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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
</div>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
</ul>',
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'description' => '<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p>Chromatin structure plays a key role in regulating gene expression by allowing DNA accessibility to transcriptional machinery and transcription factors. The packaging of DNA into nucleosomes forms a closed structure that is not highly accessible to transcriptional elements whereas the open nucleosome structure allows DNA to be accessible. Diagenode offers a number of solutions to help you analyze chromatin and the role of transcriptional machinery including ChIP kits, ChIPmentation kits, antibodies, pA-Tn5 and ATAC-seq kits.</p>
</div>
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<p><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"><img src="https://www.diagenode.com/img/banners/b-microchip-category.png" /></a></p>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<div id="portal" class="main-portal">
<div class="portal-inner"><nav class="portal-nav">
<ul class="tips-menu">
<li><a href="#workflow" class="tips portal button" style="background: #13b29c; color: #f3fbfa;">Chromatin immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation" class="tips portal button">ChIPmentation</a></li>
<li><a href="https://www.diagenode.com/en/categories/antibodies
" class="tips portal button">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">pA-Tn5</a></li>
<li><a href="https://www.diagenode.com/en/categories/atac-seq" class="tips portal button">ATAC-seq</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">CUT&Tag</a></li>
</ul>
</nav></div>
</div>
<p>Chromatin immunoprecipitation (ChIP) determines the location of DNA binding sites on the genome for a protein of interest, giving insights into gene expression regulation. ChIP involves the selective enrichment of a chromatin fraction containing a specific antigen. Antibodies that recognize a protein or protein modification are used to determine the relative abundance of that antigen at a specific locus or loci. ChIP can be used to compare enrichment of proteins, map protein modifications, or quantify a protein modification during a time course.</p>
<span class="anchor" id="workflow"></span>
<h4><span style="font-weight: 400;">The ChIP workflow</span></h4>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><img src="https://www.diagenode.com/img/categories/kits_chromatin_function/website-chip-workflow.jpg" />
<div id="chip_workflow" class="content">
<div class="row">
<table>
<tbody>
<tr>
<td width="50%">
<h3 class="text-center">Step by step workflow</h3>
</td>
<td width="50%">
<h3 class="text-center">Optimal solution from Diagenode</h3>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>1.</strong><span> </span>Crosslink to bind proteins to DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-1-workflow.png" width="192" height="24" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/chip-cross-link-gold-600-ul">ChIP Cross-link Gold</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>2.</strong><span> </span>Shear DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-2-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/bioruptor-pico-sonication-device#">Bioruptor<sup>®</sup><span> </span>Pico Sonication device</a></li>
<li><a href="https://www.diagenode.com/categories/chromatin-shearing">Shearing optimization reagent</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>3.</strong><span> </span>Immunoprecipitate with specific antibody</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-3-workflow.png" width="47" height="51" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/categories/chromatin-immunoprecipitation">ChIP-seq and ChIP-qPCR kits</a><span> </span>for transcription factors, histones, low inputs, plants</li>
<li><a href="https://www.diagenode.com/categories/chip-grade-antibodies">ChIP</a><span> </span>and<span> </span><a href="https://www.diagenode.com/categories/chip-seq-grade-antibodies">ChIP-seq grade</a><span> </span>antibodies</li>
<li><a href="https://www.diagenode.com/categories/ip-star">Automation available</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>4.</strong><span> </span>Reverse crosslinks and purify</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-4-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li>Diagenode's ChIP kits (contain optimal purification modules)</li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>5.</strong><span> </span><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">ChIP-qPCR</a><span> </span>or ChIP-seq library preparation</p>
</td>
<td>
<ul class="arrow">
<li>ChIP-seq:</li>
</ul>
<ul style="list-style-type: square;">
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x48-12-indices-48-rxns">MicroPlex Library Preparation for 50 pg - 5 ng</a></li>
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns">iDeal Library Preparation for > 5 ng</a></li>
</ul>
<ul class="arrow">
<li>ChIP qPCR</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</li>
</ul>
<p></p>
<h4><span style="font-weight: 400;">Products for chromatin study</span></h4>
<p><span style="font-weight: 400;"></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/crosslinking.png" alt="" width="35" height="35" /> Crosslinking<br /></b></span></strong><span style="font-weight: 400;">Efficient solution for protein-protein fixation.</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;"> <a href="../p/chip-cross-link-gold-600-ul
">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/chromatin-shearing.png" alt="" width="35" height="35" /> Chromatin shearing<br /></strong><strong><span style="font-weight: 400;">Perfectly sheared chromatin is critical for ChIP success.<span> </span><br /></span></strong><strong><a href="../categories/chromatin-shearing"><span style="font-weight: 400;">Read more</span></a><span style="font-weight: 400;"><span> </span>about solutions for successful chromatin preparation.<span> </span><br /></span></strong><strong><span style="font-weight: 400;"><a href="../categories/bioruptor-shearing-device">Read more</a><span> </span>about<span> </span></span><span style="font-weight: 400;">Bioruptor<span> </span></span><span style="font-weight: 400;">sonication.</span></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/immunoprecipitation.png" width="35" height="35" caption="false" /> Chromatin immunoprecipitation<br /></b></span></strong><span style="font-weight: 400;">Immunoprecipitation solutions for histone and transcription factor ChIP-qPCR and ChIP-seq for low inputs, plants, and animals including automated solutions</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;">. <a href="../categories/chromatin-immunoprecipitation">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/ChIPmentation.png" alt="" width="35" height="35" /> ChIPmentation<br /><span style="font-weight: 400;">ChIPmentation, an exclusive technology, is an end-to-end ChIP-seq solution for low and difficult inputs. <a href="../categories/chromatin-ip-chipmentation">Read more</a></span><br /></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-antibodies.png" alt="" width="35" height="35" /> ChIP and ChIP-seq antibodies<br /></b></span></strong><span style="font-weight: 400;">ChIP-grade antibodies are essential for success. <a href="../categories/antibodies">Learn more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-qPCR.png" width="35" height="35" caption="false" /> Primer pairs<br /></b></span></strong><span style="font-weight: 400;">Highly specific primer pairs for the amplification of the specific genomic regions. <a href="../categories/primer-pairs">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/cutandtag.png" width="35" height="35" caption="false" /> CUT&Tag solutions<br /></b></span></strong><span style="font-weight: 400;">An alternative to ChIP-seq that combines antibody-targeted controlled cleavage by a protein A-Tn5 fusion with NGS to identify the binding sites of DNA-associated proteins. <a href="../categories/cutandtag">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/dna-purification.png" width="35" height="35" caption="false" /> DNA purification<br /></b></span></strong><span style="font-weight: 400;"><a href="../categories/dna-and-rna-purification">Read more</a> about solutions for DNA purification</span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-seq.png" width="35" height="35" caption="false" /> Library preparation for ChIP-seq<br /></b></span></strong><span style="font-weight: 400;">Optimized solutions for the library preparation from low DNA input. <a href="../categories/library-preparation-for-ChIP-seq">Read more</a></span></span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-automation.png" alt="" width="35" height="35" /> ChIP and ChIP-seq automation<br /></b>Reproducibility, optimization simplicity, no variability. <a href="../categories/epigenetic-automation">Learn more</a></span></p>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<p class="text-justify">We offer <a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation" target="_blank">complete ChIP kits</a> or <strong>individual kit components</strong> from antibodies, buffers, beads, chromatin shearing, and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="center" style="text-align: center;"><a href="../pages/chip-kit-customizer-1"><img src="https://www.diagenode.com/img/banners/banner-customizer.png" alt="" /></a></div>
</div>
</div>
</div>
<h4>Chromatin resources</h4>
<h3>Posters</h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibody-chipseq-qc-using-the-ipstar-compact-poster"><span style="font-weight: 400;">Understanding our antibody QC</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibodies-you-can-trust-poster"><span style="font-weight: 400;">High quality ChIP antibodies</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-kit-results-with-true-microchip-kit-poster"><span style="font-weight: 400;">ChIP with only 10,000 cells</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/high-resolution-chipseq-profiles-with-ipstar-automated-platform-poster"><span style="font-weight: 400;">High resolution ChIP-seq using automation</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/bioinformatics-pipeline-for-chipseq-analyses"><span style="font-weight: 400;">ChIP-seq bioinformatics</span></a></li>
</ul>
<h3><span style="font-weight: 400;">Application notes</span></h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipettor-application-note"><span style="font-weight: 400;">Simple semi-automaton for easy and inexpensive ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipseq-from-human-tumor-tissue"><span style="font-weight: 400;">Performing ChIP-seq on human tumor tissue</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/plant-chip-seq-application-note"><span style="font-weight: 400;">Plant ChIP-seq – a successful method</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-seq-application-note"><span style="font-weight: 400;">Best workflow practices for low input ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/files/application_notes/AN-ChIP-Cas9-02_2018.pdf"><span style="font-weight: 400;">Optimize the selection of guide RNA by ChIP to keep CRISPR on-target</span></a></li>
</ul>
<h3>Publications related to ChIP</h3>
<ul>
<li><a href="https://www.diagenode.com/en/publications/view/3373">Corticosteroid receptors adopt distinct cyclical transcriptional signatures</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3347">Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3355">Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile</a></li>
</ul>
<h3><span style="font-weight: 400;">Brochures</span></h3>
<ul>
<li><a href="https://www.diagenode.com/files/brochures/Chromatin_Immunoprecipitation_Brochure.pdf"><b>Chromatin </b><span style="font-weight: 400;">products brochure</span></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Epigenetic_Antibodies_Brochure.pdf"><span style="font-weight: 400;">Epigenetic<span> </span></span><b>Antibodies</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Bioruptor_Sonicator_Brochure.pdf"><span style="font-weight: 400;">Bioruptor for<span> </span></span><b>chromatin shearing</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/IPStar_Automated_System_Brochure.pdf"><span style="font-weight: 400;">Automating<span> </span></span><b>ChIP</b><span style="font-weight: 400;"><span> </span>and<span> </span></span><b>ChIP-seq</b></a></li>
</ul>
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'meta_keywords' => 'Chromatin function,Chromatin shearing,Chromatin immunoprecipitation,Chromatin assembly',
'meta_description' => 'Diagenode offers a number of unique solutions and kits to make Diagenode offers chromatin immunoprecipitation kits have been designed to meet a wide variety of research needs and accessible',
'meta_title' => 'Chromatin Function Kit for Unique Solutions and Kits to make Chromatin Research| Diagenode',
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'name' => 'ATAC-seq Kit - Manual',
'description' => '<p class="p1">Gene expression is carefully regulated in the cells in order to manage a wide range of biological functions. The structure of chromatin is quite dynamic and contributes to this crucial regulatory process.</p>
<p class="p1">ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by nextgeneration sequencing, is a key technology to easily identify the “open” regions of the chromatin, which are usually associated with permissive gene expression. Indeed, the nuclei of the samples are incubated with a transposase, and only the genomic regions associated with open chromatin will be accessible to this transposase. During the process those regions will be cut and sequencing adaptors will be added, allowing their sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only., giving a map of the chromatin status in the whole genome of the sample.</p>
<p class="p1">The Diagenode’s ATAC-seq kit is based on a highly validated protocol, used for years in our Epigenomics Profiling Services offer and takes advantage of many successful Diagenode’s tools, such as the loaded Tagmentase (Tn5 transposase), the MicroChIP DiaPure Columns and the Primer indexes for tagmented libraries kits.</p>',
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'description' => '<p>Whether you are experienced or new to the field of chromatin immunoprecipitation, Diagenode has everything you need to make ChIP easy and convenient while ensuring consistent data between samples and experiments. As an expert in the field of epigenetics, Diagenode is committed to providing complete solutions from chromatin shearing reagents, shearing instruments such as the Bioruptor® (the gold standard for chromatin shearing), ChIP kits, the largest number of validated and trusted antibodies on the market, and the SX-8G IP-Star® Compact Automated System to achieve unparalleled productivity and reproducibility.</p>',
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'id' => '4984',
'name' => 'DNA demethylation triggers cell free DNA release in colorectal cancer cells',
'authors' => 'Valeria Pessei et al.',
'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Liquid biopsy based on cell-free DNA (cfDNA) analysis holds significant promise as a minimally invasive approach for the diagnosis, genotyping, and monitoring of solid malignancies. Human tumors release cfDNA in the bloodstream through a combination of events, including cell death, active and passive release. However, the precise mechanisms leading to cfDNA shedding remain to be characterized. Addressing this question in patients is confounded by several factors, such as tumor burden extent, anatomical and vasculature barriers, and release of nucleic acids from normal cells. In this work, we exploited cancer models to dissect basic mechanisms of DNA release.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Methods</h3>
