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'description' => '<p>pA-Tn5トランスポザーゼは、CUT＆Tagアッセイ専用に開発された高活性Tn5トランスポザーゼとプロテインAの融合タンパク質です。 融合タンパク質にはシーケンスアダプターがあらかじめロードされある、便利なプリロードです。</p>
<p>目的のタンパク質のみをターゲットとすることが重要であるため、CUT＆Tagアッセイの成功には非常に特異的な抗体が不可欠です。 厳密な検証基準を満たしている特異性が検証されているDiagenode ChIP-seqグレードの抗体は、CUT＆Tagアッセイでの高いパフォーマンスを保証します。</p>
<p class="lead">CUT＆Tagアッセイに関する推奨製品はこちら</p>
<ul>
<li>pA/Tn5 Transposase (loaded or unloaded)</li>
<li><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a></li>
<li>Negative CUT&Tag control <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">Rabbit IgG</a></li>
<li>Sequencing indexes <a href="https://www.diagenode.com/en/p/24-si-for-chipmentation">24 Single indexes</a></li>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<p class="lead">CUT＆Tagアッセイに関する推奨製品はこちら</p>
<ul>
<li>pA/Tn5 Transposase (loaded or unloaded)</li>
<li><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a></li>
<li>Negative CUT&Tag control <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">Rabbit IgG</a></li>
<li>Sequencing indexes <a href="https://www.diagenode.com/en/p/24-si-for-chipmentation">24 Single indexes</a></li>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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'meta_title' => 'pA-Tn5 Transposase (loaded) developed for the CUT&Tag assay | Diagenode.com',
'meta_keywords' => '',
'meta_description' => 'Diagenode pA-Tn5 Transposase (loaded) is a fusion protein of hyperactive Tn5 transposase and protein A developed for the CUT&Tag assay. For convenience, the fusion protein is pre-loaded with sequencing adapters.',
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'name' => 'pA-Tn5 Transposase - unloaded',
'description' => '<p><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24"> <img alt="pA-Tn5 Transposase unloaded" src="https://www.diagenode.com/img/banners/banner-cutruncuttag-small.png" /></a></p>
<p><strong>pA-Tn5 Transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For flexibility, the fusion protein is not pre-loaded with sequencing adapters. Please follow the recommended <a href="https://www.diagenode.com/en/documents/assembly-protocol-patn5-20042020-rms" target="_blank">assembly protocol</a> prior to use in CUT&Tag or similar assays (ACT-seq, CoBATCH, TIP-seq and other).</p>
<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: <a href="https://www.diagenode.com/en/products/view/3064">loaded</a> or unloaded</span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag and similar assays (eg. TIP-seq)<br /></span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> <span>- compatible with histome marks and some transcription factors</span></li>
<li>pA/Tn5 Transposase (<a href="https://www.diagenode.com/en/products/view/3064" target="_blank">loaded </a>or unloaded)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
</ul>',
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase" src="https://www.diagenode.com/img/product/cutandtag/C01070002-fig-a.jpg" width="600" height="265" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">B.<br /><center><img alt="pA-Tn5 Transposase unloaded" src="https://www.diagenode.com/img/product/cutandtag/C01070002-fig-b.jpg" /></center></div>
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<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1: Quality control of pA-Tn5 transposase loaded with sequencing adapters</strong></p>
<p>A: The Fragment Analyzer trace showing the representative cleavage pattern of gDNA. The pA-Tn5 fusion protein (Cat. No. C01070002) loaded with sequencing adapters efficiently digests gDNA to a smear. 500 ng of human genomic DNA were incubated for 7 min at 55°C with 1 μl of pATn5 fusion protein loaded with appropriated adaptors in a tagmentation buffer (40mM Tris-HCl pH7.5, 40mM MgCl2 and 12.5% DMF). The reaction was stopped by adding SDS, cleaned-up and resolved on the Fragment Analyzer to assess the cleavage.</p>
<p>B: Representative screenshot at selected locus obtained using Diagenode pA-Tn5 fusion protein (Cat. No. C01070002) lloaded with sequencing adapters and H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) following CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)).</p>
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<p><span><span style="left: 94.4882px; top: 499.039px; font-size: 15px; font-family: sans-serif; transform: scaleX(1.00223);">The negative Ctrl IgG is intended for use </span><span style="left: 94.4882px; top: 519.039px; font-size: 15px; font-family: sans-serif; transform: scaleX(1.02185);">as a negative control in ChIP, CUT&Tag, MeDIP, IF and other experiments performed with specific antibodies made in rabbit.</span></span></p>',
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<p><small> <strong>Figure 1. ChIP with the Diagenode rabbit IgG negative control antibody</strong><br />ChIP assays were performed using the Diagenode rabbit polyclonal antibody against H3K4me3 (Cat. No. C15410003) and the “iDeal ChIPseq” kit (Cat. No. C01010051) on sheared chromatin from 1 million HeLa cells. Rabbit IgG (cat. No. C15410206) was used as a negative IP control. One μg of antibody per ChIP experiment was used for both antibodies. Quantitative PCR was performed with primers specific for the promoters of the active GAPDH and EIF4A2 genes, and for the inactive MYOD1 gene and the Sat2 satellite repeat. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
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<p><small> <strong>Figure 2. Immunofluorescence with the Diagenode rabbit IgG negative control antibody</strong><br />HeLa cells were stained with the Diagenode rabbit polyclonal antibody against H3K4me3 (Cat. No. C15410003) (top) and with DAPI. Rabbit IgG (Cat. No. C15410206) was used as a negative control (bottom). Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me3 or rabbit IgG negative control antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/primer-indexes-for-tagmented-libraries_manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>The <strong>24 UDI for tagmented libraries</strong> includes 24 primer pairs for unique dual-indexing allowing the multiplexing of up to <b>24 samples </b>for sequencing on Illumina platforms. These UDI are designed and validated to be used with <a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">μChIPmentation for Histones</a> (Cat. No. C01011011), <a href="https://www.diagenode.com/en/p/chipmentation-kit-for-histones">ChIPmentation Kit for Histones</a> (Cat. No. C01011009), <a href="https://www.diagenode.com/en/p/tag-kit-for-chipmentation-24">TAG Kit for ChIPmentation</a> (Cat. No. C01011030), <a href="https://www.diagenode.com/en/categories/atac-seq">ATAC-seq Kit</a> (Cat. No. C01080002). The 24 UDI for tagmented libraries are compatible with other <b>tagmentation</b><b>-based library preparation </b>protocols, such as <a href="https://www.diagenode.com/en/categories/cutandtag">CUT&Tag</a> technologies.</p>
<p>3 sets of UDI for tagmented libraries are available:</p>
