cycle valve)</span> <em>for recommended sample volume 50 µl - 100 µl </em></p>',
'label2' => 'Available chromatin shearing kits',
'info2' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. 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>
<tbody>
<tr valign="middle">
<td></td>
<td style="text-align: center;"><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;"><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;"><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;"><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>
<p style="text-align: left;"><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">< 0.1%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">0.2%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">1%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">0.5%</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">No</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">up to 25 g of tissue</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<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;">
<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;">
<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;">
<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>
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'info3' => '<h3>Shearing Accessories</h3>
<table style="width: 641px;">
<thead>
<tr style="background-color: #dddddd; height: 37px;">
<td style="width: 300px; height: 37px;"><strong>Name</strong></td>
<td style="width: 171px; text-align: center; height: 37px;">Catalog number</td>
<td style="width: 160px; text-align: center; height: 37px;">Throughput</td>
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<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/0-5-0-65-ml-tube-holder-for-bioruptor-standard-plus-pico-1-pack">0.5/0.65 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200043</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">12 samples</span></td>
</tr>
<tr style="height: 38px;">
<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/1-5-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">1.5 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200011</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 38px;">
<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/10-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">10 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200012</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-sonication-accessories-for-bioruptor-standard-plus-pico-1-pack">15 ml sonication accessories</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200016</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">15 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200013</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">6 samples</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/50-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">50 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200014</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">3 samples</span></td>
</tr>
</tbody>
</table>
<h3>Shearing Consumables</h3>
<table style="width: 646px;">
<thead>
<tr style="background-color: #dddddd; height: 37px;">
<td style="width: 286px; height: 37px;"><strong>Name</strong></td>
<td style="width: 76px; height: 37px; text-align: center;">Catalog Number</td>
</tr>
</thead>
<tbody>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/0-5-ml-bioruptor-microtubes-500-tubes">0.5 ml Bioruptor Plus Microtubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010013</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/1-5-ml-tpx-microtubes-300-pc">1.5 ml Bioruptor Plus TPX microtubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010010</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/10-ml-tubes-100-tubes">10 ml Bioruptor Plus tubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010012</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-tpx-tubes-50-pc">15 ml Bioruptor Plus TPX tubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010009</span></td>
</tr>
</tbody>
</table>
<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor_accessories/TDS-BioruptorTubes.pdf">Find datasheet for Diagenode tubes here</a></p>
<p><a href="../documents/bioruptor-organigram-tubes">Which tubes for which Bioruptor®?</a></p>',
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<div class="small-12 medium-12 large-12 columns">The most important steps for a successful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, <strong>Diagenode's Bioruptor</strong><sup>®</sup> uses state-of-the-art ultrasound <strong>ACT</strong> (<strong>A</strong>daptive <strong>C</strong>avitation <strong>T</strong>echnology) to efficiently shear chromatin. ACT enables the highest chromatin quality for high IP efficiency and sensitivity for ChIP experiments with gentle yet highly effective shearing forces. Additionally, the Bioruptor<sup>®</sup> provides a precisely controlled temperature environment that preserves chromatin from heat degradation such that protein-DNA complexes are well-preserved for sensitive, unbiased, and accurate ChIP.<br /><br /> <strong>Diagenode's Bioruptor</strong><sup>®</sup> is the instrument of choice for chromatin shearing used for a number of downstream applications such as qPCR and ChIP-seq that require optimally sheared, unbiased chromatin.</div>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/applications/pico_dna_shearing_fig2.png" /></div>
<div class="small-10 medium-10 large-10 columns end small-offset-1"><small> <br /><strong>Panel A, 10 µl volume:</strong> Chromatin samples are sheared for 10, 20 and 30 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.1 ml Bioruptor® Microtubes (Cat. No. B01200041). <strong>Panel B, 100 µl volume:</strong> Chromatin samples are sheared for 10 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.65 ml Bioruptor® Microtubes (Cat. No. WA-005-0500). <strong>Panel C, 300 µl volume:</strong> Chromatin samples are sheared for 5, 10 and 15 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using using 1.5 ml Bioruptor microtubes (Cat. No. C30010016). Prior to de-crosslinking, samples are treated with RNase cocktail mixture at 37°C during 1 hour. The sheared chromatin is then de-crosslinked overnight and phenol/chloroform purified as described in the kit manual. 10 µl of DNA (equivalent of 500, 000 cells) are analyzed on a 2% agarose gel (MW corresponds to the 100 bp DNA molecular weight marker).</small></div>
<div class="small-12 medium-12 large-12 columns"><br /><br /></div>
<div class="small-12 medium-12 large-12 columns">
<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. 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>
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<div class="small-12 medium-12 large-12 columns">
<div class="page" title="Page 7">
<table>
<tbody>
<tr valign="middle">
<td></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histone)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/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;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-medium-sds-100-million-cells">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p>< 0.1%</p>
</td>
<td style="text-align: center;">
<p>0.2%</p>
</td>
<td style="text-align: center;">
<p>1%</p>
</td>
<td style="text-align: center;">
<p>0.5%</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>No</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>up to 25 g of tissue</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
</table>
<p><em><span style="font-weight: 400;">Table comes from our </span><a href="https://www.diagenode.com/protocols/bioruptor-pico-chromatin-preparation-guide"><span style="font-weight: 400;">Guide for successful chromatin preparation using the Bioruptor® Pico</span></a></em></p>
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<div class="large-12 columns">Diagenode's high yields FFPE DNA extraction using Bioruptor<sup><span>®</span></sup> is a superior method for extracting DNA for Next-Gen Sequencing. Our FFPE DNA Extraction kit contains optimized reagents that are added directly to the FFPE samples to remove paraffin with no toxic reagents, digest tissues, and purify DNA with high yields and low sample degradation. The DNA can then be analyzed by traditional methods or can be sheared with the Bioruptor<sup>®</sup> Pico ultrasonicator for downstream NGS library prep using the MicroPlex Library Preparation Kit.</div>
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<div class="small-12 medium-12 large-12 columns">In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniques for optimal sample preparation and genomic library construction. One of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size (depending on the sequencing platform) to enable sensitive and reliable NGS results. The <strong>Bioruptor</strong><sup>®</sup> <strong>Pico</strong> and the <strong>Megaruptor</strong><sup>®</sup> provide superior sample yields, fragment size, and consistency, which are essential for Next-Generation Sequencing workflows. 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<sup>®</sup></a>.</div>
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<div class="small-7 medium-7 large-7 columns text-center"><img src="https://www.diagenode.com/img/applications/true-flexibility-with-br-ngs.jpg" /></div>
<div class="small-5 medium-5 large-5 columns"><small><strong>Programmable DNA size distribution and high reproducibility with Bioruptor<sup>®</sup> Pico using 0.65 (panel A) or 0.1 ml (panel B) microtubes</strong>. <b>Panel A:</b> 200 bp after 13 cycles (13 sec ON/OFF) using 100 µl volume. Average size: 204; CV%:1.89%). <b>Panel B:</b> 200 bp after 20 cycles (30 sec ON/OFF) using 10 µl volume. (Average size: 215 bp; CV%: 6.6%). <b>Panel A & B:</b> peak electropherogram view. <b>Panel C & D:</b> virtual gel view.</small></div>
</div>
<p><br /><br /></p>
<div class="row">
<div class="small-10 medium-10 large-10 columns text-center end small-offset-1"><img src="https://www.diagenode.com/img/applications/megaruptor-short-frag.jpg" /></div>
<div class="small-12 medium-12 large-12 columns"><small><strong> Reproducible and narrow DNA size distribution with Megaruptor® using short fragment size Hydropores Validation using two different DNA sources and two different methods of analysis. A:</strong> Shearing of lambda phage genomic DNA (20 ng/μl; 150 μl/sample) sheared at different speed settings and analyzed on 1% agarose gel. <strong>B:</strong> Bioanalyzer profiles of human genomic DNA (20 ng/μl; 150 μl/sample) sheared at different software settings of 2 and 5 kb. Three independent experiments were run for each setting. (Agilent DNA 12000 kit was used for separation and fragment sizing).</small></div>
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<div class="small-4 medium-4 large-4 columns text-center"><img src="https://www.diagenode.com/img/applications/megaruptor-long-frag.jpg" /></div>
<div class="small-8 medium-8 large-8 columns"><small><strong> Demonstrated shearing to fragment sizes between 15 kb and 75 kb with Megaruptor® using long fragment size Hydropores. </strong>Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. DNA was analyzed by pulsed field gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software.<br /> * indicates unsheared DNA </small></div>
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[maximum depth reached]
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(int) 7 => array(
'id' => '24',
'name' => 'Western Blot - Procedure for simultaneous extraction of cytoplasmic, nuclear and chromatin protein with Bioruptor®',
'description' => '<p><span>The regular protocol for the extraction of histone requires an acid extraction, making impossible the detection of any other cytoplasmic and nuclear proteins from the same extract. Using <a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device">Bioruptor</a></span><a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device"><span>®</span></a><span>, Slimane AIT-SI-ALI and his “epigenetic and cell fate” team from the University Paris Descartes developed a protocol allowing the simultaneous extraction of histone and other proteins. </span></p>',
'image_id' => '220',
'type' => 'Protocol',
'url' => 'files/protocols/western-blot-with-bioruptor-protocol.pdf',
'slug' => 'western-blot-with-bioruptor-protocol',