<p>We measured cell loss ratio, doubling time, and cfDNA release in the supernatant of a colorectal cancer (CRC) cell line collection (<i>N</i> = 76) representative of the molecular subtypes previously identified in cancer patients. Association analyses between quantitative parameters of cfDNA release, cell proliferation, and molecular features were evaluated. Functional experiments were performed to test the impact of modulating DNA methylation on cfDNA release.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>Higher levels of supernatant cfDNA were significantly associated with slower cell cycling and increased cell death. In addition, a higher cfDNA shedding was found in non-CpG Island Methylator Phenotype (CIMP) models. These results indicate a positive correlation between lower methylation and increased cfDNA levels. To explore this further, we exploited methylation microarrays to identify a subset of probes significantly associated with cfDNA shedding and derive a methylation signature capable of discriminating high from low cfDNA releasers. We applied this signature to an independent set of 176 CRC cell lines and patient derived organoids to select 14 models predicted to be low or high releasers. The methylation profile successfully predicted the amount of cfDNA released in the supernatant. At the functional level, genetic ablation of DNA methyl-transferases increased chromatin accessibility and DNA fragmentation, leading to increased cfDNA release in isogenic CRC cell lines. Furthermore, in vitro treatment of five low releaser CRC cells with a demethylating agent was able to induce a significant increase in cfDNA shedding.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusions</h3>
<p>Methylation status of cancer cell lines contributes to the variability of cfDNA shedding in vitro. Changes in methylation pattern are associated with cfDNA release levels and might be exploited to increase sensitivity of liquid biopsy assays.</p>',
'date' => '2024-10-09',
'pmid' => 'https://link.springer.com/article/10.1186/s13073-024-01386-5',
'doi' => 'https://doi.org/10.1186/s13073-024-01386-5',
'modified' => '2024-10-14 08:56:24',
'created' => '2024-10-14 08:56:24',
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(int) 1 => array(
'id' => '4967',
'name' => 'Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila genome',
'authors' => 'Varoqui M. et al.',
'description' => '<p><span>Transposable elements (TEs), widespread genetic parasites, pose potential threats to the stability of their host genomes. Hence, the interactions observed today between TEs and their host genomes, as well as among the different TE species coexisting in the same host, likely reflect those that did not lead to the extinction of either the host or the TEs. It is not clear to what extent the expression and integration steps of the TE replication cycles are involved in this ‘peaceful’ coexistence. Here, we show that four Drosophila LTR RetroTransposable Elements (LTR-RTEs), although sharing the same overall integration mechanism, preferentially integrate into distinct open chromatin domains of the host germline. Notably, the differential expressions of the gtwin and ZAM LTR-RTEs in ovarian and embryonic somatic tissues, respectively, result in differential integration timings and targeting of accessible chromatin landscapes that differ between early and late embryonic nuclei, highlighting connections between temporal and spatial LTR-RTEs niche partitionings.</span></p>',
'date' => '2024-08-16',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.08.14.607943v1',
'doi' => 'https://doi.org/10.1101/2024.08.14.607943',
'modified' => '2024-09-02 10:29:44',
'created' => '2024-09-02 10:29:44',
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(int) 2 => array(
'id' => '4933',
'name' => 'Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches',
'authors' => 'Lee M. et al.',
'description' => '<p><span>Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.</span></p>',
'date' => '2024-04-05',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38580401/',
'doi' => '10.1101/gr.277926.123',
'modified' => '2024-04-09 00:19:18',
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'id' => '4895',
'name' => 'Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing',
'authors' => 'Santhanagopalan I. et al.',
'description' => '<p class="section-title u-h4 u-margin-l-top u-margin-xs-bottom">Highlights</p>
<div id="abssec0020">
<ul class="list">
<li class="react-xocs-list-item">
<p id="p0010">Optimized isolation of nuclei from the green model alga<span> </span><em>Chlamydomonas reinhardtii</em></p>
</li>
<li class="react-xocs-list-item">
<p id="p0010"><em></em></p>
<p id="p0015">Tag-free isolation from both cell-walled and cell wall-deficient algae strains</p>
</li>
<li class="react-xocs-list-item">
<p id="p0015"></p>
<p id="p0020">Key steps for an effective and fast isolation and quantification procedure of nuclei</p>
</li>
<li class="react-xocs-list-item">
<p><span class="list-label"></span>Extracts at a quality suitable for ATAC-sequencing</p>
</li>
</ul>
</div>',
'date' => '2024-03-15',
'pmid' => 'https://www.sciencedirect.com/science/article/pii/S2666166723007311',
'doi' => 'https://doi.org/10.1016/j.xpro.2023.102764',
'modified' => '2024-02-09 12:37:32',
'created' => '2024-01-22 13:39:58',
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(int) 4 => array(
'id' => '4917',
'name' => 'Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition',
'authors' => 'Trembley B.J.M. et al.',
'description' => '<p><span>Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in </span><i>Arabidopsis thaliana</i><span><span> </span>we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.</span></p>',
'date' => '2024-02-26',
'pmid' => 'https://www.nature.com/articles/s41467-024-46082-5',
'doi' => 'https://doi.org/10.1038/s41467-024-46082-5',
'modified' => '2024-02-29 11:56:56',
'created' => '2024-02-29 11:56:56',
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(int) 5 => array(
'id' => '4910',
'name' => 'The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation',
'authors' => 'Kim M. et al.',
'description' => '<p><span>During human pregnancy, extravillous trophoblasts play crucial roles in placental invasion into the maternal decidua and spiral artery remodeling. However, regulatory factors and their action mechanisms modulating human extravillous trophoblast specification have been unknown. By analyzing dynamic changes in transcriptome and enhancer profile during human trophoblast stem cell to extravillous trophoblast differentiation, we define stage-specific regulators, including an early-stage transcription factor, TFAP2C, and multiple late-stage transcription factors. Loss-of-function studies confirm the requirement of all transcription factors identified for adequate differentiation, and we reveal that the dynamic changes in the levels of TFAP2C are essential. Notably, TFAP2C pre-occupies the regulatory elements of the inactive extravillous trophoblast-active genes during the early stage of differentiation, and the late-stage transcription factors directly activate extravillous trophoblast-active genes, including themselves as differentiation further progresses, suggesting sequential actions of transcription factors assuring differentiation. Our results reveal stage-specific transcription factors and their inter-connected regulatory mechanisms modulating extravillous trophoblast differentiation, providing a framework for understanding early human placentation and placenta-related complications.</span></p>',
'date' => '2024-02-12',
'pmid' => 'https://www.nature.com/articles/s41467-024-45669-2',
'doi' => 'https://doi.org/10.1038/s41467-024-45669-2',
'modified' => '2024-02-15 10:43:52',
'created' => '2024-02-15 10:43:52',
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(int) 6 => array(
'id' => '4928',
'name' => 'DMSO derives Trophectoderm and Clonal Blastoid from Single Human Pluripotent Stem Cell',
'authors' => 'Alsolami S. et al.',
'description' => '<p><span>Human naïve pluripotent stem cells (nPSCs) can differentiate into extra-embryonic trophectoderm (TE), a critical step in the generation of the integrated embryo model termed blastoid. The current paradigm of blastoid generation necessitates the aggregation of dozens of nPSCs treated with multiple small molecule inhibitors, growth factors, or genetic modifications to initiate TE differentiation. The presence of complex crosstalk among pathways and cellular heterogeneity in these models complicates mechanistic study and genetic screens. Here, we show that a single small molecule, dimethyl sulfoxide (DMSO), potently induces TE differentiation in basal medium without pharmacological and genetic perturbations. DMSO enhances blastoid generation and, more importantly, is sufficient for blastoid generation by itself. DMSO blastoids resemble blastocysts in morphology and lineage composition. DMSO induces blastoid formation through PKC signaling and cell cycle regulation. Lastly, DMSO enables single nPSC-derived clonal blastoids, which could facilitate genetic screens for mechanistic understanding of human embryogenesis.</span></p>',
'date' => '2024-01-01',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2023.12.31.573770v1.abstract',
'doi' => 'https://doi.org/10.1101/2023.12.31.573770',
'modified' => '2024-03-27 15:18:04',
'created' => '2024-03-27 15:18:04',
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(int) 7 => array(
'id' => '4887',
'name' => 'In vitro production of cat-restricted Toxoplasma pre-sexual stages',
'authors' => 'Antunes, A.V. et al.',
'description' => '<p><span>Sexual reproduction of </span><i>Toxoplasma gondii</i><span>, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Farhat, D. C. et al. A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment. Nat. Microbiol. 5, 570–583 (2020)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR1" id="ref-link-section-d277698175e527">1</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 2" title="Bougdour, A. et al. Drug inhibition of HDAC3 and epigenetic control of differentiation in Apicomplexa parasites. J. Exp. Med. 206, 953–966 (2009)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR2" id="ref-link-section-d277698175e530">2</a></sup><span>. Here we found that the transcription factors AP2XII-1 and AP2XI-2 operate during the tachyzoite stage, a hallmark of acute toxoplasmosis, to silence genes necessary for merozoites, a developmental stage critical for subsequent sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a marked change in the transcriptional program, promoting a full transition from tachyzoites to merozoites. These in vitro-cultured pre-gametes have unique protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit MORC and HDAC3 (ref. </span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Farhat, D. C. et al. A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment. Nat. Microbiol. 5, 570–583 (2020)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR1" id="ref-link-section-d277698175e534">1</a></sup><span>), thereby limiting chromatin accessibility and transcription. Consequently, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. Successful production of merozoites in vitro paves the way for future studies on<span> </span></span><i>Toxoplasma</i><span><span> </span>sexual development without the need for cat infections and holds promise for the development of therapies to prevent parasite transmission.</span></p>',
'date' => '2023-12-13',
'pmid' => 'https://www.nature.com/articles/s41586-023-06821-y',
'doi' => 'https://doi.org/10.1038/s41586-023-06821-y',
'modified' => '2023-12-18 10:40:50',
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'id' => '4939',
'name' => 'Vaginal microbes alter epithelial transcriptomic and epigenomic modifications providing insight into the molecular mechanisms for susceptibility to adverse reproductive outcomes',
'authors' => 'Elovitz M. et al.',
'description' => '<p><span>The cervicovaginal microbiome is highly associated with women's health with microbial communities dominated by </span><i>Lactobacillus</i><span><span> </span>spp. being considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes including<span> </span></span><i>Gardnerella vaginalis</i><span>, have been associated with adverse reproductive outcomes. However, the molecular pathways modulated by microbe interactions with the cervicovaginal epithelia remain unclear. Using RNA-sequencing, we characterize the<span> </span></span><i>in vitro</i><span><span> </span>cervicovaginal epithelial transcriptional response to different vaginal bacteria and their culture supernatants. We showed that<span> </span></span><i>G. vaginalis</i><span><span> </span>upregulated genes were associated with an activated innate immune response including anti-microbial peptides and inflammasome pathways, represented by NLRP3-mediated increases in caspase-1, IL-1β and cell death. Cervicovaginal epithelial cells exposed to<span> </span></span><i>L. crispatus</i><span><span> </span>showed limited transcriptomic changes, while exposure to<span> </span></span><i>L. crispatus</i><span><span> </span>culture supernatants resulted in a shift in the epigenomic landscape of cervical epithelial cells. ATAC-sequencing confirmed epigenetic changes with reduced chromatin accessibility. This study reveals new insight into host-microbe interactions in the lower reproductive tract and suggest potential therapeutic strategies leveraging the vaginal microbiome to improve reproductive health.</span></p>',
'date' => '2023-11-16',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38014044/',
'doi' => '10.21203/rs.3.rs-3580132/v1',
'modified' => '2024-06-07 15:47:48',
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(int) 9 => array(
'id' => '4927',
'name' => 'Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells',
'authors' => 'Liu H. et al.',
'description' => '<p><span>Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few studies uncover the effects of inflammatory stresses on chromatin architecture. We used integrative analysis of ATAC-seq and RNA-seq data to investigate chromatin alterations in human endothelial cells in response to TNF-alpha and febrile-range heat stress exposure. Multi-omics data analysis suggests a correlation between the transcription of stress-related genes and endothelial dysfunction drivers with chromatin regions exhibiting differential accessibility. Moreover, microscopy identified the dynamics in the nuclear organization, specifically, the changes in a subset of heterochromatic nucleoli-associated chromatin domains, the centromeres. Upon inflammatory stress exposure, the centromeres decreased association with nucleoli in a p38-dependent manner and increased the number of transcripts from pericentromeric regions. Overall, we provide two lines of evidence that suggest chromatin alterations in vascular endothelial cells during inflammatory stresses.</span></p>',
'date' => '2023-10-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10614786/',
'doi' => '10.1101/2023.10.11.561959',
'modified' => '2024-03-27 15:15:21',
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(int) 10 => array(
'id' => '4880',
'name' => 'Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates',
'authors' => 'Uckelmann M. et al.',
'description' => '<p><span>The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the three dimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.</span></p>',
'date' => '2023-05-09',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2023.05.08.539931v1.abstract',
'doi' => 'https://doi.org/10.1101/2023.05.08.539931',
'modified' => '2023-11-10 15:43:37',
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'id' => '4810',
'name' => 'UMSBP2 is chromatin remodeler that functions in regulation of geneexpression and suppression of antigenic variation in trypanosomes.',
'authors' => 'Soni A. et al.',
'description' => '<p><span>Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.</span></p>',
'date' => '2023-05-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37207337',
'doi' => '10.1093/nar/gkad402',
'modified' => '2023-06-15 08:54:17',
'created' => '2023-06-13 21:11:31',