<p><strong>24 UDI for tagmented libraries - Set I</strong><br /> <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set2">24 UDI for tagmented libraries - Set II</a><br /><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set3" target="_blank">24 UDI for tagmented libraries - Set III</a><br /><br /></p>
<p><span>Each set can be used for library multiplexing up to 24. All sets can be used simultaneously for library multiplexing up to 72.</span></p>
<p>Features:</p>
<ul>
<li>Multiplexing: <b>up to 72 samples </b>(using all 3 sets simultaneously)<b><br /></b></li>
<li>Allow for <b>identification of index hopping</b></li>
<li>Compatibility: <b>tagmentation</b><b>-based library preparation protocols</b></li>
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<p>The <b>24 UDI for </b><b>tagmented</b><b> libraries </b>provides combinations of barcodes where each barcode is uniquely attributed to one sample. This is a great tool to identify mistakes during index sequencing. A phenomenon, known as index hopping, can lead to misattribution of some reads to the wrong sample. This is particularly frequent with the NovaSeq6000, and thus the use of Unique Dual Indexing (UDI) is highly recommended when using this sequencer.</p>
<p></p>
<center><img src="https://www.diagenode.com/img/product/kits/UDI-for-tagmented-fig1.png" /></center>
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<p><small><strong>Figure 1. Sequencing profiles of µChIPmentation libraries generated with 24 UDI for Tagmented libraries</strong> Chromatin preparation and immunoprecipitation have been performed on 10.000 cells using the µChIPmentation Kit for Histones (Cat. No. C01011011) and 24 UDI for Tagmented libraries – Set I (Cat. No. Cat. No. C01011034) using K562 cells. The Diagenode antibodies targeting H3K4me3 (Cat. No. C15410003) and rabbit IgG (Cat. No. C15410206) have been used. </small></p>
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'description' => '<p><a href="https://www.diagenode.com/files/application_notes/AN-iDealCUTandTag.pdf"><img src="https://www.diagenode.com/img/banners/cutandtag-appnote.png" /></a></p>
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<p><strong>CUT&Tag-sequencing</strong> (<strong>C</strong>leavage <strong>U</strong>nder <strong>T</strong>argets and <strong>Tag</strong>mentation) is a new alternative method to ChIP-seq combining antibody-targeted controlled cleavage by a protein A-Tn5 fusion with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.</p>
<p><a href="https://www.diagenode.com/files/products/kits/iDeal-CUTandTag-kit-for-histones-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
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<p>The Diagenode’s <strong>iDeal CUT&Tag kit for Histones</strong> provides an optimized protocol for a rapid chromatin profiling on <strong>histone marks</strong> and some <strong>non-histone proteins</strong>. The protocol is optimized for native cells (<strong>10,000-300,000</strong> cells per reaction) and can be completed within 1.5 days. The kit includes all reagents for cell processing, including CoA beads, pA-Tn5 and the DNA purification module. The antibodies (secondary antibodies, control antibodies) as well as primer indexes for multiplexing must be purchased separately.</p>
<p><strong>For a complete CUT&Tag protocol the following items must be purchased:</strong></p>
<ul>
<li><strong>iDeal CUT&Tag kit for Histones</strong> – including all reagents for CUT&Tag workflow (buffers, pA-Tn5, CoA beads, DNA purification)</li>
<li><strong>Antibody package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a></strong> or <strong><a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></strong> - including the secondary antibody, positive and negative control antibodies and primers</li>
<li><strong><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></strong> – for multiplexing up to 72 samples</li>
</ul>
<h3>iDeal CUT&Tag Kit features:</h3>
<ul>
<li><strong>Rapid</strong> and <strong>easy </strong>chromatin profiling assay for <strong>histones </strong>and<strong> some non-histone proteins</strong></li>
<ul style="margin-bottom: 0;">
<li>No chromatin preparation</li>
<li>Easy sample handling due to ConA magnetic beads</li>
<li>Integrated library prep</li>
</ul>
<li><strong>Low cell number</strong>: 10,000-300,000 cells</li>
<li><strong>Accurate amplification</strong> due to intermediate quantification step</li>
<li><strong>High resolution</strong> and <strong>sensitivity</strong></li>
<li><strong>Lower sequencing depth</strong></li>
</ul>
<p>The quality of antibody used in CUT&Tag is one of the crucial factors for assay success. The antibodies with confirmed high specificity will target only the protein of interest, enabling real results. Check out our selection of <strong><a href="https://www.diagenode.com/en/categories/cut-and-tag-antibodies">antibodies validated in CUT&Tag</a>.</strong></p>
<p>Looking for a standalone pA-Tn5? <a href="https://www.diagenode.com/en/products/view/3064">Read more</a>.</p>
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'info1' => '<p>The iDeal CUT&Tag protocol involves the binding of cells on a solid phase ConA magnetic beads, allowing magnetic handling of the cells for the major steps of the protocol. Bead-bound cells are permeabilized, incubated with primary antibody against a target of interest and secondary antibody. Then, Diagenode’s protein pA-Tn5 Transposase - loaded is bound to the complex. Protein A guides Tn5 transposase on chromatin to the antibody attached to its target. Tn5 transposase is activated by Mg+2 ions to insert the sequencing adaptors into genomic regions of interest. DNA is then purified and the tagmented genomic regions of interest are amplified by PCR using Diagenode’s Primer Indexes for tagmented libraries.</p>
<p></p>
<p><img alt=" pA-Tn5 Antibody package for CUT & Tag" src="https://www.diagenode.com/img/product/kits/workflow-cutandtag.jpg" /></p>',
'label2' => 'Examples of results - histone marks',
'info2' => '<p>Successful CUT&Tag results showing a low background with high region-specific enrichment are presented below. Chromatin profiling has been performed on 50,000 K562 cells, using the Diagenode’s iDeal CUT&Tag kit for Histones (Cat. No. C01070020), the Antibody Package for CUT&Tag anti rabbit (Cat. No. C01070022), the 24 UDI for Tagmented Libraries (Cat.No. C01011034) and H3K4me3 (Cat. No. C15410003), H3K27me3 (Cat. No. C15410069) or H3H9me3 antibodies (Cat. No., C15410193) as indicated. The libraries were sequenced on Illumina’s NovaSeq6000 in 2x50 bp mode.</p>
<p><br /> <img alt="CUT&Tag-sequencing" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1a.png" /> <img alt="CUT&Tag kit for Histones" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1b.png" /> <img alt="Cleavage Under Targets and Tagmentation" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1c.png" /></p>
<p><strong>Figure 1.</strong> Typical library profiles (Agilent Fragment traces) generated by the iDeal CUT&Tag protocol using 50,000 K562 cells and H3K27me3 (top), H3K4me4 (middle) primary antibodies and IgG control (bottom). Sharp peak at around 40 bp is an excess of <strong>free oligonucleotide used for pA-Tn5 loading</strong>.</p>