'meta_keywords' => '',
'meta_description' => '',
'modified' => '2016-04-29 17:39:29',
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[maximum depth reached]
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(int) 0 => array(
'id' => '4163',
'name' => 'Transcriptional programming drives Ibrutinib-resistance evolution in mantlecell lymphoma.',
'authors' => 'Zhao, Xiaohong et al.',
'description' => '<p>Ibrutinib, a bruton's tyrosine kinase (BTK) inhibitor, provokes robust clinical responses in aggressive mantle cell lymphoma (MCL), yet many patients relapse with lethal Ibrutinib-resistant (IR) disease. Here, using genomic, chemical proteomic, and drug screen profiling, we report that enhancer remodeling-mediated transcriptional activation and adaptive signaling changes drive the aggressive phenotypes of IR. Accordingly, IR MCL cells are vulnerable to inhibitors of the transcriptional machinery and especially so to inhibitors of cyclin-dependent kinase 9 (CDK9), the catalytic subunit of the positive transcription elongation factor b (P-TEFb) of RNA polymerase II (RNAPII). Further, CDK9 inhibition disables reprogrammed signaling circuits and prevents the emergence of IR in MCL. Finally, and importantly, we find that a robust and facile ex vivo image-based functional drug screening platform can predict clinical therapeutic responses of IR MCL and identify vulnerabilities that can be targeted to disable the evolution of IR.</p>',
'date' => '2021-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33730585',
'doi' => '10.1016/j.celrep.2021.108870',
'modified' => '2021-12-21 15:28:26',
'created' => '2021-12-06 15:53:19',
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[maximum depth reached]
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(int) 1 => array(
'id' => '3784',
'name' => 'Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes.',
'authors' => 'Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Hölting TLB, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hart',
'description' => '<p>Pediatric malignancies including Ewing sarcoma (EwS) feature a paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here, we demonstrate in EwS how cooperation of dominant oncogenes and regulatory germline variants determine tumor growth, patient survival and drug response. Binding of the oncogenic EWSR1-FLI1 fusion transcription factor to a polymorphic enhancer-like DNA element controls expression of the transcription factor MYBL2 mediating these phenotypes. Whole-genome and RNA sequencing reveals that variability at this locus is inherited via the germline and is associated with variable inter-tumoral MYBL2 expression. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Collectively, we establish cooperation of somatic mutations and regulatory germline variants as a major determinant of tumor progression and highlight the importance of integrating the regulatory genome in precision medicine.</p>',
'date' => '2019-09-11',
'pmid' => 'http://www.pubmed.gov/31511524',
'doi' => '10.1038/s41467-019-12071-2',
'modified' => '2019-10-02 16:48:03',
'created' => '2019-10-02 16:16:55',
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(int) 2 => array(
'id' => '3665',
'name' => 'BCL2 Amplicon Loss and Transcriptional Remodeling Drives ABT-199 Resistance in B Cell Lymphoma Models.',
'authors' => 'Zhao X, Ren Y, Lawlor M, Shah BD, Park PMC, Lwin T, Wang X, Liu K, Wang M, Gao J, Li T, Xu M, Silva AS, Lee K, Zhang T, Koomen JM, Jiang H, Sudalagunta PR, Meads MB, Cheng F, Bi C, Fu K, Fan H, Dalton WS, Moscinski LC, Shain KH, Sotomayor EM, Wang GG, Gra',
'description' => '<p>Drug-tolerant "persister" tumor cells underlie emergence of drug-resistant clones and contribute to relapse and disease progression. Here we report that resistance to the BCL-2 targeting drug ABT-199 in models of mantle cell lymphoma and double-hit lymphoma evolves from outgrowth of persister clones displaying loss of 18q21 amplicons that harbor BCL2. Further, persister status is generated via adaptive super-enhancer remodeling that reprograms transcription and offers opportunities for overcoming ABT-199 resistance. Notably, pharmacoproteomic and pharmacogenomic screens revealed that persisters are vulnerable to inhibition of the transcriptional machinery and especially to inhibition of cyclin-dependent kinase 7 (CDK7), which is essential for the transcriptional reprogramming that drives and sustains ABT-199 resistance. Thus, transcription-targeting agents offer new approaches to disable drug resistance in B-cell lymphomas.</p>',
'date' => '2019-05-13',
'pmid' => 'http://www.pubmed.gov/31085176',
'doi' => '10.1016/j.ccell.2019.04.005',
'modified' => '2019-07-01 11:37:51',
'created' => '2019-06-21 14:55:31',
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[maximum depth reached]
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(int) 3 => array(
'id' => '3690',
'name' => 'P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.',
'authors' => 'Bugai A, Quaresma AJC, Friedel CC, Lenasi T, Düster R, Sibley CR, Fujinaga K, Kukanja P, Hennig T, Blasius M, Geyer M, Ule J, Dölken L, Barborič M',
'description' => '<p>DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain ill defined. Here, we show that following genotoxic stress, the RNA-binding motif protein 7 (RBM7) stimulates RNA polymerase II (Pol II) transcription and promotes cell viability by activating the positive transcription elongation factor b (P-TEFb) via its release from the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP). This is mediated by activation of p38, which triggers enhanced binding of RBM7 with core subunits of 7SK snRNP. In turn, P-TEFb relocates to chromatin to induce transcription of short units, including key DDR genes and multiple classes of non-coding RNAs. Critically, interfering with the axis of RBM7 and P-TEFb provokes cellular hypersensitivity to DNA-damage-inducing agents due to activation of apoptosis. Our work uncovers the importance of stress-dependent stimulation of Pol II pause release, which enables a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult.</p>',
'date' => '2019-04-18',
'pmid' => 'http://www.pubmed.gov/30824372',
'doi' => '10.1016/j.molcel.2019.01.033',
'modified' => '2019-06-28 13:53:03',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
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(int) 4 => array(
'id' => '3694',
'name' => 'A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation.',
'authors' => 'Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A',
'description' => '<p>Humoral immunity depends on efficient activation of B cells and their subsequent differentiation into antibody-secreting cells (ASCs). The transcription factor NFκB cRel is critical for B cell proliferation, but incorporating its known regulatory interactions into a mathematical model of the ASC differentiation circuit prevented ASC generation in simulations. Indeed, experimental ectopic cRel expression blocked ASC differentiation by inhibiting the transcription factor Blimp1, and in wild-type (WT) cells cRel was dynamically repressed during ASC differentiation by Blimp1 binding the Rel locus. Including this bi-stable circuit of mutual cRel-Blimp1 antagonism into a multi-scale model revealed that dynamic repression of cRel controls the switch from B cell proliferation to ASC generation phases and hence the respective cell population dynamics. Our studies provide a mechanistic explanation of how dysregulation of this bi-stable circuit might result in pathologic B cell population phenotypes and thus offer new avenues for diagnostic stratification and treatment.</p>',
'date' => '2019-03-19',
'pmid' => 'http://www.pubmed.gov/30850343',
'doi' => '10.1016/j.immuni.2019.02.004',
'modified' => '2019-06-28 13:48:31',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '3717',
'name' => 'TF-ChIP Method for Tissue-Specific Gene Targets.',
'authors' => 'Perna A, Alberi LA',
'description' => '<p>Chromatin immunoprecipitation (ChIP) is an assay developed in order to define the dynamic nature of transcription processes. This method has been widely employed to identify methylated and acetylated DNA sequences in a variety of organs both in animals and humans. Nevertheless, this technique is significantly less employed to study transcriptional targets of specific nuclear signaling factors (TFs) and the data published so far have mainly used cell culture material and have been hardly reproduced in tissue. As nuclear signaling underlies important adaptive and maladaptive responses in chronic conditions such as cancer and neurodegeneration, there is a need for streamlining the upfront workflow of TF-ChIP for subsequent target sequencing. Based on the typical low concentration of the signaling transcriptional complex and the complexity/length of the ChIP Seq protocol, the field of cellular signaling has been confronted with a major roadblock in identifying clinically relevant targets of pathological and physiological signaling pathways. The present protocol offers a standardized procedure for detecting signaling targets in any whole tissue or specific dissected regions. The advantages of the protocol compared to the existing published methods are: (1) the small amount of starting material; appropriate for tissue subregions; (2) the optimization of DNA fragmentation from whole tissue; (3) suitability for sparsely populated tissues (i.e., brain); (4) the specificity of the TF-targeting readout; and (5) high DNA quality for sequencing or hybridization. The present protocol is highly detailed and can be reproduced using both fresh and fresh-frozen tissue. This is particularly relevant in the clinical setting, where specimen integrity is often the limiting step and where transcriptional target profiling is therapeutically relevant. The method is centered on Notch signaling but can be applied to a variety of nuclear signaling pathways as long as specific antibodies are available for pull down. Taken the superior yield/readout of this procedure, ChIP may finally provide relevant information about dynamic downstream gene changes for use in both basic research and clinical applications.</p>',
'date' => '2019-03-19',
'pmid' => 'http://www.pubmed.gov/30941015',
'doi' => '10.3389/fncel.2019.00095',
'modified' => '2019-07-05 13:11:18',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
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(int) 6 => array(
'id' => '3547',
'name' => 'A Lamina-Associated Domain Border Governs Nuclear Lamina Interactions, Transcription, and Recombination of the Tcrb Locus.',
'authors' => 'Chen S, Luperchio TR, Wong X, Doan EB, Byrd AT, Roy Choudhury K, Reddy KL, Krangel MS',
'description' => '<p>Tcrb locus V(D)J recombination is regulated by positioning at the nuclear periphery. Here, we used DamID to profile Tcrb locus interactions with the nuclear lamina at high resolution. We identified a lamina-associated domain (LAD) border composed of several CTCF-binding elements that segregates active non-LAD from inactive LAD regions of the locus. Deletion of the LAD border causes an enhancer-dependent spread of histone H3 lysine 27 acetylation from the active recombination center into recombination center-proximal LAD chromatin. This is associated with a disruption to nuclear lamina association, increased chromatin looping to the recombination center, and increased transcription and recombination of recombination center-proximal gene segments. Our results show that a LAD and LAD border are critical components of Tcrb locus gene regulation and suggest that LAD borders may generally function to constrain the activity of nearby enhancers.</p>',
'date' => '2018-11-13',
'pmid' => 'http://www.pubmed.gov/30428344',
'doi' => '10.1016/j.celrep.2018.10.052',
'modified' => '2019-02-27 15:40:26',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
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(int) 7 => array(
'id' => '3537',
'name' => 'spe-43 is required for sperm activation in C. elegans.',
'authors' => 'Krauchunas AR, Mendez E, Ni JZ, Druzhinina M, Mulia A, Parry J, Gu SG, Stanfield GM, Singson A',