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
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<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
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<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
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<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
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<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'description' => '<p><span>Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.</span></p>',
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
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<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
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<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
'info2' => '<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig1.png" alt="library prepared with the Diagenode ATAC-seq kit " width="500px" caption="false" /></p>
<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
</ul>',
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/atacseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
</div>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
'info2' => '<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig1.png" alt="library prepared with the Diagenode ATAC-seq kit " width="500px" caption="false" /></p>
<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
</ul>',
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<div class="small-12 medium-8 large-8 columns"><br />
<p>Chromatin structure plays a key role in regulating gene expression by allowing DNA accessibility to transcriptional machinery and transcription factors. The packaging of DNA into nucleosomes forms a closed structure that is not highly accessible to transcriptional elements whereas the open nucleosome structure allows DNA to be accessible. Diagenode offers a number of solutions to help you analyze chromatin and the role of transcriptional machinery including ChIP kits, ChIPmentation kits, antibodies, pA-Tn5 and ATAC-seq kits.</p>
</div>
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<p><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"><img src="https://www.diagenode.com/img/banners/b-microchip-category.png" /></a></p>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<div id="portal" class="main-portal">
<div class="portal-inner"><nav class="portal-nav">
<ul class="tips-menu">
<li><a href="#workflow" class="tips portal button" style="background: #13b29c; color: #f3fbfa;">Chromatin immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation" class="tips portal button">ChIPmentation</a></li>
<li><a href="https://www.diagenode.com/en/categories/antibodies
" class="tips portal button">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">pA-Tn5</a></li>
<li><a href="https://www.diagenode.com/en/categories/atac-seq" class="tips portal button">ATAC-seq</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">CUT&Tag</a></li>
</ul>
</nav></div>
</div>
<p>Chromatin immunoprecipitation (ChIP) determines the location of DNA binding sites on the genome for a protein of interest, giving insights into gene expression regulation. ChIP involves the selective enrichment of a chromatin fraction containing a specific antigen. Antibodies that recognize a protein or protein modification are used to determine the relative abundance of that antigen at a specific locus or loci. ChIP can be used to compare enrichment of proteins, map protein modifications, or quantify a protein modification during a time course.</p>
<span class="anchor" id="workflow"></span>
<h4><span style="font-weight: 400;">The ChIP workflow</span></h4>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><img src="https://www.diagenode.com/img/categories/kits_chromatin_function/website-chip-workflow.jpg" />
<div id="chip_workflow" class="content">
<div class="row">
<table>
<tbody>
<tr>
<td width="50%">
<h3 class="text-center">Step by step workflow</h3>
</td>
<td width="50%">
<h3 class="text-center">Optimal solution from Diagenode</h3>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>1.</strong><span> </span>Crosslink to bind proteins to DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-1-workflow.png" width="192" height="24" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/chip-cross-link-gold-600-ul">ChIP Cross-link Gold</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>2.</strong><span> </span>Shear DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-2-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/bioruptor-pico-sonication-device#">Bioruptor<sup>®</sup><span> </span>Pico Sonication device</a></li>
<li><a href="https://www.diagenode.com/categories/chromatin-shearing">Shearing optimization reagent</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>3.</strong><span> </span>Immunoprecipitate with specific antibody</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-3-workflow.png" width="47" height="51" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/categories/chromatin-immunoprecipitation">ChIP-seq and ChIP-qPCR kits</a><span> </span>for transcription factors, histones, low inputs, plants</li>
<li><a href="https://www.diagenode.com/categories/chip-grade-antibodies">ChIP</a><span> </span>and<span> </span><a href="https://www.diagenode.com/categories/chip-seq-grade-antibodies">ChIP-seq grade</a><span> </span>antibodies</li>
<li><a href="https://www.diagenode.com/categories/ip-star">Automation available</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>4.</strong><span> </span>Reverse crosslinks and purify</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-4-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li>Diagenode's ChIP kits (contain optimal purification modules)</li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>5.</strong><span> </span><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">ChIP-qPCR</a><span> </span>or ChIP-seq library preparation</p>
</td>
<td>
<ul class="arrow">
<li>ChIP-seq:</li>
</ul>
<ul style="list-style-type: square;">
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x48-12-indices-48-rxns">MicroPlex Library Preparation for 50 pg - 5 ng</a></li>
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns">iDeal Library Preparation for > 5 ng</a></li>
</ul>
<ul class="arrow">
<li>ChIP qPCR</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</li>
</ul>
<p></p>
<h4><span style="font-weight: 400;">Products for chromatin study</span></h4>
<p><span style="font-weight: 400;"></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/crosslinking.png" alt="" width="35" height="35" /> Crosslinking<br /></b></span></strong><span style="font-weight: 400;">Efficient solution for protein-protein fixation.</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;"> <a href="../p/chip-cross-link-gold-600-ul
">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/chromatin-shearing.png" alt="" width="35" height="35" /> Chromatin shearing<br /></strong><strong><span style="font-weight: 400;">Perfectly sheared chromatin is critical for ChIP success.<span> </span><br /></span></strong><strong><a href="../categories/chromatin-shearing"><span style="font-weight: 400;">Read more</span></a><span style="font-weight: 400;"><span> </span>about solutions for successful chromatin preparation.<span> </span><br /></span></strong><strong><span style="font-weight: 400;"><a href="../categories/bioruptor-shearing-device">Read more</a><span> </span>about<span> </span></span><span style="font-weight: 400;">Bioruptor<span> </span></span><span style="font-weight: 400;">sonication.</span></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/immunoprecipitation.png" width="35" height="35" caption="false" /> Chromatin immunoprecipitation<br /></b></span></strong><span style="font-weight: 400;">Immunoprecipitation solutions for histone and transcription factor ChIP-qPCR and ChIP-seq for low inputs, plants, and animals including automated solutions</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;">. <a href="../categories/chromatin-immunoprecipitation">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/ChIPmentation.png" alt="" width="35" height="35" /> ChIPmentation<br /><span style="font-weight: 400;">ChIPmentation, an exclusive technology, is an end-to-end ChIP-seq solution for low and difficult inputs. <a href="../categories/chromatin-ip-chipmentation">Read more</a></span><br /></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-antibodies.png" alt="" width="35" height="35" /> ChIP and ChIP-seq antibodies<br /></b></span></strong><span style="font-weight: 400;">ChIP-grade antibodies are essential for success. <a href="../categories/antibodies">Learn more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-qPCR.png" width="35" height="35" caption="false" /> Primer pairs<br /></b></span></strong><span style="font-weight: 400;">Highly specific primer pairs for the amplification of the specific genomic regions. <a href="../categories/primer-pairs">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/cutandtag.png" width="35" height="35" caption="false" /> CUT&Tag solutions<br /></b></span></strong><span style="font-weight: 400;">An alternative to ChIP-seq that combines antibody-targeted controlled cleavage by a protein A-Tn5 fusion with NGS to identify the binding sites of DNA-associated proteins. <a href="../categories/cutandtag">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/dna-purification.png" width="35" height="35" caption="false" /> DNA purification<br /></b></span></strong><span style="font-weight: 400;"><a href="../categories/dna-and-rna-purification">Read more</a> about solutions for DNA purification</span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-seq.png" width="35" height="35" caption="false" /> Library preparation for ChIP-seq<br /></b></span></strong><span style="font-weight: 400;">Optimized solutions for the library preparation from low DNA input. <a href="../categories/library-preparation-for-ChIP-seq">Read more</a></span></span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-automation.png" alt="" width="35" height="35" /> ChIP and ChIP-seq automation<br /></b>Reproducibility, optimization simplicity, no variability. <a href="../categories/epigenetic-automation">Learn more</a></span></p>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<p class="text-justify">We offer <a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation" target="_blank">complete ChIP kits</a> or <strong>individual kit components</strong> from antibodies, buffers, beads, chromatin shearing, and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="center" style="text-align: center;"><a href="../pages/chip-kit-customizer-1"><img src="https://www.diagenode.com/img/banners/banner-customizer.png" alt="" /></a></div>
</div>
</div>
</div>
<h4>Chromatin resources</h4>
<h3>Posters</h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibody-chipseq-qc-using-the-ipstar-compact-poster"><span style="font-weight: 400;">Understanding our antibody QC</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibodies-you-can-trust-poster"><span style="font-weight: 400;">High quality ChIP antibodies</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-kit-results-with-true-microchip-kit-poster"><span style="font-weight: 400;">ChIP with only 10,000 cells</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/high-resolution-chipseq-profiles-with-ipstar-automated-platform-poster"><span style="font-weight: 400;">High resolution ChIP-seq using automation</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/bioinformatics-pipeline-for-chipseq-analyses"><span style="font-weight: 400;">ChIP-seq bioinformatics</span></a></li>
</ul>
<h3><span style="font-weight: 400;">Application notes</span></h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipettor-application-note"><span style="font-weight: 400;">Simple semi-automaton for easy and inexpensive ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipseq-from-human-tumor-tissue"><span style="font-weight: 400;">Performing ChIP-seq on human tumor tissue</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/plant-chip-seq-application-note"><span style="font-weight: 400;">Plant ChIP-seq – a successful method</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-seq-application-note"><span style="font-weight: 400;">Best workflow practices for low input ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/files/application_notes/AN-ChIP-Cas9-02_2018.pdf"><span style="font-weight: 400;">Optimize the selection of guide RNA by ChIP to keep CRISPR on-target</span></a></li>
</ul>
<h3>Publications related to ChIP</h3>
<ul>
<li><a href="https://www.diagenode.com/en/publications/view/3373">Corticosteroid receptors adopt distinct cyclical transcriptional signatures</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3347">Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3355">Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile</a></li>
</ul>
<h3><span style="font-weight: 400;">Brochures</span></h3>
<ul>
<li><a href="https://www.diagenode.com/files/brochures/Chromatin_Immunoprecipitation_Brochure.pdf"><b>Chromatin </b><span style="font-weight: 400;">products brochure</span></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Epigenetic_Antibodies_Brochure.pdf"><span style="font-weight: 400;">Epigenetic<span> </span></span><b>Antibodies</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Bioruptor_Sonicator_Brochure.pdf"><span style="font-weight: 400;">Bioruptor for<span> </span></span><b>chromatin shearing</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/IPStar_Automated_System_Brochure.pdf"><span style="font-weight: 400;">Automating<span> </span></span><b>ChIP</b><span style="font-weight: 400;"><span> </span>and<span> </span></span><b>ChIP-seq</b></a></li>
</ul>
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'description' => '<p class="p1">Gene expression is carefully regulated in the cells in order to manage a wide range of biological functions. The structure of chromatin is quite dynamic and contributes to this crucial regulatory process.</p>
<p class="p1">ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by nextgeneration sequencing, is a key technology to easily identify the “open” regions of the chromatin, which are usually associated with permissive gene expression. Indeed, the nuclei of the samples are incubated with a transposase, and only the genomic regions associated with open chromatin will be accessible to this transposase. During the process those regions will be cut and sequencing adaptors will be added, allowing their sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only., giving a map of the chromatin status in the whole genome of the sample.</p>
<p class="p1">The Diagenode’s ATAC-seq kit is based on a highly validated protocol, used for years in our Epigenomics Profiling Services offer and takes advantage of many successful Diagenode’s tools, such as the loaded Tagmentase (Tn5 transposase), the MicroChIP DiaPure Columns and the Primer indexes for tagmented libraries kits.</p>',
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'description' => '<p>Whether you are experienced or new to the field of chromatin immunoprecipitation, Diagenode has everything you need to make ChIP easy and convenient while ensuring consistent data between samples and experiments. As an expert in the field of epigenetics, Diagenode is committed to providing complete solutions from chromatin shearing reagents, shearing instruments such as the Bioruptor® (the gold standard for chromatin shearing), ChIP kits, the largest number of validated and trusted antibodies on the market, and the SX-8G IP-Star® Compact Automated System to achieve unparalleled productivity and reproducibility.</p>',
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'Publication' => array(
(int) 0 => array(
'id' => '4984',
'name' => 'DNA demethylation triggers cell free DNA release in colorectal cancer cells',
'authors' => 'Valeria Pessei et al.',