<p></p>
<p><br /><br /></p>
<div class="row">
<div class="small-4 columns">
<p><img alt="iDeal CUT&Tag kit for Histones" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig2.png" /></p>
</div>
<div class="small-8 columns">
<p><strong>Figure 2.</strong> Enrichments at TSS of the CUT&Tag libraries. The heatmap shows the enrichment around 3kb upstream and downstream of the TSS for H3K4me3. H3K4me3 as an active chromatin mark is associated with active promoters shows a narrow enrichment pattern.</p>
</div>
</div>
<p><br /><br /></p>
<p><br /> <img alt="iDeal CUT&Tag experiments of K562 cells " src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig3.png" /></p>
<p><strong>Figure 3.</strong> Sequencing profiles of the CUT&Tag libraries. Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using 50,000 of K562 cells and H3K4me3 (blue), H3K27me3 (red) or H3K9me3 (green).</p>
<p><br /><br /></p>
<p><br /> <img alt="CUT&Tag experiments using 10,000 K562 cells" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig4.png" /></p>
<p><strong>Figure 4.</strong> Sequencing profiles of the CUT&Tag libraries. Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using 50,000 (blue) or 10,000 (red)) of K562 cells and H3K27me3 antibody.</p>',
'label3' => 'Examples of results - transcription factors',
'info3' => '<p>Diagenode's<strong><span> iDeal CUT&Tag Kit for Histones</span></strong><span>, </span>developed for an efficient chromatin profiling on histone marks, can be used for profiling of <span>some transcription factors and co-factors using a mild fixation as described in the manual. </span></p>
<p><strong><span>Successful CUT&Tag results using CTCF and Suz12 antibodies and iDeal CUT&Tag Kit for Histones. </span></strong></p>
<p></p>
<p><span>Chromatin profiling of <strong>Suz12</strong> has been performed on 50,000 of fixed Mouse ES-E14TG2a cells (kindly provided by Luciano Di Croce, CRG, Spain) accordingly to the protocol of Diagenode’s iDeal CUT&Tag kit for Histones (Cat. No. C01070020). Antibody Package for CUT&Tag anti rabbit (Cat. No. C01070022) and the 24 UDI for Tagmented Libraries (Cat. No. C01011034) were used. The libraries were sized using Fragment Analyzer (Agilent) (triplicates, Figure 1, top). Relative enrichment has been confirmed by qPCR using know positive (T_Bra) and negative (Actb) loci (Figure 1, bottom). Libraries were sequenced on Illumina’s NovaSeq6000 in 2x50 bp mode.</span></p>
<p></p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig1a.jpg" /><br /> <img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig1b.jpg" /></p>
<p><strong>Figure 1.</strong> Typical library profiles (top) and relative enrichment (bottom) generated by the iDeal CUT&Tag protocol using 50,000 ES-E14TG2a cells and Suz12 Antibody and IgG control (bottom). Sharp peak at around 40 bp is an excess of free oligonucleotide used for pA-Tn5 loading which does not interfere with the sequencing.</p>
<p></p>
<p>Pictures of representative loci were taken on Integrative Genome Viewer (IGV) for CTCF demonstrating the presence of high signal at promoter regions.</p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2a.jpg" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2b.jpg" /> <img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2c.jpg" /></p>
<p></p>
<p></p>
<p>Pictures of representative loci were taken on Integrative Genome Viewer (IGV) for SUZ12 and H3K27me3 triplicate samples, showing an overlap between the signal from both proteins, as part of the Polycomb Repressive Complex.</p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci1.jpg" width="100%" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci2.jpg" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci3.jpg" /></p>
<p><strong>Figure 2. IGV snapshots</strong></p>
<p></p>
<p></p>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig3.jpg" /></p>
</div>
<div class="small-8 columns">
<p><strong>Figure 3. Heatmap around the TSS</strong><br /> Heatmap of the CTCF signal around the transcription start sites (TSS) of each gene present in the murine mm10 reference genome.</p>
</div>
</div>
<p></p>
<p></p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig4.jpg" /></p>
<p><strong>Figure 4. CTCF motif</strong><br /> Presence of specific transcription factor binding motifs in the regions identified as CTCF peaks. The top3 motifs are corresponding to the CTCF binding motif.</p>
<p></p>
<p></p>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig5.jpg" /></p>
</div>
<div class="small-6 columns">
<p><strong>Figure 5. CTCF motif density</strong><br /> Location and density of the CTCF binding motif with respect to the center of the identified CTCF peaks.</p>
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<p> </p>
<p>Diagenode <b>Tagmentase</b><b> – loaded </b>is a <strong>hyperactive Tn5 transposase</strong> preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq or ChIPmentation.</p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x-1ml">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for unloaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-20-ul">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul"> (Tn5 transposase) – </a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul">unloaded</a></p>',
'label1' => 'Examples of results',
'info1' => '<p><b>Tagmentase</b><b> (Tn5 transposase) – </b><b>loaded</b> can be used in any application using tagmentation-based library preparation, like for example ChIPmentation, ATAC-seq. Here below we are showing some examples of results.</p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig1.png" width="700" alt="Tn5 transposase Enxzymes" caption="false" /></center>
<p><small><strong>Figure 1. Typical library profile of ATAC-seq library generated with the Tagmentase</strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
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<div class="small-8 columns">
<p><small><strong>Figure 2. Enrichments at TSS of ATAC-seq libraries generated with the Tagmentase</strong><br />ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). Heatmaps around the hg19 TSS were generated using deeptools plotHeatmap functionality.</small></p>
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<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig3.png" alt="Transposase enzymes for ATAC-Seq" caption="false" width="956" height="259" /></center>
<p><small><strong>Figure 3. Sequencing profiles of ATAC-seq libraries generated with the Tagmentase </strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig4.png" width="700" alt="purified Transposase enzymes " caption="false" /></center>
<p><small><strong>Figure 4. Typical library profile of ChIPmentation library generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 1,000,000 K562 cells using the ChIPmentation Kit for Histones (Cat. No. C01011010) in combination with the Diagenode antibody targeting H3K4me3 (Cat. No. C15410003) and with the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig5.png" alt="pA-Tn5 Transposase Enzymes" caption="false" width="956" height="262" /></center>