'description' => '<p>Successful fertilization requires that sperm are activated prior to contacting an oocyte. In C. elegans, this activation process, called spermiogenesis, transforms round immobile spermatids into motile, fertilization-competent spermatozoa. We describe the phenotypic and genetic characterization of spe-43, a new component of the spe-8 pathway, which is required for spermiogenesis in hermaphrodites; spe-43 hermaphrodites are self-sterile, while spe-43 males show wild-type fertility. When exposed to Pronase to activate sperm in vitro, spe-43 spermatids form long rigid spikes radiating outward from the cell periphery instead of forming a motile pseudopod, indicating that spermiogenesis initiates but is not completed. Using a combination of recombinant and deletion mapping and whole genome sequencing, we identified F09E8.1 as spe-43. SPE-43 is predicted to exist in two isoforms; one isoform appears to be a single-pass transmembrane protein while the other is predicted to be a secreted protein. SPE-43 can bind to other known sperm proteins, including SPE-4 and SPE-29, which are known to impact spermiogenesis. In summary, we have identified a membrane protein that is present in C. elegans sperm and is required for sperm activation via the hermaphrodite activation signal.</p>',
'date' => '2018-04-15',
'pmid' => 'http://www.pubmed.gov/29477340',
'doi' => '10.1016/j.ydbio.2018.02.013',
'modified' => '2019-02-28 10:40:50',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
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(int) 8 => array(
'id' => '3528',
'name' => 'Selenite and methylseleninic acid epigenetically affects distinct gene sets in myeloid leukemia: A genome wide epigenetic analysis.',
'authors' => 'Khalkar P, Ali HA, Codó P, Argelich ND, Martikainen A, Arzenani MK, Lehmann S, Walfridsson J, Ungerstedt J, Fernandes AP',
'description' => '<p>Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). Both selenite and MSA had major effects on histone marks but the effects of MSA were more pronounced. Gene ontology analysis revealed that selenite affected genes involved in response to oxygen and hypoxia, whereas MSA affected distinct gene sets associated with cell adhesion and glucocorticoid receptors, also apparent by global gene expression analysis using RNA sequencing. The correlation to adhesion was functionally confirmed by a significantly weakened ability of MSA treated cells to attach to fibronectin and linked to decreased expression of integrin beta 1. A striking loss of cellular adhesion was also confirmed in primary patient AML cells. Recent strategies to enhance the cytotoxicity of chemotherapeutic drugs by disrupting the interaction between leukemic and stromal cells in the bone marrow are of increasing interest; and organic selenium compounds like MSA might be promising candidates. In conclusion, these results provide new insight on the mechanism of action of selenium compounds, and will be of value for the understanding, usage, and development of new selenium compounds as anticancer agents.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29438720',
'doi' => '10.1016/j.freeradbiomed.2018.02.014',
'modified' => '2019-02-28 10:49:31',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
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'description' => '<p><span>Diagenode tubes were developed specifically for use with the Bioruptor<sup>®</sup>. They ensure a maximum energy delivery to samples with a minimal attenuation of ultrasound intensity. This guide helps you to choose the appropriate tubes for your application of interest and sonication on the Bioruptor<sup>®</sup> Standard, Plus, and Pico. </span></p>',
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'name' => 'Selenite and methylseleninic acid epigenetically affects distinct gene sets in myeloid leukemia: A genome wide epigenetic analysis.',
'authors' => 'Khalkar P, Ali HA, Codó P, Argelich ND, Martikainen A, Arzenani MK, Lehmann S, Walfridsson J, Ungerstedt J, Fernandes AP',
'description' => '<p>Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). Both selenite and MSA had major effects on histone marks but the effects of MSA were more pronounced. Gene ontology analysis revealed that selenite affected genes involved in response to oxygen and hypoxia, whereas MSA affected distinct gene sets associated with cell adhesion and glucocorticoid receptors, also apparent by global gene expression analysis using RNA sequencing. The correlation to adhesion was functionally confirmed by a significantly weakened ability of MSA treated cells to attach to fibronectin and linked to decreased expression of integrin beta 1. A striking loss of cellular adhesion was also confirmed in primary patient AML cells. Recent strategies to enhance the cytotoxicity of chemotherapeutic drugs by disrupting the interaction between leukemic and stromal cells in the bone marrow are of increasing interest; and organic selenium compounds like MSA might be promising candidates. In conclusion, these results provide new insight on the mechanism of action of selenium compounds, and will be of value for the understanding, usage, and development of new selenium compounds as anticancer agents.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29438720',
'doi' => '10.1016/j.freeradbiomed.2018.02.014',
'modified' => '2019-02-28 10:49:31',
'created' => '2019-02-27 12:54:44',
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<div class="small-12 medium-12 large-12 columns"><br /><br />
<p><span>The Bioruptor® uses a unique system to uniformely process multiple samples in sealed tubes of 0.5 ml to 50 ml capacity. The built-in cooling system (water cooler and Single Cycle Valve) ensures high precision temperature control resulting in higher quality samples. An excellent device for shearing chromatin, cell and tissue disruption and many other applications (see below).</span></p>
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<p></p>
<p><span></span></p>
<div class="page" title="Page 9">
<div class="section">
<div class="layoutArea">
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</div>
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</div>',
'label1' => 'Which Bioruptor® Plus configuration is right for you?',
'info1' => '<p><strong>B01020001</strong> - Bioruptor Plus<sup>®</sup> device with 1.5 ml (6 samples) tube holder <span>& temperature controlled system (water cooler + single cycle valve) </span><em>for recommended sample volume 100 µl - 300 µl</em></p>
<p><strong>B01020002</strong> - Bioruptor Plus<sup>®</sup> device with 1.5 ml (6 samples) and 15 ml tube holders <span>& temperature controlled system (water cooler + single cycle valve)</span> <em>for recommended sample volume 100 µl - 2 ml</em></p>
<p><strong>B01020003</strong> - Bioruptor Plus<sup>®</sup> device with 0.5 ml (12 samples) tube holder <span>& temperature controlled system (water cooler + single cycle valve)</span> <em>for recommended sample volume 50 µl - 100 µl </em></p>',
'label2' => 'Available chromatin shearing kits',
'info2' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. 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>
<tbody>
<tr valign="middle">
<td></td>
<td style="text-align: center;"><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;"><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;"><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;"><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>
<p style="text-align: left;"><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">< 0.1%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">0.2%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">1%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">0.5%</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">No</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">up to 25 g of tissue</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<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;">
<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;">
<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;">
<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>
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'info3' => '<h3>Shearing Accessories</h3>
<table style="width: 641px;">
<thead>
<tr style="background-color: #dddddd; height: 37px;">
<td style="width: 300px; height: 37px;"><strong>Name</strong></td>
<td style="width: 171px; text-align: center; height: 37px;">Catalog number</td>
<td style="width: 160px; text-align: center; height: 37px;">Throughput</td>
</tr>
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<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/0-5-0-65-ml-tube-holder-for-bioruptor-standard-plus-pico-1-pack">0.5/0.65 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200043</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">12 samples</span></td>
</tr>
<tr style="height: 38px;">
<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/1-5-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">1.5 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200011</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 38px;">
<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/10-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">10 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200012</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-sonication-accessories-for-bioruptor-standard-plus-pico-1-pack">15 ml sonication accessories</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200016</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">15 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200013</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">6 samples</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/50-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">50 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200014</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">3 samples</span></td>
</tr>
</tbody>
</table>
<h3>Shearing Consumables</h3>
<table style="width: 646px;">
<thead>
<tr style="background-color: #dddddd; height: 37px;">
<td style="width: 286px; height: 37px;"><strong>Name</strong></td>
<td style="width: 76px; height: 37px; text-align: center;">Catalog Number</td>
</tr>
</thead>
<tbody>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/0-5-ml-bioruptor-microtubes-500-tubes">0.5 ml Bioruptor Plus Microtubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010013</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/1-5-ml-tpx-microtubes-300-pc">1.5 ml Bioruptor Plus TPX microtubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010010</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/10-ml-tubes-100-tubes">10 ml Bioruptor Plus tubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010012</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-tpx-tubes-50-pc">15 ml Bioruptor Plus TPX tubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010009</span></td>
</tr>
</tbody>
</table>
<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor_accessories/TDS-BioruptorTubes.pdf">Find datasheet for Diagenode tubes here</a></p>
<p><a href="../documents/bioruptor-organigram-tubes">Which tubes for which Bioruptor®?</a></p>',
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<div class="small-12 medium-12 large-12 columns">The most important steps for a successful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, <strong>Diagenode's Bioruptor</strong><sup>®</sup> uses state-of-the-art ultrasound <strong>ACT</strong> (<strong>A</strong>daptive <strong>C</strong>avitation <strong>T</strong>echnology) to efficiently shear chromatin. ACT enables the highest chromatin quality for high IP efficiency and sensitivity for ChIP experiments with gentle yet highly effective shearing forces. Additionally, the Bioruptor<sup>®</sup> provides a precisely controlled temperature environment that preserves chromatin from heat degradation such that protein-DNA complexes are well-preserved for sensitive, unbiased, and accurate ChIP.<br /><br /> <strong>Diagenode's Bioruptor</strong><sup>®</sup> is the instrument of choice for chromatin shearing used for a number of downstream applications such as qPCR and ChIP-seq that require optimally sheared, unbiased chromatin.</div>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/applications/pico_dna_shearing_fig2.png" /></div>