'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Liquid biopsy based on cell-free DNA (cfDNA) analysis holds significant promise as a minimally invasive approach for the diagnosis, genotyping, and monitoring of solid malignancies. Human tumors release cfDNA in the bloodstream through a combination of events, including cell death, active and passive release. However, the precise mechanisms leading to cfDNA shedding remain to be characterized. Addressing this question in patients is confounded by several factors, such as tumor burden extent, anatomical and vasculature barriers, and release of nucleic acids from normal cells. In this work, we exploited cancer models to dissect basic mechanisms of DNA release.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Methods</h3>
<p>We measured cell loss ratio, doubling time, and cfDNA release in the supernatant of a colorectal cancer (CRC) cell line collection (<i>N</i> = 76) representative of the molecular subtypes previously identified in cancer patients. Association analyses between quantitative parameters of cfDNA release, cell proliferation, and molecular features were evaluated. Functional experiments were performed to test the impact of modulating DNA methylation on cfDNA release.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>Higher levels of supernatant cfDNA were significantly associated with slower cell cycling and increased cell death. In addition, a higher cfDNA shedding was found in non-CpG Island Methylator Phenotype (CIMP) models. These results indicate a positive correlation between lower methylation and increased cfDNA levels. To explore this further, we exploited methylation microarrays to identify a subset of probes significantly associated with cfDNA shedding and derive a methylation signature capable of discriminating high from low cfDNA releasers. We applied this signature to an independent set of 176 CRC cell lines and patient derived organoids to select 14 models predicted to be low or high releasers. The methylation profile successfully predicted the amount of cfDNA released in the supernatant. At the functional level, genetic ablation of DNA methyl-transferases increased chromatin accessibility and DNA fragmentation, leading to increased cfDNA release in isogenic CRC cell lines. Furthermore, in vitro treatment of five low releaser CRC cells with a demethylating agent was able to induce a significant increase in cfDNA shedding.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusions</h3>
<p>Methylation status of cancer cell lines contributes to the variability of cfDNA shedding in vitro. Changes in methylation pattern are associated with cfDNA release levels and might be exploited to increase sensitivity of liquid biopsy assays.</p>',
'date' => '2024-10-09',
'pmid' => 'https://link.springer.com/article/10.1186/s13073-024-01386-5',
'doi' => 'https://doi.org/10.1186/s13073-024-01386-5',
'modified' => '2024-10-14 08:56:24',
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(int) 1 => array(
'id' => '4967',
'name' => 'Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila genome',
'authors' => 'Varoqui M. et al.',
'description' => '<p><span>Transposable elements (TEs), widespread genetic parasites, pose potential threats to the stability of their host genomes. Hence, the interactions observed today between TEs and their host genomes, as well as among the different TE species coexisting in the same host, likely reflect those that did not lead to the extinction of either the host or the TEs. It is not clear to what extent the expression and integration steps of the TE replication cycles are involved in this ‘peaceful’ coexistence. Here, we show that four Drosophila LTR RetroTransposable Elements (LTR-RTEs), although sharing the same overall integration mechanism, preferentially integrate into distinct open chromatin domains of the host germline. Notably, the differential expressions of the gtwin and ZAM LTR-RTEs in ovarian and embryonic somatic tissues, respectively, result in differential integration timings and targeting of accessible chromatin landscapes that differ between early and late embryonic nuclei, highlighting connections between temporal and spatial LTR-RTEs niche partitionings.</span></p>',
'date' => '2024-08-16',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.08.14.607943v1',
'doi' => 'https://doi.org/10.1101/2024.08.14.607943',
'modified' => '2024-09-02 10:29:44',
'created' => '2024-09-02 10:29:44',
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[maximum depth reached]
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(int) 2 => array(
'id' => '4933',
'name' => 'Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches',
'authors' => 'Lee M. et al.',
'description' => '<p><span>Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.</span></p>',
'date' => '2024-04-05',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38580401/',
'doi' => '10.1101/gr.277926.123',
'modified' => '2024-04-09 00:19:18',
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'id' => '4895',
'name' => 'Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing',
'authors' => 'Santhanagopalan I. et al.',
'description' => '<p class="section-title u-h4 u-margin-l-top u-margin-xs-bottom">Highlights</p>
<div id="abssec0020">
<ul class="list">
<li class="react-xocs-list-item">
<p id="p0010">Optimized isolation of nuclei from the green model alga<span> </span><em>Chlamydomonas reinhardtii</em></p>
</li>
<li class="react-xocs-list-item">
<p id="p0010"><em></em></p>
<p id="p0015">Tag-free isolation from both cell-walled and cell wall-deficient algae strains</p>
</li>
<li class="react-xocs-list-item">
<p id="p0015"></p>
<p id="p0020">Key steps for an effective and fast isolation and quantification procedure of nuclei</p>
</li>
<li class="react-xocs-list-item">
<p><span class="list-label"></span>Extracts at a quality suitable for ATAC-sequencing</p>
</li>
</ul>
</div>',
'date' => '2024-03-15',
'pmid' => 'https://www.sciencedirect.com/science/article/pii/S2666166723007311',
'doi' => 'https://doi.org/10.1016/j.xpro.2023.102764',
'modified' => '2024-02-09 12:37:32',
'created' => '2024-01-22 13:39:58',
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(int) 4 => array(
'id' => '4917',
'name' => 'Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition',
'authors' => 'Trembley B.J.M. et al.',
'description' => '<p><span>Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in </span><i>Arabidopsis thaliana</i><span><span> </span>we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.</span></p>',
'date' => '2024-02-26',
'pmid' => 'https://www.nature.com/articles/s41467-024-46082-5',
'doi' => 'https://doi.org/10.1038/s41467-024-46082-5',
'modified' => '2024-02-29 11:56:56',
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(int) 5 => array(
'id' => '4910',
'name' => 'The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation',
'authors' => 'Kim M. et al.',
'description' => '<p><span>During human pregnancy, extravillous trophoblasts play crucial roles in placental invasion into the maternal decidua and spiral artery remodeling. However, regulatory factors and their action mechanisms modulating human extravillous trophoblast specification have been unknown. By analyzing dynamic changes in transcriptome and enhancer profile during human trophoblast stem cell to extravillous trophoblast differentiation, we define stage-specific regulators, including an early-stage transcription factor, TFAP2C, and multiple late-stage transcription factors. Loss-of-function studies confirm the requirement of all transcription factors identified for adequate differentiation, and we reveal that the dynamic changes in the levels of TFAP2C are essential. Notably, TFAP2C pre-occupies the regulatory elements of the inactive extravillous trophoblast-active genes during the early stage of differentiation, and the late-stage transcription factors directly activate extravillous trophoblast-active genes, including themselves as differentiation further progresses, suggesting sequential actions of transcription factors assuring differentiation. Our results reveal stage-specific transcription factors and their inter-connected regulatory mechanisms modulating extravillous trophoblast differentiation, providing a framework for understanding early human placentation and placenta-related complications.</span></p>',
'date' => '2024-02-12',
'pmid' => 'https://www.nature.com/articles/s41467-024-45669-2',
'doi' => 'https://doi.org/10.1038/s41467-024-45669-2',
'modified' => '2024-02-15 10:43:52',
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(int) 6 => array(
'id' => '4928',
'name' => 'DMSO derives Trophectoderm and Clonal Blastoid from Single Human Pluripotent Stem Cell',
'authors' => 'Alsolami S. et al.',
'description' => '<p><span>Human naïve pluripotent stem cells (nPSCs) can differentiate into extra-embryonic trophectoderm (TE), a critical step in the generation of the integrated embryo model termed blastoid. The current paradigm of blastoid generation necessitates the aggregation of dozens of nPSCs treated with multiple small molecule inhibitors, growth factors, or genetic modifications to initiate TE differentiation. The presence of complex crosstalk among pathways and cellular heterogeneity in these models complicates mechanistic study and genetic screens. Here, we show that a single small molecule, dimethyl sulfoxide (DMSO), potently induces TE differentiation in basal medium without pharmacological and genetic perturbations. DMSO enhances blastoid generation and, more importantly, is sufficient for blastoid generation by itself. DMSO blastoids resemble blastocysts in morphology and lineage composition. DMSO induces blastoid formation through PKC signaling and cell cycle regulation. Lastly, DMSO enables single nPSC-derived clonal blastoids, which could facilitate genetic screens for mechanistic understanding of human embryogenesis.</span></p>',
'date' => '2024-01-01',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2023.12.31.573770v1.abstract',
'doi' => 'https://doi.org/10.1101/2023.12.31.573770',
'modified' => '2024-03-27 15:18:04',
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(int) 7 => array(
'id' => '4887',
'name' => 'In vitro production of cat-restricted Toxoplasma pre-sexual stages',
'authors' => 'Antunes, A.V. et al.',
'description' => '<p><span>Sexual reproduction of </span><i>Toxoplasma gondii</i><span>, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Farhat, D. C. et al. A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment. Nat. Microbiol. 5, 570–583 (2020)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR1" id="ref-link-section-d277698175e527">1</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 2" title="Bougdour, A. et al. Drug inhibition of HDAC3 and epigenetic control of differentiation in Apicomplexa parasites. J. Exp. Med. 206, 953–966 (2009)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR2" id="ref-link-section-d277698175e530">2</a></sup><span>. Here we found that the transcription factors AP2XII-1 and AP2XI-2 operate during the tachyzoite stage, a hallmark of acute toxoplasmosis, to silence genes necessary for merozoites, a developmental stage critical for subsequent sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a marked change in the transcriptional program, promoting a full transition from tachyzoites to merozoites. These in vitro-cultured pre-gametes have unique protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit MORC and HDAC3 (ref. </span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Farhat, D. C. et al. A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment. Nat. Microbiol. 5, 570–583 (2020)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR1" id="ref-link-section-d277698175e534">1</a></sup><span>), thereby limiting chromatin accessibility and transcription. Consequently, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. Successful production of merozoites in vitro paves the way for future studies on<span> </span></span><i>Toxoplasma</i><span><span> </span>sexual development without the need for cat infections and holds promise for the development of therapies to prevent parasite transmission.</span></p>',
'date' => '2023-12-13',
'pmid' => 'https://www.nature.com/articles/s41586-023-06821-y',
'doi' => 'https://doi.org/10.1038/s41586-023-06821-y',
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'name' => 'Vaginal microbes alter epithelial transcriptomic and epigenomic modifications providing insight into the molecular mechanisms for susceptibility to adverse reproductive outcomes',
'authors' => 'Elovitz M. et al.',
'description' => '<p><span>The cervicovaginal microbiome is highly associated with women's health with microbial communities dominated by </span><i>Lactobacillus</i><span><span> </span>spp. being considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes including<span> </span></span><i>Gardnerella vaginalis</i><span>, have been associated with adverse reproductive outcomes. However, the molecular pathways modulated by microbe interactions with the cervicovaginal epithelia remain unclear. Using RNA-sequencing, we characterize the<span> </span></span><i>in vitro</i><span><span> </span>cervicovaginal epithelial transcriptional response to different vaginal bacteria and their culture supernatants. We showed that<span> </span></span><i>G. vaginalis</i><span><span> </span>upregulated genes were associated with an activated innate immune response including anti-microbial peptides and inflammasome pathways, represented by NLRP3-mediated increases in caspase-1, IL-1β and cell death. Cervicovaginal epithelial cells exposed to<span> </span></span><i>L. crispatus</i><span><span> </span>showed limited transcriptomic changes, while exposure to<span> </span></span><i>L. crispatus</i><span><span> </span>culture supernatants resulted in a shift in the epigenomic landscape of cervical epithelial cells. ATAC-sequencing confirmed epigenetic changes with reduced chromatin accessibility. This study reveals new insight into host-microbe interactions in the lower reproductive tract and suggest potential therapeutic strategies leveraging the vaginal microbiome to improve reproductive health.</span></p>',
'date' => '2023-11-16',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38014044/',
'doi' => '10.21203/rs.3.rs-3580132/v1',
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'description' => '<p><span>Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few studies uncover the effects of inflammatory stresses on chromatin architecture. We used integrative analysis of ATAC-seq and RNA-seq data to investigate chromatin alterations in human endothelial cells in response to TNF-alpha and febrile-range heat stress exposure. Multi-omics data analysis suggests a correlation between the transcription of stress-related genes and endothelial dysfunction drivers with chromatin regions exhibiting differential accessibility. Moreover, microscopy identified the dynamics in the nuclear organization, specifically, the changes in a subset of heterochromatic nucleoli-associated chromatin domains, the centromeres. Upon inflammatory stress exposure, the centromeres decreased association with nucleoli in a p38-dependent manner and increased the number of transcripts from pericentromeric regions. Overall, we provide two lines of evidence that suggest chromatin alterations in vascular endothelial cells during inflammatory stresses.</span></p>',
'date' => '2023-10-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10614786/',
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'authors' => 'Uckelmann M. et al.',
'description' => '<p><span>The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the three dimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.</span></p>',
'date' => '2023-05-09',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2023.05.08.539931v1.abstract',
'doi' => 'https://doi.org/10.1101/2023.05.08.539931',
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'authors' => 'Soni A. et al.',
'description' => '<p><span>Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.</span></p>',
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