<p><small><strong>Figure 5. Sequencing profiles of ChIPmentation libraries generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 500.000 to 1,000,000 cells using the <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones </a>(Cat. No. C01011010) in combination with the <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) – loaded </a>(Cat. No. C01070012) on K562 cells. The Diagenode antibodies targeting <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3 </a>(Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-premium-50-mg-18-ml">H3K27ac </a>(Cat. No. C15410196), <a href="https://www.diagenode.com/en/p/h3k36me3-polyclonal-antibody-premium-50-mg">H3K36me3 </a>(Cat. No. C15410192), <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (Cat. No. C15410195) and rabbit <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">IgG </a>(Cat. No. C15410206) have been used.</small></p>
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'info2' => '<p><strong>Tagmentase (Tn5 transposase) - loaded </strong></p>
<div>Protein Molecular weight: 53.3 kDa</div>
<p>Expressed: in Escherichia coli</p>
<p></p>
<p><strong>Product description:</strong> Diagenode Tagmentase – loaded is a hyperactive Tn5 transposase preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments. The Tagmentase is pre-loaded with sequencing adapters compatible with Illumina Nextera platforms, as shown below. The oligos loaded on the Tagmentase are inserted into DNA upon a tagmentation reaction.</p>
<div>Mosaic end_reverse: 5’ [PHO]<span style="text-decoration: underline;">CTGTCTCTTATACACATCT</span> 3’</div>
<div>Mosaic end_Adapter A: 5’ TCGTCGGCAGCGTC<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</div>
<p>Mosaic end_Adapter B: 5’ GTCTCGTGGGCTCGG<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</p>
<p></p>
<div><span style="text-decoration: underline;">Underlined regions</span> correspond to the double-stranded part of the adapter, recognized by the Tagmentase. The final libraries can be amplified using Diagenode Primer indexes for tagmented libraries:</div>
<div>24 SI for tagmented libraries, Cat. No. C01011032</div>
<div>24 UDI fortagmented libraries - Set I, Cat. No. C0101134</div>
<div>24 UDI for tagmented libraries - Set II, Cat. No. C0101136</div>
<p>24 UDI for tagmented libraries - Set III, Cat. No. C0101137</p>
<p></p>
<p><strong>Storage conditions: </strong>Store at -20°C. Guaranteed stable for 6 months from date of receipt when stored properly.</p>
<p><strong>Storage buffer:</strong> Supplied in solution containing 50% v/v glycerol.</p>
<p><strong>Properties & Usage: </strong>Tagmentase is dependent on Mg++ for activity. Avoid chelators, such as EDTA/EGTA, in reaction buffers. The enzyme is active at pH 7.5-8 at 37-55°C. SDS, EDTA/EGTA or heating to 65°C will inactivate the enzyme.</p>
<p><strong>Applications:</strong> Tagmentase (Tn5 transposase) – loaded can be used in a variety of applications to construct library for second-generation sequencing. Please note that an additional optimization might be required for custom protocols including the enzyme dose- and time-response experiments.</p>
<div>For ATAC-seq and ChIPmentation, we recommend using Diagenode validated protocols:</div>
<div>ATAC-seq kit, Cat. No. C01080002</div>
<div>ATAC-seq package for tissue, Cat. No. <span>C01080006</span></div>
<div>ChIPmentation Kit for Histones, Cat. No. C01011009</div>
<div>µChIPmentation Kit for Histones, Cat. No. C01011011</div>
<div>TAG Kit for ChIPmentation, Cat. No. C01011030</div>
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<p><strong>CUT&Tag</strong>-sequencing (<strong>C</strong>leavage <strong>U</strong>nder <strong>T</strong>argets and <strong>Tag</strong>mentation) is a new alternative method to ChIP-seq combining antibody-targeted controlled cleavage by a protein A-Tn5 fusion with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. At Diagenode we offer a complete solution for CUT&Tag – our iDeal CUT&Tag for Histones (developped for histone marks and some non-histone proteins), but also stand-alone fusion protein – pA-Tn5 Transposase. Moreover, we have validated our <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a> in <a href="https://www.diagenode.com/en/categories/cut-and-tag-antibodies">CUT&Tag</a> proving their high performance in this assay.</p>
<br /> <a href="https://www.diagenode.com/files/application_notes/AN-iDealCUTandTag.pdf"><img src="https://www.diagenode.com/img/banners/cutandtag-appnote.png" /></a><br /><br /></div>
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<li class="accordion-navigation"><a href="#v5" style="color: #13b29c;"><i class="fa fa-caret-right"></i> How does it work?</a>
<div id="v5" class="content">
<p>The iDeal CUT&Tag protocol involves the binding of cells on a solid phase ConA magnetic beads, allowing magnetic handling of the cells for the major steps of the protocol. Bead-bound cells are permeabilized, incubated with primary antibody against a target of interest and secondary antibody. Then, Diagenode’s protein pA-Tn5 Transposase - loaded is bound to the complex. Protein A guides Tn5 transposase on chromatin to the antibody attached to its target. Tn5 transposase is activated by Mg+2 ions to insert the sequencing adaptors into genomic regions of interest. DNA is then purified and the tagmented genomic regions of interest are amplified by PCR using Diagenode’s Primer Indexes for tagmented libraries.</p>
<img src="https://www.diagenode.com/img/product/kits/workflow-cutandtag.jpg" /></div>
<h2>Products for CUT&Tag assay</h2>
<h3 class="diacol">Complete solutions</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24" target="_blank">iDeal CUT&Tag kit for Histones</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24" target="_blank">Antibody package for CUT&Tag (anti-rabbit)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24" target="_blank">Antibody package for CUT&Tag (anti-mouse)</a></li>
</ul>
<h3 class="diacol">Fusion protein</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/products/view/3064" target="_blank">pA/Tn5 Transposase (loaded)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">pA/Tn5 Transposase (unloaded)</a></li>
</ul>
<h3 class="diacol">CUT&Tag grade antibodies</h3>
<ul class="nobullet">
<li>Antibodies <a href="https://www.diagenode.com/en/applications/cut-and-tag">validated in CUT&Tag</a></li>
<li>Check out our list of <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies" target="_blank">ChIP-seq grade antibodies</a></li>
<li>Read more about the performance of Diagenode antibodies in <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">CUT&Tag</a></li>
</ul>
<h3 class="diacol">Positive & Negative CUT&Tag control</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24" target="_blank">Antibody package for CUT&Tag (anti-rabbit)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24" target="_blank">Antibody package for CUT&Tag (anti-mouse)</a></li>
</ul>
<h3 class="diacol">DNA purification</h3>
<p style="padding-left: 30px;"><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2<br /></a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></p>