<div class="small-10 medium-10 large-10 columns end small-offset-1"><small> <br /><strong>Panel A, 10 µl volume:</strong> Chromatin samples are sheared for 10, 20 and 30 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.1 ml Bioruptor® Microtubes (Cat. No. B01200041). <strong>Panel B, 100 µl volume:</strong> Chromatin samples are sheared for 10 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.65 ml Bioruptor® Microtubes (Cat. No. WA-005-0500). <strong>Panel C, 300 µl volume:</strong> Chromatin samples are sheared for 5, 10 and 15 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using using 1.5 ml Bioruptor microtubes (Cat. No. C30010016). Prior to de-crosslinking, samples are treated with RNase cocktail mixture at 37°C during 1 hour. The sheared chromatin is then de-crosslinked overnight and phenol/chloroform purified as described in the kit manual. 10 µl of DNA (equivalent of 500, 000 cells) are analyzed on a 2% agarose gel (MW corresponds to the 100 bp DNA molecular weight marker).</small></div>
<div class="small-12 medium-12 large-12 columns"><br /><br /></div>
<div class="small-12 medium-12 large-12 columns">
<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. 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>
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<div class="small-12 medium-12 large-12 columns">
<div class="page" title="Page 7">
<table>
<tbody>
<tr valign="middle">
<td></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histone)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/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;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-medium-sds-100-million-cells">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p>< 0.1%</p>
</td>
<td style="text-align: center;">
<p>0.2%</p>
</td>
<td style="text-align: center;">
<p>1%</p>
</td>
<td style="text-align: center;">
<p>0.5%</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>No</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>up to 25 g of tissue</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
</table>
<p><em><span style="font-weight: 400;">Table comes from our </span><a href="https://www.diagenode.com/protocols/bioruptor-pico-chromatin-preparation-guide"><span style="font-weight: 400;">Guide for successful chromatin preparation using the Bioruptor® Pico</span></a></em></p>
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<div class="large-12 columns">Diagenode's high yields FFPE DNA extraction using Bioruptor<sup><span>®</span></sup> is a superior method for extracting DNA for Next-Gen Sequencing. Our FFPE DNA Extraction kit contains optimized reagents that are added directly to the FFPE samples to remove paraffin with no toxic reagents, digest tissues, and purify DNA with high yields and low sample degradation. The DNA can then be analyzed by traditional methods or can be sheared with the Bioruptor<sup>®</sup> Pico ultrasonicator for downstream NGS library prep using the MicroPlex Library Preparation Kit.</div>
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<div class="small-12 medium-12 large-12 columns">In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniques for optimal sample preparation and genomic library construction. One of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size (depending on the sequencing platform) to enable sensitive and reliable NGS results. The <strong>Bioruptor</strong><sup>®</sup> <strong>Pico</strong> and the <strong>Megaruptor</strong><sup>®</sup> provide superior sample yields, fragment size, and consistency, which are essential for Next-Generation Sequencing workflows. 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<sup>®</sup></a>.</div>
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<p></p>
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<div class="small-7 medium-7 large-7 columns text-center"><img src="https://www.diagenode.com/img/applications/true-flexibility-with-br-ngs.jpg" /></div>
<div class="small-5 medium-5 large-5 columns"><small><strong>Programmable DNA size distribution and high reproducibility with Bioruptor<sup>®</sup> Pico using 0.65 (panel A) or 0.1 ml (panel B) microtubes</strong>. <b>Panel A:</b> 200 bp after 13 cycles (13 sec ON/OFF) using 100 µl volume. Average size: 204; CV%:1.89%). <b>Panel B:</b> 200 bp after 20 cycles (30 sec ON/OFF) using 10 µl volume. (Average size: 215 bp; CV%: 6.6%). <b>Panel A & B:</b> peak electropherogram view. <b>Panel C & D:</b> virtual gel view.</small></div>
</div>
<p><br /><br /></p>
<div class="row">
<div class="small-10 medium-10 large-10 columns text-center end small-offset-1"><img src="https://www.diagenode.com/img/applications/megaruptor-short-frag.jpg" /></div>
<div class="small-12 medium-12 large-12 columns"><small><strong> Reproducible and narrow DNA size distribution with Megaruptor® using short fragment size Hydropores Validation using two different DNA sources and two different methods of analysis. A:</strong> Shearing of lambda phage genomic DNA (20 ng/μl; 150 μl/sample) sheared at different speed settings and analyzed on 1% agarose gel. <strong>B:</strong> Bioanalyzer profiles of human genomic DNA (20 ng/μl; 150 μl/sample) sheared at different software settings of 2 and 5 kb. Three independent experiments were run for each setting. (Agilent DNA 12000 kit was used for separation and fragment sizing).</small></div>
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<p><br /><br /></p>
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<div class="small-4 medium-4 large-4 columns text-center"><img src="https://www.diagenode.com/img/applications/megaruptor-long-frag.jpg" /></div>
<div class="small-8 medium-8 large-8 columns"><small><strong> Demonstrated shearing to fragment sizes between 15 kb and 75 kb with Megaruptor® using long fragment size Hydropores. </strong>Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. DNA was analyzed by pulsed field gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software.<br /> * indicates unsheared DNA </small></div>
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'name' => 'TAP-TAG - Procedure for the purification of a chromatin protein with Bioruptor®',
'description' => '<p><span>The Tandem Affinity Purification (TAP) is a general procedure for the purification of protein complex. The fusion of the TAP tag to the protein of interest allows the rapid purification under a native environment. Molecular complexes can then be isolated and used for various applications for the identification of partners. Slimane AIT-SI-ALI and his “epigenetic and cell fate” team from the University Paris Descartes combined the TAP tagging with the Bioruptor</span><span>®</span><span>. This combination is essential for the efficient purification of a chromatin protein. </span></p>',
'image_id' => null,
'type' => 'Protocol',
'url' => 'files/protocols/TAP-TAG-procedure-for-bioruptor.pdf',
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[maximum depth reached]
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(int) 7 => array(
'id' => '24',
'name' => 'Western Blot - Procedure for simultaneous extraction of cytoplasmic, nuclear and chromatin protein with Bioruptor®',
'description' => '<p><span>The regular protocol for the extraction of histone requires an acid extraction, making impossible the detection of any other cytoplasmic and nuclear proteins from the same extract. Using <a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device">Bioruptor</a></span><a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device"><span>®</span></a><span>, Slimane AIT-SI-ALI and his “epigenetic and cell fate” team from the University Paris Descartes developed a protocol allowing the simultaneous extraction of histone and other proteins. </span></p>',
'image_id' => '220',
'type' => 'Protocol',
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(int) 0 => array(
'id' => '4163',
'name' => 'Transcriptional programming drives Ibrutinib-resistance evolution in mantlecell lymphoma.',
'authors' => 'Zhao, Xiaohong et al.',
'description' => '<p>Ibrutinib, a bruton's tyrosine kinase (BTK) inhibitor, provokes robust clinical responses in aggressive mantle cell lymphoma (MCL), yet many patients relapse with lethal Ibrutinib-resistant (IR) disease. Here, using genomic, chemical proteomic, and drug screen profiling, we report that enhancer remodeling-mediated transcriptional activation and adaptive signaling changes drive the aggressive phenotypes of IR. Accordingly, IR MCL cells are vulnerable to inhibitors of the transcriptional machinery and especially so to inhibitors of cyclin-dependent kinase 9 (CDK9), the catalytic subunit of the positive transcription elongation factor b (P-TEFb) of RNA polymerase II (RNAPII). Further, CDK9 inhibition disables reprogrammed signaling circuits and prevents the emergence of IR in MCL. Finally, and importantly, we find that a robust and facile ex vivo image-based functional drug screening platform can predict clinical therapeutic responses of IR MCL and identify vulnerabilities that can be targeted to disable the evolution of IR.</p>',
'date' => '2021-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33730585',
'doi' => '10.1016/j.celrep.2021.108870',
'modified' => '2021-12-21 15:28:26',
'created' => '2021-12-06 15:53:19',
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(int) 1 => array(
'id' => '3784',
'name' => 'Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes.',
'authors' => 'Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Hölting TLB, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hart',
'description' => '<p>Pediatric malignancies including Ewing sarcoma (EwS) feature a paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here, we demonstrate in EwS how cooperation of dominant oncogenes and regulatory germline variants determine tumor growth, patient survival and drug response. Binding of the oncogenic EWSR1-FLI1 fusion transcription factor to a polymorphic enhancer-like DNA element controls expression of the transcription factor MYBL2 mediating these phenotypes. Whole-genome and RNA sequencing reveals that variability at this locus is inherited via the germline and is associated with variable inter-tumoral MYBL2 expression. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Collectively, we establish cooperation of somatic mutations and regulatory germline variants as a major determinant of tumor progression and highlight the importance of integrating the regulatory genome in precision medicine.</p>',
'date' => '2019-09-11',
'pmid' => 'http://www.pubmed.gov/31511524',
'doi' => '10.1038/s41467-019-12071-2',
'modified' => '2019-10-02 16:48:03',
'created' => '2019-10-02 16:16:55',
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(int) 2 => array(
'id' => '3665',
'name' => 'BCL2 Amplicon Loss and Transcriptional Remodeling Drives ABT-199 Resistance in B Cell Lymphoma Models.',
'authors' => 'Zhao X, Ren Y, Lawlor M, Shah BD, Park PMC, Lwin T, Wang X, Liu K, Wang M, Gao J, Li T, Xu M, Silva AS, Lee K, Zhang T, Koomen JM, Jiang H, Sudalagunta PR, Meads MB, Cheng F, Bi C, Fu K, Fan H, Dalton WS, Moscinski LC, Shain KH, Sotomayor EM, Wang GG, Gra',
'description' => '<p>Drug-tolerant "persister" tumor cells underlie emergence of drug-resistant clones and contribute to relapse and disease progression. Here we report that resistance to the BCL-2 targeting drug ABT-199 in models of mantle cell lymphoma and double-hit lymphoma evolves from outgrowth of persister clones displaying loss of 18q21 amplicons that harbor BCL2. Further, persister status is generated via adaptive super-enhancer remodeling that reprograms transcription and offers opportunities for overcoming ABT-199 resistance. Notably, pharmacoproteomic and pharmacogenomic screens revealed that persisters are vulnerable to inhibition of the transcriptional machinery and especially to inhibition of cyclin-dependent kinase 7 (CDK7), which is essential for the transcriptional reprogramming that drives and sustains ABT-199 resistance. Thus, transcription-targeting agents offer new approaches to disable drug resistance in B-cell lymphomas.</p>',
'date' => '2019-05-13',
'pmid' => 'http://www.pubmed.gov/31085176',
'doi' => '10.1016/j.ccell.2019.04.005',
'modified' => '2019-07-01 11:37:51',
'created' => '2019-06-21 14:55:31',
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[maximum depth reached]
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(int) 3 => array(
'id' => '3690',
'name' => 'P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.',
'authors' => 'Bugai A, Quaresma AJC, Friedel CC, Lenasi T, Düster R, Sibley CR, Fujinaga K, Kukanja P, Hennig T, Blasius M, Geyer M, Ule J, Dölken L, Barborič M',