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<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'description' => '<p><span>Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.</span></p>',
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
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<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
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<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
</div>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<div class="small-12 medium-8 large-8 columns"><br />
<p>Chromatin structure plays a key role in regulating gene expression by allowing DNA accessibility to transcriptional machinery and transcription factors. The packaging of DNA into nucleosomes forms a closed structure that is not highly accessible to transcriptional elements whereas the open nucleosome structure allows DNA to be accessible. Diagenode offers a number of solutions to help you analyze chromatin and the role of transcriptional machinery including ChIP kits, ChIPmentation kits, antibodies, pA-Tn5 and ATAC-seq kits.</p>
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<p><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"><img src="https://www.diagenode.com/img/banners/b-microchip-category.png" /></a></p>
<div class="row">
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<div id="portal" class="main-portal">
<div class="portal-inner"><nav class="portal-nav">
<ul class="tips-menu">
<li><a href="#workflow" class="tips portal button" style="background: #13b29c; color: #f3fbfa;">Chromatin immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation" class="tips portal button">ChIPmentation</a></li>
<li><a href="https://www.diagenode.com/en/categories/antibodies
" class="tips portal button">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">pA-Tn5</a></li>
<li><a href="https://www.diagenode.com/en/categories/atac-seq" class="tips portal button">ATAC-seq</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">CUT&Tag</a></li>
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</nav></div>
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<p>Chromatin immunoprecipitation (ChIP) determines the location of DNA binding sites on the genome for a protein of interest, giving insights into gene expression regulation. ChIP involves the selective enrichment of a chromatin fraction containing a specific antigen. Antibodies that recognize a protein or protein modification are used to determine the relative abundance of that antigen at a specific locus or loci. ChIP can be used to compare enrichment of proteins, map protein modifications, or quantify a protein modification during a time course.</p>
<span class="anchor" id="workflow"></span>
<h4><span style="font-weight: 400;">The ChIP workflow</span></h4>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><img src="https://www.diagenode.com/img/categories/kits_chromatin_function/website-chip-workflow.jpg" />
<div id="chip_workflow" class="content">
<div class="row">
<table>
<tbody>
<tr>
<td width="50%">
<h3 class="text-center">Step by step workflow</h3>
</td>
<td width="50%">
<h3 class="text-center">Optimal solution from Diagenode</h3>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>1.</strong><span> </span>Crosslink to bind proteins to DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-1-workflow.png" width="192" height="24" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/chip-cross-link-gold-600-ul">ChIP Cross-link Gold</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>2.</strong><span> </span>Shear DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-2-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/bioruptor-pico-sonication-device#">Bioruptor<sup>®</sup><span> </span>Pico Sonication device</a></li>
<li><a href="https://www.diagenode.com/categories/chromatin-shearing">Shearing optimization reagent</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>3.</strong><span> </span>Immunoprecipitate with specific antibody</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-3-workflow.png" width="47" height="51" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/categories/chromatin-immunoprecipitation">ChIP-seq and ChIP-qPCR kits</a><span> </span>for transcription factors, histones, low inputs, plants</li>
<li><a href="https://www.diagenode.com/categories/chip-grade-antibodies">ChIP</a><span> </span>and<span> </span><a href="https://www.diagenode.com/categories/chip-seq-grade-antibodies">ChIP-seq grade</a><span> </span>antibodies</li>
<li><a href="https://www.diagenode.com/categories/ip-star">Automation available</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>4.</strong><span> </span>Reverse crosslinks and purify</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-4-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li>Diagenode's ChIP kits (contain optimal purification modules)</li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>5.</strong><span> </span><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">ChIP-qPCR</a><span> </span>or ChIP-seq library preparation</p>
</td>
<td>
<ul class="arrow">
<li>ChIP-seq:</li>
</ul>
<ul style="list-style-type: square;">
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x48-12-indices-48-rxns">MicroPlex Library Preparation for 50 pg - 5 ng</a></li>
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns">iDeal Library Preparation for > 5 ng</a></li>
</ul>
<ul class="arrow">
<li>ChIP qPCR</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</li>
</ul>
<p></p>
<h4><span style="font-weight: 400;">Products for chromatin study</span></h4>
<p><span style="font-weight: 400;"></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/crosslinking.png" alt="" width="35" height="35" /> Crosslinking<br /></b></span></strong><span style="font-weight: 400;">Efficient solution for protein-protein fixation.</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;"> <a href="../p/chip-cross-link-gold-600-ul
">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/chromatin-shearing.png" alt="" width="35" height="35" /> Chromatin shearing<br /></strong><strong><span style="font-weight: 400;">Perfectly sheared chromatin is critical for ChIP success.<span> </span><br /></span></strong><strong><a href="../categories/chromatin-shearing"><span style="font-weight: 400;">Read more</span></a><span style="font-weight: 400;"><span> </span>about solutions for successful chromatin preparation.<span> </span><br /></span></strong><strong><span style="font-weight: 400;"><a href="../categories/bioruptor-shearing-device">Read more</a><span> </span>about<span> </span></span><span style="font-weight: 400;">Bioruptor<span> </span></span><span style="font-weight: 400;">sonication.</span></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/immunoprecipitation.png" width="35" height="35" caption="false" /> Chromatin immunoprecipitation<br /></b></span></strong><span style="font-weight: 400;">Immunoprecipitation solutions for histone and transcription factor ChIP-qPCR and ChIP-seq for low inputs, plants, and animals including automated solutions</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;">. <a href="../categories/chromatin-immunoprecipitation">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/ChIPmentation.png" alt="" width="35" height="35" /> ChIPmentation<br /><span style="font-weight: 400;">ChIPmentation, an exclusive technology, is an end-to-end ChIP-seq solution for low and difficult inputs. <a href="../categories/chromatin-ip-chipmentation">Read more</a></span><br /></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-antibodies.png" alt="" width="35" height="35" /> ChIP and ChIP-seq antibodies<br /></b></span></strong><span style="font-weight: 400;">ChIP-grade antibodies are essential for success. <a href="../categories/antibodies">Learn more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-qPCR.png" width="35" height="35" caption="false" /> Primer pairs<br /></b></span></strong><span style="font-weight: 400;">Highly specific primer pairs for the amplification of the specific genomic regions. <a href="../categories/primer-pairs">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/cutandtag.png" width="35" height="35" caption="false" /> CUT&Tag solutions<br /></b></span></strong><span style="font-weight: 400;">An alternative to ChIP-seq that combines antibody-targeted controlled cleavage by a protein A-Tn5 fusion with NGS to identify the binding sites of DNA-associated proteins. <a href="../categories/cutandtag">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/dna-purification.png" width="35" height="35" caption="false" /> DNA purification<br /></b></span></strong><span style="font-weight: 400;"><a href="../categories/dna-and-rna-purification">Read more</a> about solutions for DNA purification</span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-seq.png" width="35" height="35" caption="false" /> Library preparation for ChIP-seq<br /></b></span></strong><span style="font-weight: 400;">Optimized solutions for the library preparation from low DNA input. <a href="../categories/library-preparation-for-ChIP-seq">Read more</a></span></span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-automation.png" alt="" width="35" height="35" /> ChIP and ChIP-seq automation<br /></b>Reproducibility, optimization simplicity, no variability. <a href="../categories/epigenetic-automation">Learn more</a></span></p>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<p class="text-justify">We offer <a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation" target="_blank">complete ChIP kits</a> or <strong>individual kit components</strong> from antibodies, buffers, beads, chromatin shearing, and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="center" style="text-align: center;"><a href="../pages/chip-kit-customizer-1"><img src="https://www.diagenode.com/img/banners/banner-customizer.png" alt="" /></a></div>
</div>
</div>
</div>
<h4>Chromatin resources</h4>
<h3>Posters</h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibody-chipseq-qc-using-the-ipstar-compact-poster"><span style="font-weight: 400;">Understanding our antibody QC</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibodies-you-can-trust-poster"><span style="font-weight: 400;">High quality ChIP antibodies</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-kit-results-with-true-microchip-kit-poster"><span style="font-weight: 400;">ChIP with only 10,000 cells</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/high-resolution-chipseq-profiles-with-ipstar-automated-platform-poster"><span style="font-weight: 400;">High resolution ChIP-seq using automation</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/bioinformatics-pipeline-for-chipseq-analyses"><span style="font-weight: 400;">ChIP-seq bioinformatics</span></a></li>
</ul>
<h3><span style="font-weight: 400;">Application notes</span></h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipettor-application-note"><span style="font-weight: 400;">Simple semi-automaton for easy and inexpensive ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipseq-from-human-tumor-tissue"><span style="font-weight: 400;">Performing ChIP-seq on human tumor tissue</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/plant-chip-seq-application-note"><span style="font-weight: 400;">Plant ChIP-seq – a successful method</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-seq-application-note"><span style="font-weight: 400;">Best workflow practices for low input ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/files/application_notes/AN-ChIP-Cas9-02_2018.pdf"><span style="font-weight: 400;">Optimize the selection of guide RNA by ChIP to keep CRISPR on-target</span></a></li>
</ul>
<h3>Publications related to ChIP</h3>
<ul>
<li><a href="https://www.diagenode.com/en/publications/view/3373">Corticosteroid receptors adopt distinct cyclical transcriptional signatures</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3347">Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3355">Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile</a></li>
</ul>
<h3><span style="font-weight: 400;">Brochures</span></h3>
<ul>
<li><a href="https://www.diagenode.com/files/brochures/Chromatin_Immunoprecipitation_Brochure.pdf"><b>Chromatin </b><span style="font-weight: 400;">products brochure</span></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Epigenetic_Antibodies_Brochure.pdf"><span style="font-weight: 400;">Epigenetic<span> </span></span><b>Antibodies</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Bioruptor_Sonicator_Brochure.pdf"><span style="font-weight: 400;">Bioruptor for<span> </span></span><b>chromatin shearing</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/IPStar_Automated_System_Brochure.pdf"><span style="font-weight: 400;">Automating<span> </span></span><b>ChIP</b><span style="font-weight: 400;"><span> </span>and<span> </span></span><b>ChIP-seq</b></a></li>
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<p class="p1">ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by nextgeneration sequencing, is a key technology to easily identify the “open” regions of the chromatin, which are usually associated with permissive gene expression. Indeed, the nuclei of the samples are incubated with a transposase, and only the genomic regions associated with open chromatin will be accessible to this transposase. During the process those regions will be cut and sequencing adaptors will be added, allowing their sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only., giving a map of the chromatin status in the whole genome of the sample.</p>
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'authors' => 'Valeria Pessei et al.',
'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Liquid biopsy based on cell-free DNA (cfDNA) analysis holds significant promise as a minimally invasive approach for the diagnosis, genotyping, and monitoring of solid malignancies. Human tumors release cfDNA in the bloodstream through a combination of events, including cell death, active and passive release. However, the precise mechanisms leading to cfDNA shedding remain to be characterized. Addressing this question in patients is confounded by several factors, such as tumor burden extent, anatomical and vasculature barriers, and release of nucleic acids from normal cells. In this work, we exploited cancer models to dissect basic mechanisms of DNA release.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Methods</h3>
<p>We measured cell loss ratio, doubling time, and cfDNA release in the supernatant of a colorectal cancer (CRC) cell line collection (<i>N</i> = 76) representative of the molecular subtypes previously identified in cancer patients. Association analyses between quantitative parameters of cfDNA release, cell proliferation, and molecular features were evaluated. Functional experiments were performed to test the impact of modulating DNA methylation on cfDNA release.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>Higher levels of supernatant cfDNA were significantly associated with slower cell cycling and increased cell death. In addition, a higher cfDNA shedding was found in non-CpG Island Methylator Phenotype (CIMP) models. These results indicate a positive correlation between lower methylation and increased cfDNA levels. To explore this further, we exploited methylation microarrays to identify a subset of probes significantly associated with cfDNA shedding and derive a methylation signature capable of discriminating high from low cfDNA releasers. We applied this signature to an independent set of 176 CRC cell lines and patient derived organoids to select 14 models predicted to be low or high releasers. The methylation profile successfully predicted the amount of cfDNA released in the supernatant. At the functional level, genetic ablation of DNA methyl-transferases increased chromatin accessibility and DNA fragmentation, leading to increased cfDNA release in isogenic CRC cell lines. Furthermore, in vitro treatment of five low releaser CRC cells with a demethylating agent was able to induce a significant increase in cfDNA shedding.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusions</h3>