<h3 class="diacol">Sequencing indexes</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries" target="_blank">Primer indexes for tagmented libraries</a></li>
</ul>
</li>
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'name' => 'The molecular consequences of FOXF1 missense mutations associated with alveolar capillary dysplasia with misalignment of pulmonary veins',
'authors' => 'G. G. Edel et al.',
'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a fatal congenital lung disorder strongly associated with genomic alterations in the Forkhead box F1 (FOXF1) gene and its regulatory region. However, little is known about how FOXF1 genomic alterations cause ACD/MPV and what molecular mechanisms are affected by these mutations. Therefore, the effect of ACD/MPV patient-specific mutations in the<span> </span><i>FOXF1</i><span> </span>gene on the molecular function of FOXF1 was studied.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Methods</h3>
<p>Epitope-tagged FOXF1 constructs containing one of the ACD/MPV-associated mutations were expressed in mammalian cell lines to study the effect of FOXF1 mutations on protein function. EMSA binding assays and luciferase assays were performed to study the effect on target gene binding and activation. Immunoprecipitation followed by SDS‒PAGE and western blotting were used to study protein‒protein interactions. Protein phosphorylation was studied using phos-tag western blotting.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>An overview of the localization of ACD/MPV-associated FOXF1 mutations revealed that the G91-S101 region was frequently mutated. A three-dimensional model of the forkhead DNA-binding domain of FOXF1 showed that the G91-S101 region consists of an α-helix and is predicted to be important for DNA binding. We showed that FOXF1 missense mutations in this region differentially affect the DNA binding of the FOXF1 protein and influence the transcriptional regulation of target genes depending on the location of the mutation. Furthermore, we showed that some of these mutations can affect the FOXF1 protein at the posttranscriptional level, as shown by altered phosphorylation by MST1 and MST2 kinases.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusion</h3>
<p>Missense mutations in the coding region of the<span> </span><i>FOXF1</i><span> </span>gene alter the molecular function of the FOXF1 protein at multiple levels, such as phosphorylation, DNA binding and target gene activation. These results indicate that FOXF1 molecular pathways may be differentially affected in ACD/MPV patients carrying missense mutations in the DNA-binding domain and may explain the phenotypic heterogeneity of ACD/MPV.</p>',
'date' => '2024-11-04',
'pmid' => 'https://link.springer.com/article/10.1186/s12929-024-01088-5',
'doi' => 'https://doi.org/10.1186/s12929-024-01088-5',
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'name' => 'Two-factor authentication underpins the precision of the piRNA pathway',
'authors' => 'Dias Mirandela M. et al.',
'description' => '<p><span>The PIWI-interacting RNA (piRNA) pathway guides the DNA methylation of young, active transposons during germline development in male mice</span><span>. piRNAs tether the PIWI protein MIWI2 (PIWIL4) to the nascent transposon transcript, resulting in DNA methylation through SPOCD1</span><span>. Transposon methylation requires great precision: every copy needs to be methylated but off-target methylation must be avoided. However, the underlying mechanisms that ensure this precision remain unknown. Here, we show that SPOCD1 interacts directly with SPIN1 (SPINDLIN1), a chromatin reader that primarily binds to H3K4me3-K9me3</span><span>. The prevailing assumption is that all the molecular events required for piRNA-directed DNA methylation occur after the engagement of MIWI2. We find that SPIN1 expression precedes that of both SPOCD1 and MIWI2. Furthermore, we demonstrate that young LINE1 copies, but not old ones, are marked by H3K4me3, H3K9me3 and SPIN1 before the initiation of piRNA-directed DNA methylation. We generated a<span> </span></span><i>Spocd1</i><span><span> </span>separation-of-function allele in the mouse that encodes a SPOCD1 variant that no longer interacts with SPIN1. We found that the interaction between SPOCD1 and SPIN1 is essential for spermatogenesis and piRNA-directed DNA methylation of young LINE1 elements. We propose that piRNA-directed LINE1 DNA methylation requires a developmentally timed two-factor authentication process. The first authentication is the recruitment of SPIN1–SPOCD1 to the young LINE1 promoter, and the second is MIWI2 engagement with the nascent transcript. In summary, independent authentication events underpin the precision of piRNA-directed LINE1 DNA methylation.</span></p>',
'date' => '2024-09-18',
'pmid' => 'https://www.nature.com/articles/s41586-024-07963-3',
'doi' => 'https://doi.org/10.1038/s41586-024-07963-3',
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'name' => 'Transcription factor EGR2 controls homing and pathogenicity of T17cells in the central nervous system.',
'authors' => 'Gao Y. et al.',
'description' => '<p>CD4 T helper 17 (T17) cells protect barrier tissues but also trigger autoimmunity. The mechanisms behind these opposing processes remain unclear. Here, we found that the transcription factor EGR2 controlled the transcriptional program of pathogenic T17 cells in the central nervous system (CNS) but not that of protective T17 cells at barrier sites. EGR2 was significantly elevated in myelin-reactive CD4 T cells from patients with multiple sclerosis and mice with autoimmune neuroinflammation. The EGR2 transcriptional program was intricately woven within the T17 cell transcriptional regulatory network and showed high interconnectivity with core T17 cell-specific transcription factors. Mechanistically, EGR2 enhanced T17 cell differentiation and myeloid cell recruitment to the CNS by upregulating pathogenesis-associated genes and myelomonocytic chemokines. T cell-specific deletion of Egr2 attenuated neuroinflammation without compromising the host's ability to control infections. Our study shows that EGR2 regulates tissue-specific and disease-specific functions in pathogenic T17 cells in the CNS.</p>',
'date' => '2023-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37443284',
'doi' => '10.1038/s41590-023-01553-7',
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'name' => 'The Hdc GC box is critical for Hdc gene transcription andhistamine-mediated anaphylaxis.',