'description' => '<p>DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain ill defined. Here, we show that following genotoxic stress, the RNA-binding motif protein 7 (RBM7) stimulates RNA polymerase II (Pol II) transcription and promotes cell viability by activating the positive transcription elongation factor b (P-TEFb) via its release from the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP). This is mediated by activation of p38, which triggers enhanced binding of RBM7 with core subunits of 7SK snRNP. In turn, P-TEFb relocates to chromatin to induce transcription of short units, including key DDR genes and multiple classes of non-coding RNAs. Critically, interfering with the axis of RBM7 and P-TEFb provokes cellular hypersensitivity to DNA-damage-inducing agents due to activation of apoptosis. Our work uncovers the importance of stress-dependent stimulation of Pol II pause release, which enables a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult.</p>',
'date' => '2019-04-18',
'pmid' => 'http://www.pubmed.gov/30824372',
'doi' => '10.1016/j.molcel.2019.01.033',
'modified' => '2019-06-28 13:53:03',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
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(int) 4 => array(
'id' => '3694',
'name' => 'A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation.',
'authors' => 'Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A',
'description' => '<p>Humoral immunity depends on efficient activation of B cells and their subsequent differentiation into antibody-secreting cells (ASCs). The transcription factor NFκB cRel is critical for B cell proliferation, but incorporating its known regulatory interactions into a mathematical model of the ASC differentiation circuit prevented ASC generation in simulations. Indeed, experimental ectopic cRel expression blocked ASC differentiation by inhibiting the transcription factor Blimp1, and in wild-type (WT) cells cRel was dynamically repressed during ASC differentiation by Blimp1 binding the Rel locus. Including this bi-stable circuit of mutual cRel-Blimp1 antagonism into a multi-scale model revealed that dynamic repression of cRel controls the switch from B cell proliferation to ASC generation phases and hence the respective cell population dynamics. Our studies provide a mechanistic explanation of how dysregulation of this bi-stable circuit might result in pathologic B cell population phenotypes and thus offer new avenues for diagnostic stratification and treatment.</p>',
'date' => '2019-03-19',
'pmid' => 'http://www.pubmed.gov/30850343',
'doi' => '10.1016/j.immuni.2019.02.004',
'modified' => '2019-06-28 13:48:31',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '3717',
'name' => 'TF-ChIP Method for Tissue-Specific Gene Targets.',
'authors' => 'Perna A, Alberi LA',
'description' => '<p>Chromatin immunoprecipitation (ChIP) is an assay developed in order to define the dynamic nature of transcription processes. This method has been widely employed to identify methylated and acetylated DNA sequences in a variety of organs both in animals and humans. Nevertheless, this technique is significantly less employed to study transcriptional targets of specific nuclear signaling factors (TFs) and the data published so far have mainly used cell culture material and have been hardly reproduced in tissue. As nuclear signaling underlies important adaptive and maladaptive responses in chronic conditions such as cancer and neurodegeneration, there is a need for streamlining the upfront workflow of TF-ChIP for subsequent target sequencing. Based on the typical low concentration of the signaling transcriptional complex and the complexity/length of the ChIP Seq protocol, the field of cellular signaling has been confronted with a major roadblock in identifying clinically relevant targets of pathological and physiological signaling pathways. The present protocol offers a standardized procedure for detecting signaling targets in any whole tissue or specific dissected regions. The advantages of the protocol compared to the existing published methods are: (1) the small amount of starting material; appropriate for tissue subregions; (2) the optimization of DNA fragmentation from whole tissue; (3) suitability for sparsely populated tissues (i.e., brain); (4) the specificity of the TF-targeting readout; and (5) high DNA quality for sequencing or hybridization. The present protocol is highly detailed and can be reproduced using both fresh and fresh-frozen tissue. This is particularly relevant in the clinical setting, where specimen integrity is often the limiting step and where transcriptional target profiling is therapeutically relevant. The method is centered on Notch signaling but can be applied to a variety of nuclear signaling pathways as long as specific antibodies are available for pull down. Taken the superior yield/readout of this procedure, ChIP may finally provide relevant information about dynamic downstream gene changes for use in both basic research and clinical applications.</p>',
'date' => '2019-03-19',
'pmid' => 'http://www.pubmed.gov/30941015',
'doi' => '10.3389/fncel.2019.00095',
'modified' => '2019-07-05 13:11:18',
'created' => '2019-07-04 10:42:34',
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[maximum depth reached]
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(int) 6 => array(
'id' => '3547',
'name' => 'A Lamina-Associated Domain Border Governs Nuclear Lamina Interactions, Transcription, and Recombination of the Tcrb Locus.',
'authors' => 'Chen S, Luperchio TR, Wong X, Doan EB, Byrd AT, Roy Choudhury K, Reddy KL, Krangel MS',
'description' => '<p>Tcrb locus V(D)J recombination is regulated by positioning at the nuclear periphery. Here, we used DamID to profile Tcrb locus interactions with the nuclear lamina at high resolution. We identified a lamina-associated domain (LAD) border composed of several CTCF-binding elements that segregates active non-LAD from inactive LAD regions of the locus. Deletion of the LAD border causes an enhancer-dependent spread of histone H3 lysine 27 acetylation from the active recombination center into recombination center-proximal LAD chromatin. This is associated with a disruption to nuclear lamina association, increased chromatin looping to the recombination center, and increased transcription and recombination of recombination center-proximal gene segments. Our results show that a LAD and LAD border are critical components of Tcrb locus gene regulation and suggest that LAD borders may generally function to constrain the activity of nearby enhancers.</p>',
'date' => '2018-11-13',
'pmid' => 'http://www.pubmed.gov/30428344',
'doi' => '10.1016/j.celrep.2018.10.052',
'modified' => '2019-02-27 15:40:26',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
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(int) 7 => array(
'id' => '3537',
'name' => 'spe-43 is required for sperm activation in C. elegans.',
'authors' => 'Krauchunas AR, Mendez E, Ni JZ, Druzhinina M, Mulia A, Parry J, Gu SG, Stanfield GM, Singson A',
'description' => '<p>Successful fertilization requires that sperm are activated prior to contacting an oocyte. In C. elegans, this activation process, called spermiogenesis, transforms round immobile spermatids into motile, fertilization-competent spermatozoa. We describe the phenotypic and genetic characterization of spe-43, a new component of the spe-8 pathway, which is required for spermiogenesis in hermaphrodites; spe-43 hermaphrodites are self-sterile, while spe-43 males show wild-type fertility. When exposed to Pronase to activate sperm in vitro, spe-43 spermatids form long rigid spikes radiating outward from the cell periphery instead of forming a motile pseudopod, indicating that spermiogenesis initiates but is not completed. Using a combination of recombinant and deletion mapping and whole genome sequencing, we identified F09E8.1 as spe-43. SPE-43 is predicted to exist in two isoforms; one isoform appears to be a single-pass transmembrane protein while the other is predicted to be a secreted protein. SPE-43 can bind to other known sperm proteins, including SPE-4 and SPE-29, which are known to impact spermiogenesis. In summary, we have identified a membrane protein that is present in C. elegans sperm and is required for sperm activation via the hermaphrodite activation signal.</p>',
'date' => '2018-04-15',
'pmid' => 'http://www.pubmed.gov/29477340',
'doi' => '10.1016/j.ydbio.2018.02.013',
'modified' => '2019-02-28 10:40:50',
'created' => '2019-02-27 12:54:44',
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[maximum depth reached]
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(int) 8 => array(
'id' => '3528',
'name' => 'Selenite and methylseleninic acid epigenetically affects distinct gene sets in myeloid leukemia: A genome wide epigenetic analysis.',
'authors' => 'Khalkar P, Ali HA, Codó P, Argelich ND, Martikainen A, Arzenani MK, Lehmann S, Walfridsson J, Ungerstedt J, Fernandes AP',
'description' => '<p>Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). Both selenite and MSA had major effects on histone marks but the effects of MSA were more pronounced. Gene ontology analysis revealed that selenite affected genes involved in response to oxygen and hypoxia, whereas MSA affected distinct gene sets associated with cell adhesion and glucocorticoid receptors, also apparent by global gene expression analysis using RNA sequencing. The correlation to adhesion was functionally confirmed by a significantly weakened ability of MSA treated cells to attach to fibronectin and linked to decreased expression of integrin beta 1. A striking loss of cellular adhesion was also confirmed in primary patient AML cells. Recent strategies to enhance the cytotoxicity of chemotherapeutic drugs by disrupting the interaction between leukemic and stromal cells in the bone marrow are of increasing interest; and organic selenium compounds like MSA might be promising candidates. In conclusion, these results provide new insight on the mechanism of action of selenium compounds, and will be of value for the understanding, usage, and development of new selenium compounds as anticancer agents.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29438720',
'doi' => '10.1016/j.freeradbiomed.2018.02.014',
'modified' => '2019-02-28 10:49:31',
'created' => '2019-02-27 12:54:44',
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'description' => '<p><span>The regular protocol for the extraction of histone requires an acid extraction, making impossible the detection of any other cytoplasmic and nuclear proteins from the same extract. Using <a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device">Bioruptor</a></span><a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device"><span>®</span></a><span>, Slimane AIT-SI-ALI and his “epigenetic and cell fate” team from the University Paris Descartes developed a protocol allowing the simultaneous extraction of histone and other proteins. </span></p>',
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'description' => '<p><span>Diagenode tubes were developed specifically for use with the Bioruptor<sup>®</sup>. They ensure a maximum energy delivery to samples with a minimal attenuation of ultrasound intensity. This guide helps you to choose the appropriate tubes for your application of interest and sonication on the Bioruptor<sup>®</sup> Standard, Plus, and Pico. </span></p>',
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'modified' => '2022-02-23 12:18:51',
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'name' => 'Selenite and methylseleninic acid epigenetically affects distinct gene sets in myeloid leukemia: A genome wide epigenetic analysis.',
'authors' => 'Khalkar P, Ali HA, Codó P, Argelich ND, Martikainen A, Arzenani MK, Lehmann S, Walfridsson J, Ungerstedt J, Fernandes AP',