<p>Methylation status of cancer cell lines contributes to the variability of cfDNA shedding in vitro. Changes in methylation pattern are associated with cfDNA release levels and might be exploited to increase sensitivity of liquid biopsy assays.</p>',
'date' => '2024-10-09',
'pmid' => 'https://link.springer.com/article/10.1186/s13073-024-01386-5',
'doi' => 'https://doi.org/10.1186/s13073-024-01386-5',
'modified' => '2024-10-14 08:56:24',
'created' => '2024-10-14 08:56:24',
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[maximum depth reached]
)
),
(int) 1 => array(
'id' => '4967',
'name' => 'Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila genome',
'authors' => 'Varoqui M. et al.',
'description' => '<p><span>Transposable elements (TEs), widespread genetic parasites, pose potential threats to the stability of their host genomes. Hence, the interactions observed today between TEs and their host genomes, as well as among the different TE species coexisting in the same host, likely reflect those that did not lead to the extinction of either the host or the TEs. It is not clear to what extent the expression and integration steps of the TE replication cycles are involved in this ‘peaceful’ coexistence. Here, we show that four Drosophila LTR RetroTransposable Elements (LTR-RTEs), although sharing the same overall integration mechanism, preferentially integrate into distinct open chromatin domains of the host germline. Notably, the differential expressions of the gtwin and ZAM LTR-RTEs in ovarian and embryonic somatic tissues, respectively, result in differential integration timings and targeting of accessible chromatin landscapes that differ between early and late embryonic nuclei, highlighting connections between temporal and spatial LTR-RTEs niche partitionings.</span></p>',
'date' => '2024-08-16',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.08.14.607943v1',
'doi' => 'https://doi.org/10.1101/2024.08.14.607943',
'modified' => '2024-09-02 10:29:44',
'created' => '2024-09-02 10:29:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'id' => '4933',
'name' => 'Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches',
'authors' => 'Lee M. et al.',
'description' => '<p><span>Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.</span></p>',
'date' => '2024-04-05',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38580401/',
'doi' => '10.1101/gr.277926.123',
'modified' => '2024-04-09 00:19:18',
'created' => '2024-04-09 00:19:18',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'id' => '4895',
'name' => 'Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing',
'authors' => 'Santhanagopalan I. et al.',
'description' => '<p class="section-title u-h4 u-margin-l-top u-margin-xs-bottom">Highlights</p>
<div id="abssec0020">
<ul class="list">
<li class="react-xocs-list-item">
<p id="p0010">Optimized isolation of nuclei from the green model alga<span> </span><em>Chlamydomonas reinhardtii</em></p>
</li>
<li class="react-xocs-list-item">
<p id="p0010"><em></em></p>
<p id="p0015">Tag-free isolation from both cell-walled and cell wall-deficient algae strains</p>
</li>
<li class="react-xocs-list-item">
<p id="p0015"></p>
<p id="p0020">Key steps for an effective and fast isolation and quantification procedure of nuclei</p>
</li>
<li class="react-xocs-list-item">
<p><span class="list-label"></span>Extracts at a quality suitable for ATAC-sequencing</p>
</li>
</ul>
</div>',
'date' => '2024-03-15',
'pmid' => 'https://www.sciencedirect.com/science/article/pii/S2666166723007311',
'doi' => 'https://doi.org/10.1016/j.xpro.2023.102764',
'modified' => '2024-02-09 12:37:32',
'created' => '2024-01-22 13:39:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '4917',
'name' => 'Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition',
'authors' => 'Trembley B.J.M. et al.',
'description' => '<p><span>Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in </span><i>Arabidopsis thaliana</i><span><span> </span>we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.</span></p>',
'date' => '2024-02-26',
'pmid' => 'https://www.nature.com/articles/s41467-024-46082-5',
'doi' => 'https://doi.org/10.1038/s41467-024-46082-5',
'modified' => '2024-02-29 11:56:56',
'created' => '2024-02-29 11:56:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '4910',
'name' => 'The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation',
'authors' => 'Kim M. et al.',
'description' => '<p><span>During human pregnancy, extravillous trophoblasts play crucial roles in placental invasion into the maternal decidua and spiral artery remodeling. However, regulatory factors and their action mechanisms modulating human extravillous trophoblast specification have been unknown. By analyzing dynamic changes in transcriptome and enhancer profile during human trophoblast stem cell to extravillous trophoblast differentiation, we define stage-specific regulators, including an early-stage transcription factor, TFAP2C, and multiple late-stage transcription factors. Loss-of-function studies confirm the requirement of all transcription factors identified for adequate differentiation, and we reveal that the dynamic changes in the levels of TFAP2C are essential. Notably, TFAP2C pre-occupies the regulatory elements of the inactive extravillous trophoblast-active genes during the early stage of differentiation, and the late-stage transcription factors directly activate extravillous trophoblast-active genes, including themselves as differentiation further progresses, suggesting sequential actions of transcription factors assuring differentiation. Our results reveal stage-specific transcription factors and their inter-connected regulatory mechanisms modulating extravillous trophoblast differentiation, providing a framework for understanding early human placentation and placenta-related complications.</span></p>',
'date' => '2024-02-12',
'pmid' => 'https://www.nature.com/articles/s41467-024-45669-2',
'doi' => 'https://doi.org/10.1038/s41467-024-45669-2',
'modified' => '2024-02-15 10:43:52',
'created' => '2024-02-15 10:43:52',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'id' => '4928',
'name' => 'DMSO derives Trophectoderm and Clonal Blastoid from Single Human Pluripotent Stem Cell',
'authors' => 'Alsolami S. et al.',
'description' => '<p><span>Human naïve pluripotent stem cells (nPSCs) can differentiate into extra-embryonic trophectoderm (TE), a critical step in the generation of the integrated embryo model termed blastoid. The current paradigm of blastoid generation necessitates the aggregation of dozens of nPSCs treated with multiple small molecule inhibitors, growth factors, or genetic modifications to initiate TE differentiation. The presence of complex crosstalk among pathways and cellular heterogeneity in these models complicates mechanistic study and genetic screens. Here, we show that a single small molecule, dimethyl sulfoxide (DMSO), potently induces TE differentiation in basal medium without pharmacological and genetic perturbations. DMSO enhances blastoid generation and, more importantly, is sufficient for blastoid generation by itself. DMSO blastoids resemble blastocysts in morphology and lineage composition. DMSO induces blastoid formation through PKC signaling and cell cycle regulation. Lastly, DMSO enables single nPSC-derived clonal blastoids, which could facilitate genetic screens for mechanistic understanding of human embryogenesis.</span></p>',
'date' => '2024-01-01',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2023.12.31.573770v1.abstract',
'doi' => 'https://doi.org/10.1101/2023.12.31.573770',
'modified' => '2024-03-27 15:18:04',
'created' => '2024-03-27 15:18:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '4887',
'name' => 'In vitro production of cat-restricted Toxoplasma pre-sexual stages',
'authors' => 'Antunes, A.V. et al.',
'description' => '<p><span>Sexual reproduction of </span><i>Toxoplasma gondii</i><span>, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Farhat, D. C. et al. A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment. Nat. Microbiol. 5, 570–583 (2020)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR1" id="ref-link-section-d277698175e527">1</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 2" title="Bougdour, A. et al. Drug inhibition of HDAC3 and epigenetic control of differentiation in Apicomplexa parasites. J. Exp. Med. 206, 953–966 (2009)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR2" id="ref-link-section-d277698175e530">2</a></sup><span>. Here we found that the transcription factors AP2XII-1 and AP2XI-2 operate during the tachyzoite stage, a hallmark of acute toxoplasmosis, to silence genes necessary for merozoites, a developmental stage critical for subsequent sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a marked change in the transcriptional program, promoting a full transition from tachyzoites to merozoites. These in vitro-cultured pre-gametes have unique protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit MORC and HDAC3 (ref. </span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Farhat, D. C. et al. A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment. Nat. Microbiol. 5, 570–583 (2020)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR1" id="ref-link-section-d277698175e534">1</a></sup><span>), thereby limiting chromatin accessibility and transcription. Consequently, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. Successful production of merozoites in vitro paves the way for future studies on<span> </span></span><i>Toxoplasma</i><span><span> </span>sexual development without the need for cat infections and holds promise for the development of therapies to prevent parasite transmission.</span></p>',
'date' => '2023-12-13',
'pmid' => 'https://www.nature.com/articles/s41586-023-06821-y',
'doi' => 'https://doi.org/10.1038/s41586-023-06821-y',
'modified' => '2023-12-18 10:40:50',
'created' => '2023-12-18 10:40:50',
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[maximum depth reached]
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(int) 8 => array(
'id' => '4939',
'name' => 'Vaginal microbes alter epithelial transcriptomic and epigenomic modifications providing insight into the molecular mechanisms for susceptibility to adverse reproductive outcomes',
'authors' => 'Elovitz M. et al.',
'description' => '<p><span>The cervicovaginal microbiome is highly associated with women's health with microbial communities dominated by </span><i>Lactobacillus</i><span><span> </span>spp. being considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes including<span> </span></span><i>Gardnerella vaginalis</i><span>, have been associated with adverse reproductive outcomes. However, the molecular pathways modulated by microbe interactions with the cervicovaginal epithelia remain unclear. Using RNA-sequencing, we characterize the<span> </span></span><i>in vitro</i><span><span> </span>cervicovaginal epithelial transcriptional response to different vaginal bacteria and their culture supernatants. We showed that<span> </span></span><i>G. vaginalis</i><span><span> </span>upregulated genes were associated with an activated innate immune response including anti-microbial peptides and inflammasome pathways, represented by NLRP3-mediated increases in caspase-1, IL-1β and cell death. Cervicovaginal epithelial cells exposed to<span> </span></span><i>L. crispatus</i><span><span> </span>showed limited transcriptomic changes, while exposure to<span> </span></span><i>L. crispatus</i><span><span> </span>culture supernatants resulted in a shift in the epigenomic landscape of cervical epithelial cells. ATAC-sequencing confirmed epigenetic changes with reduced chromatin accessibility. This study reveals new insight into host-microbe interactions in the lower reproductive tract and suggest potential therapeutic strategies leveraging the vaginal microbiome to improve reproductive health.</span></p>',
'date' => '2023-11-16',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38014044/',
'doi' => '10.21203/rs.3.rs-3580132/v1',
'modified' => '2024-06-07 15:47:48',
'created' => '2024-06-07 15:47:48',
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[maximum depth reached]
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(int) 9 => array(
'id' => '4927',
'name' => 'Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells',
'authors' => 'Liu H. et al.',
'description' => '<p><span>Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few studies uncover the effects of inflammatory stresses on chromatin architecture. We used integrative analysis of ATAC-seq and RNA-seq data to investigate chromatin alterations in human endothelial cells in response to TNF-alpha and febrile-range heat stress exposure. Multi-omics data analysis suggests a correlation between the transcription of stress-related genes and endothelial dysfunction drivers with chromatin regions exhibiting differential accessibility. Moreover, microscopy identified the dynamics in the nuclear organization, specifically, the changes in a subset of heterochromatic nucleoli-associated chromatin domains, the centromeres. Upon inflammatory stress exposure, the centromeres decreased association with nucleoli in a p38-dependent manner and increased the number of transcripts from pericentromeric regions. Overall, we provide two lines of evidence that suggest chromatin alterations in vascular endothelial cells during inflammatory stresses.</span></p>',
'date' => '2023-10-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10614786/',
'doi' => '10.1101/2023.10.11.561959',
'modified' => '2024-03-27 15:15:21',
'created' => '2024-03-27 15:15:21',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '4880',
'name' => 'Dynamic PRC1-CBX8 stabilizes a porous structure of chromatin condensates',
'authors' => 'Uckelmann M. et al.',
'description' => '<p><span>The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the three dimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.</span></p>',
'date' => '2023-05-09',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2023.05.08.539931v1.abstract',
'doi' => 'https://doi.org/10.1101/2023.05.08.539931',
'modified' => '2023-11-10 15:43:37',
'created' => '2023-11-10 15:43:37',
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[maximum depth reached]
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(int) 11 => array(
'id' => '4810',
'name' => 'UMSBP2 is chromatin remodeler that functions in regulation of geneexpression and suppression of antigenic variation in trypanosomes.',
'authors' => 'Soni A. et al.',
'description' => '<p><span>Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.</span></p>',
'date' => '2023-05-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37207337',
'doi' => '10.1093/nar/gkad402',
'modified' => '2023-06-15 08:54:17',
'created' => '2023-06-13 21:11:31',
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/atacseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
'info2' => '<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig1.png" alt="library prepared with the Diagenode ATAC-seq kit " width="500px" caption="false" /></p>
<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'description' => '<p><span>Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.</span></p>',
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
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<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
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<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
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<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
</ul>',
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/atacseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
</div>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">primer indexes for multiplexing</a> are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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'info2' => '<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig1.png" alt="library prepared with the Diagenode ATAC-seq kit " width="500px" caption="false" /></p>