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'description' => '<p>BACKGROUND: Histamine is a critical mediator of anaphylaxis, a neurotransmitter, and a regulator of gastric acid secretion. Histidine decarboxylase is a rate-limiting enzyme for histamine synthesis. However, in vivo regulation of Hdc, the gene that encodes histidine decarboxylase is poorly understood. OBJECTIVE: We sought to investigate how enhancers regulate Hdc gene transcription and histamine synthesis in resting conditions and in a mouse model of anaphylaxis. METHODS: H3K27 acetylation histone modification and chromatin accessibility were used to identify candidate enhancers; The enhancer activity of candidate enhancers was measured in a reporter gene assay; and the function enhancers were validated using CRISPR deletion. RESULTS: Deletion of the GC box, which binds to zinc finger transcription factors, in the proximal Hdc enhancer, reduced Hdc gene transcription and histamine synthesis in the mouse and human mast cell lines. Mast cells, basophils, brain cells, and stomach cells from GC box-deficient mice transcribed the Hdc gene much less than similar cells from wild-type mice and Hdc GC box-deficient mice failed to develop anaphylaxis. CONCLUSION: Our results demonstrate that the HDC GC box within the proximal enhancer in the mouse and human HDC gene is essential for Hdc gene transcription, histamine synthesis, and histamine-mediated anaphylaxis in vitro and in vivo.</p>',
'date' => '2023-02-01',
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'date' => '2023-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36823354',
'doi' => '10.1038/s41587-023-01683-1',
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'name' => 'Simultaneous profiling of histone modifications and DNA methylation viananopore sequencing.',
'authors' => 'Yue X. et al.',
'description' => '<p>The interplay between histone modifications and DNA methylation drives the establishment and maintenance of the cellular epigenomic landscape, but it remains challenging to investigate the complex relationship between these epigenetic marks across the genome. Here we describe a nanopore-sequencing-based-method, nanoHiMe-seq, for interrogating the genome-wide localization of histone modifications and DNA methylation from single DNA molecules. nanoHiMe-seq leverages a nonspecific methyltransferase to exogenously label adenine bases proximal to antibody-targeted modified nucleosomes in situ. The labelled adenines and the endogenous methylated CpG sites are simultaneously detected on individual nanopore reads using a hidden Markov model, which is implemented in the nanoHiMe software package. We demonstrate the utility, robustness and sensitivity of nanoHiMe-seq by jointly profiling DNA methylation and histone modifications at low coverage depths, concurrently determining phased patterns of DNA methylation and histone modifications, and probing the intrinsic connectivity between these epigenetic marks across the genome.</p>',
'date' => '2022-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36566265',
'doi' => '10.1038/s41467-022-35650-2',
'modified' => '2023-03-28 08:59:26',
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'name' => 'A SOX2-engineered epigenetic silencer factor represses the glioblastomagenetic program and restrains tumor development.',
'authors' => 'Benedetti V. et al.',
'description' => '<p>Current therapies remain unsatisfactory in preventing the recurrence of glioblastoma multiforme (GBM), which leads to poor patient survival. By rational engineering of the transcription factor SOX2, a key promoter of GBM malignancy, together with the Kruppel-associated box and DNA methyltransferase3A/L catalytic domains, we generated a synthetic repressor named SOX2 epigenetic silencer (SES), which induces the transcriptional silencing of its original targets. By doing so, SES kills both glioma cell lines and patient-derived cancer stem cells in vitro and in vivo. SES expression, through local viral delivery in mouse xenografts, induces strong regression of human tumors and survival rescue. Conversely, SES is not harmful to neurons and glia, also thanks to a minimal promoter that restricts its expression in mitotically active cells, rarely present in the brain parenchyma. Collectively, SES produces a significant silencing of a large fraction of the SOX2 transcriptional network, achieving high levels of efficacy in repressing aggressive brain tumors.</p>',
'date' => '2022-08-01',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/35921410/',
'doi' => '10.1126/sciadv.abn3986',
'modified' => '2023-09-28 11:26:02',
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'id' => '4836',
'name' => 'Caffeine intake exerts dual genome-wide effects on hippocampal metabolismand learning-dependent transcription.',
'authors' => 'Paiva I. et al.',
'description' => '<p>Caffeine is the most widely consumed psychoactive substance in the world. Strikingly, the molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal omics techniques. Our results revealed that chronic caffeine exerts concerted pleiotropic effects in the hippocampus at the epigenomic, proteomic, and metabolomic levels. Caffeine lowered metabolism-related processes (e.g., at the level of metabolomics and gene expression) in bulk tissue, while it induced neuron-specific epigenetic changes at synaptic transmission/plasticity-related genes and increased experience-driven transcriptional activity. Altogether, these findings suggest that regular caffeine intake improves the signal-to-noise ratio during information encoding, in part through fine-tuning of metabolic genes, while boosting the salience of information processing during learning in neuronal circuits.</p>',
'date' => '2022-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35536645',
'doi' => '10.1172/JCI149371',
'modified' => '2023-08-01 13:52:29',
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'name' => 'ATRX regulates glial identity and the tumor microenvironment inIDH-mutant glioma',
'authors' => 'Babikir, Husam and Wang, Lin and Shamardani, Karin andCatalan, Francisca and Sudhir, Sweta and Aghi, Manish K. andRaleigh, David R. and Phillips, Joanna J. and Diaz, AaronA.',
'description' => '<p>Background Recent single-cell transcriptomic studies report that IDH-mutant gliomas share a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the genetic differences between IDH-mutant glioma subtypes are prognostic, predictive of response to chemotherapy, and correlate with distinct tumor microenvironments. Results To reconcile these findings, we profile 22 human IDH-mutant gliomas using scATAC-seq and scRNA-seq. We determine the cell-type-specific differences in transcription factor expression and associated regulatory grammars between IDH-mutant glioma subtypes. We find that while IDH-mutant gliomas do share a common distribution of cell types, there are significant differences in the expression and targeting of transcription factors that regulate glial identity and cytokine elaboration. We knock out the chromatin remodeler ATRX, which suffers loss-of-function alterations in most IDH-mutant astrocytomas, in an IDH-mutant immunocompetent intracranial murine model. We find that both human ATRX-mutant gliomas and murine ATRX-knockout gliomas are more heavily infiltrated by immunosuppressive monocytic-lineage cells derived from circulation than ATRX-intact gliomas, in an IDH-mutant background. ATRX knockout in murine glioma recapitulates gene expression and open chromatin signatures that are specific to human ATRX-mutant astrocytomas, including drivers of astrocytic lineage and immune-cell chemotaxis. Through single-cell cleavage under targets and tagmentation assays and meta-analysis of public data, we show that ATRX loss leads to a global depletion in CCCTC-binding factor association with DNA, gene dysregulation along associated chromatin loops, and protection from therapy-induced senescence. Conclusions These studies explain how IDH-mutant gliomas from different subtypes maintain distinct phenotypes and tumor microenvironments despite a common lineage hierarchy. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02535-4.</p>',