'description' => '<p>Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). Both selenite and MSA had major effects on histone marks but the effects of MSA were more pronounced. Gene ontology analysis revealed that selenite affected genes involved in response to oxygen and hypoxia, whereas MSA affected distinct gene sets associated with cell adhesion and glucocorticoid receptors, also apparent by global gene expression analysis using RNA sequencing. The correlation to adhesion was functionally confirmed by a significantly weakened ability of MSA treated cells to attach to fibronectin and linked to decreased expression of integrin beta 1. A striking loss of cellular adhesion was also confirmed in primary patient AML cells. Recent strategies to enhance the cytotoxicity of chemotherapeutic drugs by disrupting the interaction between leukemic and stromal cells in the bone marrow are of increasing interest; and organic selenium compounds like MSA might be promising candidates. In conclusion, these results provide new insight on the mechanism of action of selenium compounds, and will be of value for the understanding, usage, and development of new selenium compounds as anticancer agents.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29438720',
'doi' => '10.1016/j.freeradbiomed.2018.02.014',
'modified' => '2019-02-28 10:49:31',
'created' => '2019-02-27 12:54:44',
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<div class="small-12 medium-12 large-12 columns"><br /><br />
<p><span>The Bioruptor® uses a unique system to uniformely process multiple samples in sealed tubes of 0.5 ml to 50 ml capacity. The built-in cooling system (water cooler and Single Cycle Valve) ensures high precision temperature control resulting in higher quality samples. An excellent device for shearing chromatin, cell and tissue disruption and many other applications (see below).</span></p>
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<p></p>
<p><span></span></p>
<div class="page" title="Page 9">
<div class="section">
<div class="layoutArea">
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</div>
</div>
</div>',
'label1' => 'Which Bioruptor® Plus configuration is right for you?',
'info1' => '<p><strong>B01020001</strong> - Bioruptor Plus<sup>®</sup> device with 1.5 ml (6 samples) tube holder <span>& temperature controlled system (water cooler + single cycle valve) </span><em>for recommended sample volume 100 µl - 300 µl</em></p>
<p><strong>B01020002</strong> - Bioruptor Plus<sup>®</sup> device with 1.5 ml (6 samples) and 15 ml tube holders <span>& temperature controlled system (water cooler + single cycle valve)</span> <em>for recommended sample volume 100 µl - 2 ml</em></p>
<p><strong>B01020003</strong> - Bioruptor Plus<sup>®</sup> device with 0.5 ml (12 samples) tube holder <span>& temperature controlled system (water cooler + single cycle valve)</span> <em>for recommended sample volume 50 µl - 100 µl </em></p>',
'label2' => 'Available chromatin shearing kits',
'info2' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. 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>
<tbody>
<tr valign="middle">
<td></td>
<td style="text-align: center;"><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;"><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;"><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;"><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>
<p style="text-align: left;"><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">< 0.1%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">0.2%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">1%</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">0.5%</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">No</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">Yes</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center;">
<p style="text-align: center;">up to 25 g of tissue</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td>
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<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;">
<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;">
<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;">
<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>
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'info3' => '<h3>Shearing Accessories</h3>
<table style="width: 641px;">
<thead>
<tr style="background-color: #dddddd; height: 37px;">
<td style="width: 300px; height: 37px;"><strong>Name</strong></td>
<td style="width: 171px; text-align: center; height: 37px;">Catalog number</td>
<td style="width: 160px; text-align: center; height: 37px;">Throughput</td>
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<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/0-5-0-65-ml-tube-holder-for-bioruptor-standard-plus-pico-1-pack">0.5/0.65 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200043</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">12 samples</span></td>
</tr>
<tr style="height: 38px;">
<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/1-5-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">1.5 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200011</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 38px;">
<td style="width: 300px; height: 38px;"><a href="https://www.diagenode.com/en/p/10-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">10 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 38px;"><span style="font-weight: 400;">B01200012</span></td>
<td style="width: 160px; text-align: center; height: 38px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-sonication-accessories-for-bioruptor-standard-plus-pico-1-pack">15 ml sonication accessories</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200016</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">6 samples<br /></span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">15 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200013</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">6 samples</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 300px; height: 37px;"><a href="https://www.diagenode.com/en/p/50-ml-tube-holder-for-bioruptor-standard-bioruptor-plus-1-pack">50 ml tube holder</a></td>
<td style="width: 171px; text-align: center; height: 37px;"><span style="font-weight: 400;">B01200014</span></td>
<td style="width: 160px; text-align: center; height: 37px;"><span style="font-weight: 400;">3 samples</span></td>
</tr>
</tbody>
</table>
<h3>Shearing Consumables</h3>
<table style="width: 646px;">
<thead>
<tr style="background-color: #dddddd; height: 37px;">
<td style="width: 286px; height: 37px;"><strong>Name</strong></td>
<td style="width: 76px; height: 37px; text-align: center;">Catalog Number</td>
</tr>
</thead>
<tbody>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/0-5-ml-bioruptor-microtubes-500-tubes">0.5 ml Bioruptor Plus Microtubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010013</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/1-5-ml-tpx-microtubes-300-pc">1.5 ml Bioruptor Plus TPX microtubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010010</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/10-ml-tubes-100-tubes">10 ml Bioruptor Plus tubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010012</span></td>
</tr>
<tr style="height: 37px;">
<td style="width: 286px; height: 37px;"><a href="https://www.diagenode.com/en/p/15-ml-tpx-tubes-50-pc">15 ml Bioruptor Plus TPX tubes</a></td>
<td style="width: 76px; height: 37px; text-align: center;"><span style="font-weight: 400;">C30010009</span></td>
</tr>
</tbody>
</table>
<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor_accessories/TDS-BioruptorTubes.pdf">Find datasheet for Diagenode tubes here</a></p>
<p><a href="../documents/bioruptor-organigram-tubes">Which tubes for which Bioruptor®?</a></p>',
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<div class="small-12 medium-12 large-12 columns">The most important steps for a successful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, <strong>Diagenode's Bioruptor</strong><sup>®</sup> uses state-of-the-art ultrasound <strong>ACT</strong> (<strong>A</strong>daptive <strong>C</strong>avitation <strong>T</strong>echnology) to efficiently shear chromatin. ACT enables the highest chromatin quality for high IP efficiency and sensitivity for ChIP experiments with gentle yet highly effective shearing forces. Additionally, the Bioruptor<sup>®</sup> provides a precisely controlled temperature environment that preserves chromatin from heat degradation such that protein-DNA complexes are well-preserved for sensitive, unbiased, and accurate ChIP.<br /><br /> <strong>Diagenode's Bioruptor</strong><sup>®</sup> is the instrument of choice for chromatin shearing used for a number of downstream applications such as qPCR and ChIP-seq that require optimally sheared, unbiased chromatin.</div>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/applications/pico_dna_shearing_fig2.png" /></div>
<div class="small-10 medium-10 large-10 columns end small-offset-1"><small> <br /><strong>Panel A, 10 µl volume:</strong> Chromatin samples are sheared for 10, 20 and 30 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.1 ml Bioruptor® Microtubes (Cat. No. B01200041). <strong>Panel B, 100 µl volume:</strong> Chromatin samples are sheared for 10 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.65 ml Bioruptor® Microtubes (Cat. No. WA-005-0500). <strong>Panel C, 300 µl volume:</strong> Chromatin samples are sheared for 5, 10 and 15 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using using 1.5 ml Bioruptor microtubes (Cat. No. C30010016). Prior to de-crosslinking, samples are treated with RNase cocktail mixture at 37°C during 1 hour. The sheared chromatin is then de-crosslinked overnight and phenol/chloroform purified as described in the kit manual. 10 µl of DNA (equivalent of 500, 000 cells) are analyzed on a 2% agarose gel (MW corresponds to the 100 bp DNA molecular weight marker).</small></div>
<div class="small-12 medium-12 large-12 columns"><br /><br /></div>
<div class="small-12 medium-12 large-12 columns">
<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. 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>
</div>
<div class="small-12 medium-12 large-12 columns">
<div class="page" title="Page 7">
<table>
<tbody>
<tr valign="middle">
<td></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histone)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/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;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-medium-sds-100-million-cells">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p>< 0.1%</p>
</td>
<td style="text-align: center;">
<p>0.2%</p>
</td>
<td style="text-align: center;">
<p>1%</p>
</td>
<td style="text-align: center;">
<p>0.5%</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>No</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>up to 25 g of tissue</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
</table>
<p><em><span style="font-weight: 400;">Table comes from our </span><a href="https://www.diagenode.com/protocols/bioruptor-pico-chromatin-preparation-guide"><span style="font-weight: 400;">Guide for successful chromatin preparation using the Bioruptor® Pico</span></a></em></p>
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<div class="large-12 columns">Diagenode's high yields FFPE DNA extraction using Bioruptor<sup><span>®</span></sup> is a superior method for extracting DNA for Next-Gen Sequencing. Our FFPE DNA Extraction kit contains optimized reagents that are added directly to the FFPE samples to remove paraffin with no toxic reagents, digest tissues, and purify DNA with high yields and low sample degradation. The DNA can then be analyzed by traditional methods or can be sheared with the Bioruptor<sup>®</sup> Pico ultrasonicator for downstream NGS library prep using the MicroPlex Library Preparation Kit.</div>
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<div class="small-12 medium-12 large-12 columns">In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniques for optimal sample preparation and genomic library construction. One of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size (depending on the sequencing platform) to enable sensitive and reliable NGS results. The <strong>Bioruptor</strong><sup>®</sup> <strong>Pico</strong> and the <strong>Megaruptor</strong><sup>®</sup> provide superior sample yields, fragment size, and consistency, which are essential for Next-Generation Sequencing workflows. 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<sup>®</sup></a>.</div>
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<div class="small-7 medium-7 large-7 columns text-center"><img src="https://www.diagenode.com/img/applications/true-flexibility-with-br-ngs.jpg" /></div>