<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
</ul>',
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<div class="small-12 medium-8 large-8 columns"><br />
<p>Chromatin structure plays a key role in regulating gene expression by allowing DNA accessibility to transcriptional machinery and transcription factors. The packaging of DNA into nucleosomes forms a closed structure that is not highly accessible to transcriptional elements whereas the open nucleosome structure allows DNA to be accessible. Diagenode offers a number of solutions to help you analyze chromatin and the role of transcriptional machinery including ChIP kits, ChIPmentation kits, antibodies, pA-Tn5 and ATAC-seq kits.</p>
</div>
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<p><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"><img src="https://www.diagenode.com/img/banners/b-microchip-category.png" /></a></p>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<div id="portal" class="main-portal">
<div class="portal-inner"><nav class="portal-nav">
<ul class="tips-menu">
<li><a href="#workflow" class="tips portal button" style="background: #13b29c; color: #f3fbfa;">Chromatin immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation" class="tips portal button">ChIPmentation</a></li>
<li><a href="https://www.diagenode.com/en/categories/antibodies
" class="tips portal button">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">pA-Tn5</a></li>
<li><a href="https://www.diagenode.com/en/categories/atac-seq" class="tips portal button">ATAC-seq</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">CUT&Tag</a></li>
</ul>
</nav></div>
</div>
<p>Chromatin immunoprecipitation (ChIP) determines the location of DNA binding sites on the genome for a protein of interest, giving insights into gene expression regulation. ChIP involves the selective enrichment of a chromatin fraction containing a specific antigen. Antibodies that recognize a protein or protein modification are used to determine the relative abundance of that antigen at a specific locus or loci. ChIP can be used to compare enrichment of proteins, map protein modifications, or quantify a protein modification during a time course.</p>
<span class="anchor" id="workflow"></span>
<h4><span style="font-weight: 400;">The ChIP workflow</span></h4>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><img src="https://www.diagenode.com/img/categories/kits_chromatin_function/website-chip-workflow.jpg" />
<div id="chip_workflow" class="content">
<div class="row">
<table>
<tbody>
<tr>
<td width="50%">
<h3 class="text-center">Step by step workflow</h3>
</td>
<td width="50%">
<h3 class="text-center">Optimal solution from Diagenode</h3>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>1.</strong><span> </span>Crosslink to bind proteins to DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-1-workflow.png" width="192" height="24" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/chip-cross-link-gold-600-ul">ChIP Cross-link Gold</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>2.</strong><span> </span>Shear DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-2-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/bioruptor-pico-sonication-device#">Bioruptor<sup>®</sup><span> </span>Pico Sonication device</a></li>
<li><a href="https://www.diagenode.com/categories/chromatin-shearing">Shearing optimization reagent</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>3.</strong><span> </span>Immunoprecipitate with specific antibody</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-3-workflow.png" width="47" height="51" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/categories/chromatin-immunoprecipitation">ChIP-seq and ChIP-qPCR kits</a><span> </span>for transcription factors, histones, low inputs, plants</li>
<li><a href="https://www.diagenode.com/categories/chip-grade-antibodies">ChIP</a><span> </span>and<span> </span><a href="https://www.diagenode.com/categories/chip-seq-grade-antibodies">ChIP-seq grade</a><span> </span>antibodies</li>
<li><a href="https://www.diagenode.com/categories/ip-star">Automation available</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>4.</strong><span> </span>Reverse crosslinks and purify</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-4-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li>Diagenode's ChIP kits (contain optimal purification modules)</li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>5.</strong><span> </span><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">ChIP-qPCR</a><span> </span>or ChIP-seq library preparation</p>
</td>
<td>
<ul class="arrow">
<li>ChIP-seq:</li>
</ul>
<ul style="list-style-type: square;">
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x48-12-indices-48-rxns">MicroPlex Library Preparation for 50 pg - 5 ng</a></li>
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns">iDeal Library Preparation for > 5 ng</a></li>
</ul>
<ul class="arrow">
<li>ChIP qPCR</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</li>
</ul>
<p></p>
<h4><span style="font-weight: 400;">Products for chromatin study</span></h4>
<p><span style="font-weight: 400;"></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/crosslinking.png" alt="" width="35" height="35" /> Crosslinking<br /></b></span></strong><span style="font-weight: 400;">Efficient solution for protein-protein fixation.</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;"> <a href="../p/chip-cross-link-gold-600-ul
">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/chromatin-shearing.png" alt="" width="35" height="35" /> Chromatin shearing<br /></strong><strong><span style="font-weight: 400;">Perfectly sheared chromatin is critical for ChIP success.<span> </span><br /></span></strong><strong><a href="../categories/chromatin-shearing"><span style="font-weight: 400;">Read more</span></a><span style="font-weight: 400;"><span> </span>about solutions for successful chromatin preparation.<span> </span><br /></span></strong><strong><span style="font-weight: 400;"><a href="../categories/bioruptor-shearing-device">Read more</a><span> </span>about<span> </span></span><span style="font-weight: 400;">Bioruptor<span> </span></span><span style="font-weight: 400;">sonication.</span></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/immunoprecipitation.png" width="35" height="35" caption="false" /> Chromatin immunoprecipitation<br /></b></span></strong><span style="font-weight: 400;">Immunoprecipitation solutions for histone and transcription factor ChIP-qPCR and ChIP-seq for low inputs, plants, and animals including automated solutions</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;">. <a href="../categories/chromatin-immunoprecipitation">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/ChIPmentation.png" alt="" width="35" height="35" /> ChIPmentation<br /><span style="font-weight: 400;">ChIPmentation, an exclusive technology, is an end-to-end ChIP-seq solution for low and difficult inputs. <a href="../categories/chromatin-ip-chipmentation">Read more</a></span><br /></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-antibodies.png" alt="" width="35" height="35" /> ChIP and ChIP-seq antibodies<br /></b></span></strong><span style="font-weight: 400;">ChIP-grade antibodies are essential for success. <a href="../categories/antibodies">Learn more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-qPCR.png" width="35" height="35" caption="false" /> Primer pairs<br /></b></span></strong><span style="font-weight: 400;">Highly specific primer pairs for the amplification of the specific genomic regions. <a href="../categories/primer-pairs">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/cutandtag.png" width="35" height="35" caption="false" /> CUT&Tag solutions<br /></b></span></strong><span style="font-weight: 400;">An alternative to ChIP-seq that combines antibody-targeted controlled cleavage by a protein A-Tn5 fusion with NGS to identify the binding sites of DNA-associated proteins. <a href="../categories/cutandtag">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/dna-purification.png" width="35" height="35" caption="false" /> DNA purification<br /></b></span></strong><span style="font-weight: 400;"><a href="../categories/dna-and-rna-purification">Read more</a> about solutions for DNA purification</span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-seq.png" width="35" height="35" caption="false" /> Library preparation for ChIP-seq<br /></b></span></strong><span style="font-weight: 400;">Optimized solutions for the library preparation from low DNA input. <a href="../categories/library-preparation-for-ChIP-seq">Read more</a></span></span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-automation.png" alt="" width="35" height="35" /> ChIP and ChIP-seq automation<br /></b>Reproducibility, optimization simplicity, no variability. <a href="../categories/epigenetic-automation">Learn more</a></span></p>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<p class="text-justify">We offer <a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation" target="_blank">complete ChIP kits</a> or <strong>individual kit components</strong> from antibodies, buffers, beads, chromatin shearing, and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="center" style="text-align: center;"><a href="../pages/chip-kit-customizer-1"><img src="https://www.diagenode.com/img/banners/banner-customizer.png" alt="" /></a></div>
</div>
</div>
</div>
<h4>Chromatin resources</h4>
<h3>Posters</h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibody-chipseq-qc-using-the-ipstar-compact-poster"><span style="font-weight: 400;">Understanding our antibody QC</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibodies-you-can-trust-poster"><span style="font-weight: 400;">High quality ChIP antibodies</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-kit-results-with-true-microchip-kit-poster"><span style="font-weight: 400;">ChIP with only 10,000 cells</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/high-resolution-chipseq-profiles-with-ipstar-automated-platform-poster"><span style="font-weight: 400;">High resolution ChIP-seq using automation</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/bioinformatics-pipeline-for-chipseq-analyses"><span style="font-weight: 400;">ChIP-seq bioinformatics</span></a></li>
</ul>
<h3><span style="font-weight: 400;">Application notes</span></h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipettor-application-note"><span style="font-weight: 400;">Simple semi-automaton for easy and inexpensive ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipseq-from-human-tumor-tissue"><span style="font-weight: 400;">Performing ChIP-seq on human tumor tissue</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/plant-chip-seq-application-note"><span style="font-weight: 400;">Plant ChIP-seq – a successful method</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-seq-application-note"><span style="font-weight: 400;">Best workflow practices for low input ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/files/application_notes/AN-ChIP-Cas9-02_2018.pdf"><span style="font-weight: 400;">Optimize the selection of guide RNA by ChIP to keep CRISPR on-target</span></a></li>
</ul>
<h3>Publications related to ChIP</h3>
<ul>
<li><a href="https://www.diagenode.com/en/publications/view/3373">Corticosteroid receptors adopt distinct cyclical transcriptional signatures</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3347">Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3355">Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile</a></li>
</ul>
<h3><span style="font-weight: 400;">Brochures</span></h3>
<ul>
<li><a href="https://www.diagenode.com/files/brochures/Chromatin_Immunoprecipitation_Brochure.pdf"><b>Chromatin </b><span style="font-weight: 400;">products brochure</span></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Epigenetic_Antibodies_Brochure.pdf"><span style="font-weight: 400;">Epigenetic<span> </span></span><b>Antibodies</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Bioruptor_Sonicator_Brochure.pdf"><span style="font-weight: 400;">Bioruptor for<span> </span></span><b>chromatin shearing</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/IPStar_Automated_System_Brochure.pdf"><span style="font-weight: 400;">Automating<span> </span></span><b>ChIP</b><span style="font-weight: 400;"><span> </span>and<span> </span></span><b>ChIP-seq</b></a></li>
</ul>
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'meta_description' => 'Diagenode offers a number of unique solutions and kits to make Diagenode offers chromatin immunoprecipitation kits have been designed to meet a wide variety of research needs and accessible',
'meta_title' => 'Chromatin Function Kit for Unique Solutions and Kits to make Chromatin Research| Diagenode',
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'description' => '<p class="p1">Gene expression is carefully regulated in the cells in order to manage a wide range of biological functions. The structure of chromatin is quite dynamic and contributes to this crucial regulatory process.</p>
<p class="p1">ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by nextgeneration sequencing, is a key technology to easily identify the “open” regions of the chromatin, which are usually associated with permissive gene expression. Indeed, the nuclei of the samples are incubated with a transposase, and only the genomic regions associated with open chromatin will be accessible to this transposase. During the process those regions will be cut and sequencing adaptors will be added, allowing their sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only., giving a map of the chromatin status in the whole genome of the sample.</p>
<p class="p1">The Diagenode’s ATAC-seq kit is based on a highly validated protocol, used for years in our Epigenomics Profiling Services offer and takes advantage of many successful Diagenode’s tools, such as the loaded Tagmentase (Tn5 transposase), the MicroChIP DiaPure Columns and the Primer indexes for tagmented libraries kits.</p>',
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'description' => '<p>Whether you are experienced or new to the field of chromatin immunoprecipitation, Diagenode has everything you need to make ChIP easy and convenient while ensuring consistent data between samples and experiments. As an expert in the field of epigenetics, Diagenode is committed to providing complete solutions from chromatin shearing reagents, shearing instruments such as the Bioruptor® (the gold standard for chromatin shearing), ChIP kits, the largest number of validated and trusted antibodies on the market, and the SX-8G IP-Star® Compact Automated System to achieve unparalleled productivity and reproducibility.</p>',
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(int) 0 => array(
'id' => '4984',
'name' => 'DNA demethylation triggers cell free DNA release in colorectal cancer cells',
'authors' => 'Valeria Pessei et al.',
'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Liquid biopsy based on cell-free DNA (cfDNA) analysis holds significant promise as a minimally invasive approach for the diagnosis, genotyping, and monitoring of solid malignancies. Human tumors release cfDNA in the bloodstream through a combination of events, including cell death, active and passive release. However, the precise mechanisms leading to cfDNA shedding remain to be characterized. Addressing this question in patients is confounded by several factors, such as tumor burden extent, anatomical and vasculature barriers, and release of nucleic acids from normal cells. In this work, we exploited cancer models to dissect basic mechanisms of DNA release.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Methods</h3>