'date' => '2021-11-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34763709',
'doi' => '10.1186/s13059-021-02535-4',
'modified' => '2022-05-20 09:50:12',
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'name' => 'Autocrine Vitamin D-signaling switches off pro-inflammatory programsof Th1 cells',
'authors' => 'Chauss D.et al.',
'description' => '<p>The molecular mechanisms governing orderly shutdown and retraction of CD4+ T helper (Th)1 responses remain poorly understood. Here, we show that complement triggers contraction of Th1 responses by inducing intrinsic expression of the vitamin D (VitD) receptor (VDR) and the VitD-activating enzyme CYP27B1, permitting T cells to both activate and respond to VitD. VitD then initiated transition from pro-inflammatory IFN-γ + Th1 cells to suppressive IL-10+ cells. This process was primed by dynamic changes in the epigenetic landscape of CD4+ T cells, generating super-enhancers and recruiting several transcription factors, notably c-JUN, STAT3 and BACH2, which together with VDR shaped the transcriptional response to VitD. Accordingly, VitD did not induce IL-10 in cells with dysfunctional BACH2 or STAT3. Bronchoalveolar lavage fluid CD4+ T cells of COVID-19 patients were Th1-skewed and showed de-repression of genes down-regulated by VitD, either from lack of substrate (VitD deficiency) and/or abnormal regulation of this system.</p>',
'date' => '2021-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34764490',
'doi' => '10.1038/s41590-021-01080-3',
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<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
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<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<div class="row extra-spaced">
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
</div>
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<div class="row extra-spaced">
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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'name' => 'pA-Tn5',
'description' => '<p>We are really happy to use the loaded pA-Tn5 for CUT&Tag. Easy to use and reproductible for samples with a starting low number of cells. Besides, Diagenode has a great customer service and technical support which are really responsive.</p>',
'author' => 'Cathy NGUYEN, CNRGH, Evry-Courcouronnes, France.',
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<p><strong><input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/></strong>Tagmentase (Tn5 transposase) - loaded個カートに追加。</p>
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<p> </p>
<p>Diagenode <b>Tagmentase</b><b> – loaded </b>is a <strong>hyperactive Tn5 transposase</strong> preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq or ChIPmentation.</p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x-1ml">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for unloaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-20-ul">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul"> (Tn5 transposase) – </a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul">unloaded</a></p>',
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'info1' => '<p><b>Tagmentase</b><b> (Tn5 transposase) – </b><b>loaded</b> can be used in any application using tagmentation-based library preparation, like for example ChIPmentation, ATAC-seq. Here below we are showing some examples of results.</p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig1.png" width="700" alt="Tn5 transposase Enxzymes" caption="false" /></center>
<p><small><strong>Figure 1. Typical library profile of ATAC-seq library generated with the Tagmentase</strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<div class="row">
<div class="small-8 columns">
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<div class="small-8 columns">
<p><small><strong>Figure 2. Enrichments at TSS of ATAC-seq libraries generated with the Tagmentase</strong><br />ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). Heatmaps around the hg19 TSS were generated using deeptools plotHeatmap functionality.</small></p>
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<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig3.png" alt="Transposase enzymes for ATAC-Seq" caption="false" width="956" height="259" /></center>
<p><small><strong>Figure 3. Sequencing profiles of ATAC-seq libraries generated with the Tagmentase </strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig4.png" width="700" alt="purified Transposase enzymes " caption="false" /></center>
<p><small><strong>Figure 4. Typical library profile of ChIPmentation library generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 1,000,000 K562 cells using the ChIPmentation Kit for Histones (Cat. No. C01011010) in combination with the Diagenode antibody targeting H3K4me3 (Cat. No. C15410003) and with the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig5.png" alt="pA-Tn5 Transposase Enzymes" caption="false" width="956" height="262" /></center>
<p><small><strong>Figure 5. Sequencing profiles of ChIPmentation libraries generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 500.000 to 1,000,000 cells using the <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones </a>(Cat. No. C01011010) in combination with the <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) – loaded </a>(Cat. No. C01070012) on K562 cells. The Diagenode antibodies targeting <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3 </a>(Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-premium-50-mg-18-ml">H3K27ac </a>(Cat. No. C15410196), <a href="https://www.diagenode.com/en/p/h3k36me3-polyclonal-antibody-premium-50-mg">H3K36me3 </a>(Cat. No. C15410192), <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (Cat. No. C15410195) and rabbit <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">IgG </a>(Cat. No. C15410206) have been used.</small></p>
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<div>Protein Molecular weight: 53.3 kDa</div>
<p>Expressed: in Escherichia coli</p>
<p></p>
<p><strong>Product description:</strong> Diagenode Tagmentase – loaded is a hyperactive Tn5 transposase preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments. The Tagmentase is pre-loaded with sequencing adapters compatible with Illumina Nextera platforms, as shown below. The oligos loaded on the Tagmentase are inserted into DNA upon a tagmentation reaction.</p>
<div>Mosaic end_reverse: 5’ [PHO]<span style="text-decoration: underline;">CTGTCTCTTATACACATCT</span> 3’</div>
<div>Mosaic end_Adapter A: 5’ TCGTCGGCAGCGTC<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</div>
<p>Mosaic end_Adapter B: 5’ GTCTCGTGGGCTCGG<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</p>