<div class="small-5 medium-5 large-5 columns"><small><strong>Programmable DNA size distribution and high reproducibility with Bioruptor<sup>®</sup> Pico using 0.65 (panel A) or 0.1 ml (panel B) microtubes</strong>. <b>Panel A:</b> 200 bp after 13 cycles (13 sec ON/OFF) using 100 µl volume. Average size: 204; CV%:1.89%). <b>Panel B:</b> 200 bp after 20 cycles (30 sec ON/OFF) using 10 µl volume. (Average size: 215 bp; CV%: 6.6%). <b>Panel A & B:</b> peak electropherogram view. <b>Panel C & D:</b> virtual gel view.</small></div>
</div>
<p><br /><br /></p>
<div class="row">
<div class="small-10 medium-10 large-10 columns text-center end small-offset-1"><img src="https://www.diagenode.com/img/applications/megaruptor-short-frag.jpg" /></div>
<div class="small-12 medium-12 large-12 columns"><small><strong> Reproducible and narrow DNA size distribution with Megaruptor® using short fragment size Hydropores Validation using two different DNA sources and two different methods of analysis. A:</strong> Shearing of lambda phage genomic DNA (20 ng/μl; 150 μl/sample) sheared at different speed settings and analyzed on 1% agarose gel. <strong>B:</strong> Bioanalyzer profiles of human genomic DNA (20 ng/μl; 150 μl/sample) sheared at different software settings of 2 and 5 kb. Three independent experiments were run for each setting. (Agilent DNA 12000 kit was used for separation and fragment sizing).</small></div>
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<p><br /><br /></p>
<div class="row">
<div class="small-4 medium-4 large-4 columns text-center"><img src="https://www.diagenode.com/img/applications/megaruptor-long-frag.jpg" /></div>
<div class="small-8 medium-8 large-8 columns"><small><strong> Demonstrated shearing to fragment sizes between 15 kb and 75 kb with Megaruptor® using long fragment size Hydropores. </strong>Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. DNA was analyzed by pulsed field gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software.<br /> * indicates unsheared DNA </small></div>
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'id' => '26',
'name' => 'RNA extraction from tissue using Bioruptor® (Standard/Plus) and RNA extraction kit',
'description' => '<p><span>Isolation of intact RNA is essential for many techniques used in gene expression analysis. Efficient disruption and homogenization of animal tissues are required to ensure high yield of RNA. Disruption releases RNA, while homogenization reduces sample viscosity to facilitate RNA purification. Diagenode’s Bioruptor</span><span>® </span><span>Sonicator uses state-of-the-art ultrasound technology to efficiently disrupt and homogenize tissues in one step. Diagenode’s RNA extraction reagent (included in the RNA extraction kit) is used as sonication medium and maintains the integrity of RNA while disrupting cells and dissolving cell components. </span></p>',
'image_id' => '216',
'type' => 'Protocol',
'url' => 'files/protocols/RNA_Extraction_from_Tissue_with_Bioruptor_Standard_Plus_protocol.pdf',
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'name' => 'TAP-TAG - Procedure for the purification of a chromatin protein with Bioruptor®',
'description' => '<p><span>The Tandem Affinity Purification (TAP) is a general procedure for the purification of protein complex. The fusion of the TAP tag to the protein of interest allows the rapid purification under a native environment. Molecular complexes can then be isolated and used for various applications for the identification of partners. Slimane AIT-SI-ALI and his “epigenetic and cell fate” team from the University Paris Descartes combined the TAP tagging with the Bioruptor</span><span>®</span><span>. This combination is essential for the efficient purification of a chromatin protein. </span></p>',
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'id' => '24',
'name' => 'Western Blot - Procedure for simultaneous extraction of cytoplasmic, nuclear and chromatin protein with Bioruptor®',
'description' => '<p><span>The regular protocol for the extraction of histone requires an acid extraction, making impossible the detection of any other cytoplasmic and nuclear proteins from the same extract. Using <a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device">Bioruptor</a></span><a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device"><span>®</span></a><span>, Slimane AIT-SI-ALI and his “epigenetic and cell fate” team from the University Paris Descartes developed a protocol allowing the simultaneous extraction of histone and other proteins. </span></p>',
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'id' => '4163',
'name' => 'Transcriptional programming drives Ibrutinib-resistance evolution in mantlecell lymphoma.',
'authors' => 'Zhao, Xiaohong et al.',
'description' => '<p>Ibrutinib, a bruton's tyrosine kinase (BTK) inhibitor, provokes robust clinical responses in aggressive mantle cell lymphoma (MCL), yet many patients relapse with lethal Ibrutinib-resistant (IR) disease. Here, using genomic, chemical proteomic, and drug screen profiling, we report that enhancer remodeling-mediated transcriptional activation and adaptive signaling changes drive the aggressive phenotypes of IR. Accordingly, IR MCL cells are vulnerable to inhibitors of the transcriptional machinery and especially so to inhibitors of cyclin-dependent kinase 9 (CDK9), the catalytic subunit of the positive transcription elongation factor b (P-TEFb) of RNA polymerase II (RNAPII). Further, CDK9 inhibition disables reprogrammed signaling circuits and prevents the emergence of IR in MCL. Finally, and importantly, we find that a robust and facile ex vivo image-based functional drug screening platform can predict clinical therapeutic responses of IR MCL and identify vulnerabilities that can be targeted to disable the evolution of IR.</p>',
'date' => '2021-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33730585',
'doi' => '10.1016/j.celrep.2021.108870',
'modified' => '2021-12-21 15:28:26',
'created' => '2021-12-06 15:53:19',
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'id' => '3784',
'name' => 'Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes.',
'authors' => 'Musa J, Cidre-Aranaz F, Aynaud MM, Orth MF, Knott MML, Mirabeau O, Mazor G, Varon M, Hölting TLB, Grossetête S, Gartlgruber M, Surdez D, Gerke JS, Ohmura S, Marchetto A, Dallmayer M, Baldauf MC, Stein S, Sannino G, Li J, Romero-Pérez L, Westermann F, Hart',
'description' => '<p>Pediatric malignancies including Ewing sarcoma (EwS) feature a paucity of somatic alterations except for pathognomonic driver-mutations that cannot explain overt variations in clinical outcome. Here, we demonstrate in EwS how cooperation of dominant oncogenes and regulatory germline variants determine tumor growth, patient survival and drug response. Binding of the oncogenic EWSR1-FLI1 fusion transcription factor to a polymorphic enhancer-like DNA element controls expression of the transcription factor MYBL2 mediating these phenotypes. Whole-genome and RNA sequencing reveals that variability at this locus is inherited via the germline and is associated with variable inter-tumoral MYBL2 expression. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Collectively, we establish cooperation of somatic mutations and regulatory germline variants as a major determinant of tumor progression and highlight the importance of integrating the regulatory genome in precision medicine.</p>',
'date' => '2019-09-11',
'pmid' => 'http://www.pubmed.gov/31511524',
'doi' => '10.1038/s41467-019-12071-2',
'modified' => '2019-10-02 16:48:03',
'created' => '2019-10-02 16:16:55',
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'id' => '3665',
'name' => 'BCL2 Amplicon Loss and Transcriptional Remodeling Drives ABT-199 Resistance in B Cell Lymphoma Models.',
'authors' => 'Zhao X, Ren Y, Lawlor M, Shah BD, Park PMC, Lwin T, Wang X, Liu K, Wang M, Gao J, Li T, Xu M, Silva AS, Lee K, Zhang T, Koomen JM, Jiang H, Sudalagunta PR, Meads MB, Cheng F, Bi C, Fu K, Fan H, Dalton WS, Moscinski LC, Shain KH, Sotomayor EM, Wang GG, Gra',
'description' => '<p>Drug-tolerant "persister" tumor cells underlie emergence of drug-resistant clones and contribute to relapse and disease progression. Here we report that resistance to the BCL-2 targeting drug ABT-199 in models of mantle cell lymphoma and double-hit lymphoma evolves from outgrowth of persister clones displaying loss of 18q21 amplicons that harbor BCL2. Further, persister status is generated via adaptive super-enhancer remodeling that reprograms transcription and offers opportunities for overcoming ABT-199 resistance. Notably, pharmacoproteomic and pharmacogenomic screens revealed that persisters are vulnerable to inhibition of the transcriptional machinery and especially to inhibition of cyclin-dependent kinase 7 (CDK7), which is essential for the transcriptional reprogramming that drives and sustains ABT-199 resistance. Thus, transcription-targeting agents offer new approaches to disable drug resistance in B-cell lymphomas.</p>',
'date' => '2019-05-13',
'pmid' => 'http://www.pubmed.gov/31085176',
'doi' => '10.1016/j.ccell.2019.04.005',
'modified' => '2019-07-01 11:37:51',
'created' => '2019-06-21 14:55:31',
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(int) 3 => array(
'id' => '3690',
'name' => 'P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.',
'authors' => 'Bugai A, Quaresma AJC, Friedel CC, Lenasi T, Düster R, Sibley CR, Fujinaga K, Kukanja P, Hennig T, Blasius M, Geyer M, Ule J, Dölken L, Barborič M',
'description' => '<p>DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain ill defined. Here, we show that following genotoxic stress, the RNA-binding motif protein 7 (RBM7) stimulates RNA polymerase II (Pol II) transcription and promotes cell viability by activating the positive transcription elongation factor b (P-TEFb) via its release from the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP). This is mediated by activation of p38, which triggers enhanced binding of RBM7 with core subunits of 7SK snRNP. In turn, P-TEFb relocates to chromatin to induce transcription of short units, including key DDR genes and multiple classes of non-coding RNAs. Critically, interfering with the axis of RBM7 and P-TEFb provokes cellular hypersensitivity to DNA-damage-inducing agents due to activation of apoptosis. Our work uncovers the importance of stress-dependent stimulation of Pol II pause release, which enables a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult.</p>',
'date' => '2019-04-18',
'pmid' => 'http://www.pubmed.gov/30824372',
'doi' => '10.1016/j.molcel.2019.01.033',
'modified' => '2019-06-28 13:53:03',
'created' => '2019-06-21 14:55:31',
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'id' => '3694',
'name' => 'A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation.',
'authors' => 'Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A',
'description' => '<p>Humoral immunity depends on efficient activation of B cells and their subsequent differentiation into antibody-secreting cells (ASCs). The transcription factor NFκB cRel is critical for B cell proliferation, but incorporating its known regulatory interactions into a mathematical model of the ASC differentiation circuit prevented ASC generation in simulations. Indeed, experimental ectopic cRel expression blocked ASC differentiation by inhibiting the transcription factor Blimp1, and in wild-type (WT) cells cRel was dynamically repressed during ASC differentiation by Blimp1 binding the Rel locus. Including this bi-stable circuit of mutual cRel-Blimp1 antagonism into a multi-scale model revealed that dynamic repression of cRel controls the switch from B cell proliferation to ASC generation phases and hence the respective cell population dynamics. Our studies provide a mechanistic explanation of how dysregulation of this bi-stable circuit might result in pathologic B cell population phenotypes and thus offer new avenues for diagnostic stratification and treatment.</p>',
'date' => '2019-03-19',
'pmid' => 'http://www.pubmed.gov/30850343',
'doi' => '10.1016/j.immuni.2019.02.004',
'modified' => '2019-06-28 13:48:31',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '3717',
'name' => 'TF-ChIP Method for Tissue-Specific Gene Targets.',
'authors' => 'Perna A, Alberi LA',