<p>We measured cell loss ratio, doubling time, and cfDNA release in the supernatant of a colorectal cancer (CRC) cell line collection (<i>N</i> = 76) representative of the molecular subtypes previously identified in cancer patients. Association analyses between quantitative parameters of cfDNA release, cell proliferation, and molecular features were evaluated. Functional experiments were performed to test the impact of modulating DNA methylation on cfDNA release.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>Higher levels of supernatant cfDNA were significantly associated with slower cell cycling and increased cell death. In addition, a higher cfDNA shedding was found in non-CpG Island Methylator Phenotype (CIMP) models. These results indicate a positive correlation between lower methylation and increased cfDNA levels. To explore this further, we exploited methylation microarrays to identify a subset of probes significantly associated with cfDNA shedding and derive a methylation signature capable of discriminating high from low cfDNA releasers. We applied this signature to an independent set of 176 CRC cell lines and patient derived organoids to select 14 models predicted to be low or high releasers. The methylation profile successfully predicted the amount of cfDNA released in the supernatant. At the functional level, genetic ablation of DNA methyl-transferases increased chromatin accessibility and DNA fragmentation, leading to increased cfDNA release in isogenic CRC cell lines. Furthermore, in vitro treatment of five low releaser CRC cells with a demethylating agent was able to induce a significant increase in cfDNA shedding.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusions</h3>
<p>Methylation status of cancer cell lines contributes to the variability of cfDNA shedding in vitro. Changes in methylation pattern are associated with cfDNA release levels and might be exploited to increase sensitivity of liquid biopsy assays.</p>',
'date' => '2024-10-09',
'pmid' => 'https://link.springer.com/article/10.1186/s13073-024-01386-5',
'doi' => 'https://doi.org/10.1186/s13073-024-01386-5',
'modified' => '2024-10-14 08:56:24',
'created' => '2024-10-14 08:56:24',
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(int) 1 => array(
'id' => '4967',
'name' => 'Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila genome',
'authors' => 'Varoqui M. et al.',
'description' => '<p><span>Transposable elements (TEs), widespread genetic parasites, pose potential threats to the stability of their host genomes. Hence, the interactions observed today between TEs and their host genomes, as well as among the different TE species coexisting in the same host, likely reflect those that did not lead to the extinction of either the host or the TEs. It is not clear to what extent the expression and integration steps of the TE replication cycles are involved in this ‘peaceful’ coexistence. Here, we show that four Drosophila LTR RetroTransposable Elements (LTR-RTEs), although sharing the same overall integration mechanism, preferentially integrate into distinct open chromatin domains of the host germline. Notably, the differential expressions of the gtwin and ZAM LTR-RTEs in ovarian and embryonic somatic tissues, respectively, result in differential integration timings and targeting of accessible chromatin landscapes that differ between early and late embryonic nuclei, highlighting connections between temporal and spatial LTR-RTEs niche partitionings.</span></p>',
'date' => '2024-08-16',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.08.14.607943v1',
'doi' => 'https://doi.org/10.1101/2024.08.14.607943',
'modified' => '2024-09-02 10:29:44',
'created' => '2024-09-02 10:29:44',
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[maximum depth reached]
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(int) 2 => array(
'id' => '4933',
'name' => 'Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches',
'authors' => 'Lee M. et al.',
'description' => '<p><span>Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.</span></p>',
'date' => '2024-04-05',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38580401/',
'doi' => '10.1101/gr.277926.123',
'modified' => '2024-04-09 00:19:18',
'created' => '2024-04-09 00:19:18',
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'id' => '4895',
'name' => 'Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing',
'authors' => 'Santhanagopalan I. et al.',
'description' => '<p class="section-title u-h4 u-margin-l-top u-margin-xs-bottom">Highlights</p>
<div id="abssec0020">
<ul class="list">
<li class="react-xocs-list-item">
<p id="p0010">Optimized isolation of nuclei from the green model alga<span> </span><em>Chlamydomonas reinhardtii</em></p>
</li>
<li class="react-xocs-list-item">
<p id="p0010"><em></em></p>
<p id="p0015">Tag-free isolation from both cell-walled and cell wall-deficient algae strains</p>
</li>
<li class="react-xocs-list-item">
<p id="p0015"></p>
<p id="p0020">Key steps for an effective and fast isolation and quantification procedure of nuclei</p>
</li>
<li class="react-xocs-list-item">
<p><span class="list-label"></span>Extracts at a quality suitable for ATAC-sequencing</p>
</li>
</ul>
</div>',
'date' => '2024-03-15',
'pmid' => 'https://www.sciencedirect.com/science/article/pii/S2666166723007311',
'doi' => 'https://doi.org/10.1016/j.xpro.2023.102764',
'modified' => '2024-02-09 12:37:32',
'created' => '2024-01-22 13:39:58',
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(int) 4 => array(
'id' => '4917',
'name' => 'Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition',
'authors' => 'Trembley B.J.M. et al.',
'description' => '<p><span>Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in </span><i>Arabidopsis thaliana</i><span><span> </span>we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.</span></p>',
'date' => '2024-02-26',
'pmid' => 'https://www.nature.com/articles/s41467-024-46082-5',
'doi' => 'https://doi.org/10.1038/s41467-024-46082-5',
'modified' => '2024-02-29 11:56:56',
'created' => '2024-02-29 11:56:56',
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(int) 5 => array(
'id' => '4910',
'name' => 'The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation',
'authors' => 'Kim M. et al.',
'description' => '<p><span>During human pregnancy, extravillous trophoblasts play crucial roles in placental invasion into the maternal decidua and spiral artery remodeling. However, regulatory factors and their action mechanisms modulating human extravillous trophoblast specification have been unknown. By analyzing dynamic changes in transcriptome and enhancer profile during human trophoblast stem cell to extravillous trophoblast differentiation, we define stage-specific regulators, including an early-stage transcription factor, TFAP2C, and multiple late-stage transcription factors. Loss-of-function studies confirm the requirement of all transcription factors identified for adequate differentiation, and we reveal that the dynamic changes in the levels of TFAP2C are essential. Notably, TFAP2C pre-occupies the regulatory elements of the inactive extravillous trophoblast-active genes during the early stage of differentiation, and the late-stage transcription factors directly activate extravillous trophoblast-active genes, including themselves as differentiation further progresses, suggesting sequential actions of transcription factors assuring differentiation. Our results reveal stage-specific transcription factors and their inter-connected regulatory mechanisms modulating extravillous trophoblast differentiation, providing a framework for understanding early human placentation and placenta-related complications.</span></p>',
'date' => '2024-02-12',
'pmid' => 'https://www.nature.com/articles/s41467-024-45669-2',
'doi' => 'https://doi.org/10.1038/s41467-024-45669-2',
'modified' => '2024-02-15 10:43:52',
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(int) 6 => array(
'id' => '4928',
'name' => 'DMSO derives Trophectoderm and Clonal Blastoid from Single Human Pluripotent Stem Cell',
'authors' => 'Alsolami S. et al.',
'description' => '<p><span>Human naïve pluripotent stem cells (nPSCs) can differentiate into extra-embryonic trophectoderm (TE), a critical step in the generation of the integrated embryo model termed blastoid. The current paradigm of blastoid generation necessitates the aggregation of dozens of nPSCs treated with multiple small molecule inhibitors, growth factors, or genetic modifications to initiate TE differentiation. The presence of complex crosstalk among pathways and cellular heterogeneity in these models complicates mechanistic study and genetic screens. Here, we show that a single small molecule, dimethyl sulfoxide (DMSO), potently induces TE differentiation in basal medium without pharmacological and genetic perturbations. DMSO enhances blastoid generation and, more importantly, is sufficient for blastoid generation by itself. DMSO blastoids resemble blastocysts in morphology and lineage composition. DMSO induces blastoid formation through PKC signaling and cell cycle regulation. Lastly, DMSO enables single nPSC-derived clonal blastoids, which could facilitate genetic screens for mechanistic understanding of human embryogenesis.</span></p>',
'date' => '2024-01-01',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2023.12.31.573770v1.abstract',
'doi' => 'https://doi.org/10.1101/2023.12.31.573770',
'modified' => '2024-03-27 15:18:04',
'created' => '2024-03-27 15:18:04',
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(int) 7 => array(
'id' => '4887',
'name' => 'In vitro production of cat-restricted Toxoplasma pre-sexual stages',
'authors' => 'Antunes, A.V. et al.',
'description' => '<p><span>Sexual reproduction of </span><i>Toxoplasma gondii</i><span>, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Farhat, D. C. et al. A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment. Nat. Microbiol. 5, 570–583 (2020)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR1" id="ref-link-section-d277698175e527">1</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 2" title="Bougdour, A. et al. Drug inhibition of HDAC3 and epigenetic control of differentiation in Apicomplexa parasites. J. Exp. Med. 206, 953–966 (2009)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR2" id="ref-link-section-d277698175e530">2</a></sup><span>. Here we found that the transcription factors AP2XII-1 and AP2XI-2 operate during the tachyzoite stage, a hallmark of acute toxoplasmosis, to silence genes necessary for merozoites, a developmental stage critical for subsequent sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a marked change in the transcriptional program, promoting a full transition from tachyzoites to merozoites. These in vitro-cultured pre-gametes have unique protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit MORC and HDAC3 (ref. </span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Farhat, D. C. et al. A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment. Nat. Microbiol. 5, 570–583 (2020)." href="https://www.nature.com/articles/s41586-023-06821-y#ref-CR1" id="ref-link-section-d277698175e534">1</a></sup><span>), thereby limiting chromatin accessibility and transcription. Consequently, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. Successful production of merozoites in vitro paves the way for future studies on<span> </span></span><i>Toxoplasma</i><span><span> </span>sexual development without the need for cat infections and holds promise for the development of therapies to prevent parasite transmission.</span></p>',
'date' => '2023-12-13',
'pmid' => 'https://www.nature.com/articles/s41586-023-06821-y',
'doi' => 'https://doi.org/10.1038/s41586-023-06821-y',
'modified' => '2023-12-18 10:40:50',
'created' => '2023-12-18 10:40:50',
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(int) 8 => array(
'id' => '4939',
'name' => 'Vaginal microbes alter epithelial transcriptomic and epigenomic modifications providing insight into the molecular mechanisms for susceptibility to adverse reproductive outcomes',
'authors' => 'Elovitz M. et al.',
'description' => '<p><span>The cervicovaginal microbiome is highly associated with women's health with microbial communities dominated by </span><i>Lactobacillus</i><span><span> </span>spp. being considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes including<span> </span></span><i>Gardnerella vaginalis</i><span>, have been associated with adverse reproductive outcomes. However, the molecular pathways modulated by microbe interactions with the cervicovaginal epithelia remain unclear. Using RNA-sequencing, we characterize the<span> </span></span><i>in vitro</i><span><span> </span>cervicovaginal epithelial transcriptional response to different vaginal bacteria and their culture supernatants. We showed that<span> </span></span><i>G. vaginalis</i><span><span> </span>upregulated genes were associated with an activated innate immune response including anti-microbial peptides and inflammasome pathways, represented by NLRP3-mediated increases in caspase-1, IL-1β and cell death. Cervicovaginal epithelial cells exposed to<span> </span></span><i>L. crispatus</i><span><span> </span>showed limited transcriptomic changes, while exposure to<span> </span></span><i>L. crispatus</i><span><span> </span>culture supernatants resulted in a shift in the epigenomic landscape of cervical epithelial cells. ATAC-sequencing confirmed epigenetic changes with reduced chromatin accessibility. This study reveals new insight into host-microbe interactions in the lower reproductive tract and suggest potential therapeutic strategies leveraging the vaginal microbiome to improve reproductive health.</span></p>',
'date' => '2023-11-16',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38014044/',
'doi' => '10.21203/rs.3.rs-3580132/v1',
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'description' => '<p><span>The compaction of chromatin is a prevalent paradigm in gene repression. Chromatin compaction is commonly thought to repress transcription by restricting chromatin accessibility. However, the spatial organisation and dynamics of chromatin compacted by gene-repressing factors are unknown. Using cryo-electron tomography, we solved the three dimensional structure of chromatin condensed by the Polycomb Repressive Complex 1 (PRC1) in a complex with CBX8. PRC1-condensed chromatin is porous and stabilised through multivalent dynamic interactions of PRC1 with chromatin. Within condensates, PRC1 remains dynamic while maintaining a static chromatin structure. In differentiated mouse embryonic stem cells, CBX8-bound chromatin remains accessible. These findings challenge the idea of rigidly compacted polycomb domains and instead provides a mechanistic framework for dynamic and accessible PRC1-chromatin condensates.</span></p>',
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'description' => '<p><span>Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.</span></p>',
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
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<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
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<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
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<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
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<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
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<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'meta_description' => 'Diagenode’s ATAC-seq kit provides a robust protocol for assessing genome-wide chromatin accessibility',
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/atacseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
'info2' => '<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig1.png" alt="library prepared with the Diagenode ATAC-seq kit " width="500px" caption="false" /></p>
<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'name' => 'UMSBP2 is chromatin remodeler that functions in regulation of geneexpression and suppression of antigenic variation in trypanosomes.',
'authors' => 'Soni A. et al.',
'description' => '<p><span>Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.</span></p>',
'date' => '2023-05-01',
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