'description' => '<p>Chromatin immunoprecipitation (ChIP) is an assay developed in order to define the dynamic nature of transcription processes. This method has been widely employed to identify methylated and acetylated DNA sequences in a variety of organs both in animals and humans. Nevertheless, this technique is significantly less employed to study transcriptional targets of specific nuclear signaling factors (TFs) and the data published so far have mainly used cell culture material and have been hardly reproduced in tissue. As nuclear signaling underlies important adaptive and maladaptive responses in chronic conditions such as cancer and neurodegeneration, there is a need for streamlining the upfront workflow of TF-ChIP for subsequent target sequencing. Based on the typical low concentration of the signaling transcriptional complex and the complexity/length of the ChIP Seq protocol, the field of cellular signaling has been confronted with a major roadblock in identifying clinically relevant targets of pathological and physiological signaling pathways. The present protocol offers a standardized procedure for detecting signaling targets in any whole tissue or specific dissected regions. The advantages of the protocol compared to the existing published methods are: (1) the small amount of starting material; appropriate for tissue subregions; (2) the optimization of DNA fragmentation from whole tissue; (3) suitability for sparsely populated tissues (i.e., brain); (4) the specificity of the TF-targeting readout; and (5) high DNA quality for sequencing or hybridization. The present protocol is highly detailed and can be reproduced using both fresh and fresh-frozen tissue. This is particularly relevant in the clinical setting, where specimen integrity is often the limiting step and where transcriptional target profiling is therapeutically relevant. The method is centered on Notch signaling but can be applied to a variety of nuclear signaling pathways as long as specific antibodies are available for pull down. Taken the superior yield/readout of this procedure, ChIP may finally provide relevant information about dynamic downstream gene changes for use in both basic research and clinical applications.</p>',
'date' => '2019-03-19',
'pmid' => 'http://www.pubmed.gov/30941015',
'doi' => '10.3389/fncel.2019.00095',
'modified' => '2019-07-05 13:11:18',
'created' => '2019-07-04 10:42:34',
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[maximum depth reached]
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(int) 6 => array(
'id' => '3547',
'name' => 'A Lamina-Associated Domain Border Governs Nuclear Lamina Interactions, Transcription, and Recombination of the Tcrb Locus.',
'authors' => 'Chen S, Luperchio TR, Wong X, Doan EB, Byrd AT, Roy Choudhury K, Reddy KL, Krangel MS',
'description' => '<p>Tcrb locus V(D)J recombination is regulated by positioning at the nuclear periphery. Here, we used DamID to profile Tcrb locus interactions with the nuclear lamina at high resolution. We identified a lamina-associated domain (LAD) border composed of several CTCF-binding elements that segregates active non-LAD from inactive LAD regions of the locus. Deletion of the LAD border causes an enhancer-dependent spread of histone H3 lysine 27 acetylation from the active recombination center into recombination center-proximal LAD chromatin. This is associated with a disruption to nuclear lamina association, increased chromatin looping to the recombination center, and increased transcription and recombination of recombination center-proximal gene segments. Our results show that a LAD and LAD border are critical components of Tcrb locus gene regulation and suggest that LAD borders may generally function to constrain the activity of nearby enhancers.</p>',
'date' => '2018-11-13',
'pmid' => 'http://www.pubmed.gov/30428344',
'doi' => '10.1016/j.celrep.2018.10.052',
'modified' => '2019-02-27 15:40:26',
'created' => '2019-02-27 12:54:44',
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[maximum depth reached]
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'id' => '3537',
'name' => 'spe-43 is required for sperm activation in C. elegans.',
'authors' => 'Krauchunas AR, Mendez E, Ni JZ, Druzhinina M, Mulia A, Parry J, Gu SG, Stanfield GM, Singson A',
'description' => '<p>Successful fertilization requires that sperm are activated prior to contacting an oocyte. In C. elegans, this activation process, called spermiogenesis, transforms round immobile spermatids into motile, fertilization-competent spermatozoa. We describe the phenotypic and genetic characterization of spe-43, a new component of the spe-8 pathway, which is required for spermiogenesis in hermaphrodites; spe-43 hermaphrodites are self-sterile, while spe-43 males show wild-type fertility. When exposed to Pronase to activate sperm in vitro, spe-43 spermatids form long rigid spikes radiating outward from the cell periphery instead of forming a motile pseudopod, indicating that spermiogenesis initiates but is not completed. Using a combination of recombinant and deletion mapping and whole genome sequencing, we identified F09E8.1 as spe-43. SPE-43 is predicted to exist in two isoforms; one isoform appears to be a single-pass transmembrane protein while the other is predicted to be a secreted protein. SPE-43 can bind to other known sperm proteins, including SPE-4 and SPE-29, which are known to impact spermiogenesis. In summary, we have identified a membrane protein that is present in C. elegans sperm and is required for sperm activation via the hermaphrodite activation signal.</p>',
'date' => '2018-04-15',
'pmid' => 'http://www.pubmed.gov/29477340',
'doi' => '10.1016/j.ydbio.2018.02.013',
'modified' => '2019-02-28 10:40:50',
'created' => '2019-02-27 12:54:44',
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[maximum depth reached]
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(int) 8 => array(
'id' => '3528',
'name' => 'Selenite and methylseleninic acid epigenetically affects distinct gene sets in myeloid leukemia: A genome wide epigenetic analysis.',
'authors' => 'Khalkar P, Ali HA, Codó P, Argelich ND, Martikainen A, Arzenani MK, Lehmann S, Walfridsson J, Ungerstedt J, Fernandes AP',
'description' => '<p>Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). Both selenite and MSA had major effects on histone marks but the effects of MSA were more pronounced. Gene ontology analysis revealed that selenite affected genes involved in response to oxygen and hypoxia, whereas MSA affected distinct gene sets associated with cell adhesion and glucocorticoid receptors, also apparent by global gene expression analysis using RNA sequencing. The correlation to adhesion was functionally confirmed by a significantly weakened ability of MSA treated cells to attach to fibronectin and linked to decreased expression of integrin beta 1. A striking loss of cellular adhesion was also confirmed in primary patient AML cells. Recent strategies to enhance the cytotoxicity of chemotherapeutic drugs by disrupting the interaction between leukemic and stromal cells in the bone marrow are of increasing interest; and organic selenium compounds like MSA might be promising candidates. In conclusion, these results provide new insight on the mechanism of action of selenium compounds, and will be of value for the understanding, usage, and development of new selenium compounds as anticancer agents.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29438720',
'doi' => '10.1016/j.freeradbiomed.2018.02.014',
'modified' => '2019-02-28 10:49:31',
'created' => '2019-02-27 12:54:44',
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'id' => '4129',
'product_id' => '2830',
'related_id' => '1792'
),
'Image' => array(
(int) 0 => array(
'id' => '126',
'name' => 'product/shearing_technologies/B01200040_tube_holder.jpg',
'alt' => 'some alt',
'modified' => '2018-11-28 19:48:50',
'created' => '2015-06-10 17:28:55',
'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 = ''
$country_code = 'US'
$label = '<img src="/img/banners/banner-customizer-back.png" alt=""/>'
$protocol = array(
'id' => '24',
'name' => 'Western Blot - Procedure for simultaneous extraction of cytoplasmic, nuclear and chromatin protein with Bioruptor®',
'description' => '<p><span>The regular protocol for the extraction of histone requires an acid extraction, making impossible the detection of any other cytoplasmic and nuclear proteins from the same extract. Using <a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device">Bioruptor</a></span><a href="https://www.diagenode.com/categories/bioruptor-shearing-device" title="Bioruptor Shearing device"><span>®</span></a><span>, Slimane AIT-SI-ALI and his “epigenetic and cell fate” team from the University Paris Descartes developed a protocol allowing the simultaneous extraction of histone and other proteins. </span></p>',
'image_id' => '220',
'type' => 'Protocol',
'url' => 'files/protocols/western-blot-with-bioruptor-protocol.pdf',
'slug' => 'western-blot-with-bioruptor-protocol',
'meta_keywords' => '',
'meta_description' => '',
'modified' => '2016-04-29 17:39:29',
'created' => '2015-07-20 10:35:07',
'ProductsProtocol' => array(
'id' => '206',
'product_id' => '2830',
'protocol_id' => '24'
)
)
$document = array(
'id' => '791',
'name' => 'Which tubes for which Bioruptor<sup>®</sup>? ',
'description' => '<p><span>Diagenode tubes were developed specifically for use with the Bioruptor<sup>®</sup>. They ensure a maximum energy delivery to samples with a minimal attenuation of ultrasound intensity. This guide helps you to choose the appropriate tubes for your application of interest and sonication on the Bioruptor<sup>®</sup> Standard, Plus, and Pico. </span></p>',
'image_id' => null,
'type' => 'Quick guide',
'url' => 'files/organigram/bioruptor-organigram-tubes.pdf',
'slug' => 'bioruptor-organigram-tubes',
'meta_keywords' => '',
'meta_description' => '',
'modified' => '2022-02-23 12:18:51',
'created' => '2015-07-24 16:46:15',
'ProductsDocument' => array(
'id' => '2200',
'product_id' => '2830',
'document_id' => '791'
)
)
$publication = array(
'id' => '3528',
'name' => 'Selenite and methylseleninic acid epigenetically affects distinct gene sets in myeloid leukemia: A genome wide epigenetic analysis.',
'authors' => 'Khalkar P, Ali HA, Codó P, Argelich ND, Martikainen A, Arzenani MK, Lehmann S, Walfridsson J, Ungerstedt J, Fernandes AP',
'description' => '<p>Selenium compounds have emerged as promising chemotherapeutic agents with proposed epigenetic effects, however the mechanisms and downstream effects are yet to be studied. Here we assessed the effects of the inorganic selenium compound selenite and the organic form methylseleninic acid (MSA) in a leukemic cell line K562, on active (histone H3 lysine 9 acetylation, H3K9ac and histone H3 lysine 4 tri-methylation, H3K4me3) and repressive (histone H3 lysine 9 tri-methylation, H3K9me3) histone marks by Chromatin immunoprecipitation followed by DNA sequencing (ChIP-Seq). Both selenite and MSA had major effects on histone marks but the effects of MSA were more pronounced. Gene ontology analysis revealed that selenite affected genes involved in response to oxygen and hypoxia, whereas MSA affected distinct gene sets associated with cell adhesion and glucocorticoid receptors, also apparent by global gene expression analysis using RNA sequencing. The correlation to adhesion was functionally confirmed by a significantly weakened ability of MSA treated cells to attach to fibronectin and linked to decreased expression of integrin beta 1. A striking loss of cellular adhesion was also confirmed in primary patient AML cells. Recent strategies to enhance the cytotoxicity of chemotherapeutic drugs by disrupting the interaction between leukemic and stromal cells in the bone marrow are of increasing interest; and organic selenium compounds like MSA might be promising candidates. In conclusion, these results provide new insight on the mechanism of action of selenium compounds, and will be of value for the understanding, usage, and development of new selenium compounds as anticancer agents.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29438720',
'doi' => '10.1016/j.freeradbiomed.2018.02.014',
'modified' => '2019-02-28 10:49:31',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
'id' => '3277',
'product_id' => '2830',
'publication_id' => '3528'
)
)
$externalLink = ' <a href="http://www.pubmed.gov/29438720" target="_blank"><i class="fa fa-external-link"></i></a>'include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118
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