<p></p>
<div><span style="text-decoration: underline;">Underlined regions</span> correspond to the double-stranded part of the adapter, recognized by the Tagmentase. The final libraries can be amplified using Diagenode Primer indexes for tagmented libraries:</div>
<div>24 SI for tagmented libraries, Cat. No. C01011032</div>
<div>24 UDI fortagmented libraries - Set I, Cat. No. C0101134</div>
<div>24 UDI for tagmented libraries - Set II, Cat. No. C0101136</div>
<p>24 UDI for tagmented libraries - Set III, Cat. No. C0101137</p>
<p></p>
<p><strong>Storage conditions: </strong>Store at -20°C. Guaranteed stable for 6 months from date of receipt when stored properly.</p>
<p><strong>Storage buffer:</strong> Supplied in solution containing 50% v/v glycerol.</p>
<p><strong>Properties & Usage: </strong>Tagmentase is dependent on Mg++ for activity. Avoid chelators, such as EDTA/EGTA, in reaction buffers. The enzyme is active at pH 7.5-8 at 37-55°C. SDS, EDTA/EGTA or heating to 65°C will inactivate the enzyme.</p>
<p><strong>Applications:</strong> Tagmentase (Tn5 transposase) – loaded can be used in a variety of applications to construct library for second-generation sequencing. Please note that an additional optimization might be required for custom protocols including the enzyme dose- and time-response experiments.</p>
<div>For ATAC-seq and ChIPmentation, we recommend using Diagenode validated protocols:</div>
<div>ATAC-seq kit, Cat. No. C01080002</div>
<div>ATAC-seq package for tissue, Cat. No. <span>C01080006</span></div>
<div>ChIPmentation Kit for Histones, Cat. No. C01011009</div>
<div>µChIPmentation Kit for Histones, Cat. No. C01011011</div>
<div>TAG Kit for ChIPmentation, Cat. No. C01011030</div>
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<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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'description' => '<p>pA-Tn5トランスポザーゼは、CUT＆Tagアッセイ専用に開発された高活性Tn5トランスポザーゼとプロテインAの融合タンパク質です。 融合タンパク質にはシーケンスアダプターがあらかじめロードされある、便利なプリロードです。</p>
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<p class="lead">CUT＆Tagアッセイに関する推奨製品はこちら</p>
<ul>
<li>pA/Tn5 Transposase (loaded or unloaded)</li>
<li><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a></li>
<li>Negative CUT&Tag control <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">Rabbit IgG</a></li>
<li>Sequencing indexes <a href="https://www.diagenode.com/en/p/24-si-for-chipmentation">24 Single indexes</a></li>
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'description' => '<p>pA-Tn5トランスポザーゼは、CUT＆Tagアッセイ専用に開発された高活性Tn5トランスポザーゼとプロテインAの融合タンパク質です。 融合タンパク質にはシーケンスアダプターがあらかじめロードされある、便利なプリロードです。</p>
<p>目的のタンパク質のみをターゲットとすることが重要であるため、CUT＆Tagアッセイの成功には非常に特異的な抗体が不可欠です。 厳密な検証基準を満たしている特異性が検証されているDiagenode ChIP-seqグレードの抗体は、CUT＆Tagアッセイでの高いパフォーマンスを保証します。</p>
<p class="lead">CUT＆Tagアッセイに関する推奨製品はこちら</p>
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<li>pA/Tn5 Transposase (loaded or unloaded)</li>
<li><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a></li>
<li>Negative CUT&Tag control <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">Rabbit IgG</a></li>
<li>Sequencing indexes <a href="https://www.diagenode.com/en/p/24-si-for-chipmentation">24 Single indexes</a></li>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="row extra-spaced">
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<p><strong>pA-Tn5 Transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For flexibility, the fusion protein is not pre-loaded with sequencing adapters. Please follow the recommended <a href="https://www.diagenode.com/en/documents/assembly-protocol-patn5-20042020-rms" target="_blank">assembly protocol</a> prior to use in CUT&Tag or similar assays (ACT-seq, CoBATCH, TIP-seq and other).</p>
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<li><span style="font-weight: 400;">Flexible versions: <a href="https://www.diagenode.com/en/products/view/3064">loaded</a> or unloaded</span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag and similar assays (eg. TIP-seq)<br /></span></li>
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<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> <span>- compatible with histome marks and some transcription factors</span></li>
<li>pA/Tn5 Transposase (<a href="https://www.diagenode.com/en/products/view/3064" target="_blank">loaded </a>or unloaded)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase" src="https://www.diagenode.com/img/product/cutandtag/C01070002-fig-a.jpg" width="600" height="265" /></center></div>
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<div class="small-12 medium-12 large-12 columns">B.<br /><center><img alt="pA-Tn5 Transposase unloaded" src="https://www.diagenode.com/img/product/cutandtag/C01070002-fig-b.jpg" /></center></div>
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<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1: Quality control of pA-Tn5 transposase loaded with sequencing adapters</strong></p>
<p>A: The Fragment Analyzer trace showing the representative cleavage pattern of gDNA. The pA-Tn5 fusion protein (Cat. No. C01070002) loaded with sequencing adapters efficiently digests gDNA to a smear. 500 ng of human genomic DNA were incubated for 7 min at 55°C with 1 μl of pATn5 fusion protein loaded with appropriated adaptors in a tagmentation buffer (40mM Tris-HCl pH7.5, 40mM MgCl2 and 12.5% DMF). The reaction was stopped by adding SDS, cleaned-up and resolved on the Fragment Analyzer to assess the cleavage.</p>
<p>B: Representative screenshot at selected locus obtained using Diagenode pA-Tn5 fusion protein (Cat. No. C01070002) lloaded with sequencing adapters and H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) following CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)).</p>
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'description' => '<p><span>The negative Ctrl IgG from rabbit has been extensively validated in chromatin immunoprecipitation assays (ChIP). It contains a spectrum of the IgG subclasses present in serum of healthy animals. This IgG preparation is intended for use as a negative control in ChIP experiments for specific antibodies made in rabbit. The negative Ctrl IgG from rabbit should be used for ChIP in parallel with specific antibody at the same concentration as the specific antibody. </span></p>
<p><span><span style="left: 94.4882px; top: 499.039px; font-size: 15px; font-family: sans-serif; transform: scaleX(1.00223);">The negative Ctrl IgG is intended for use </span><span style="left: 94.4882px; top: 519.039px; font-size: 15px; font-family: sans-serif; transform: scaleX(1.02185);">as a negative control in ChIP, CUT&Tag, MeDIP, IF and other experiments performed with specific antibodies made in rabbit.</span></span></p>',
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410206-chip.jpg" alt="Rabbit IgG Antibody ChIP Grade" /></p>
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<div class="small-8 columns">
<p><small> <strong>Figure 1. ChIP with the Diagenode rabbit IgG negative control antibody</strong><br />ChIP assays were performed using the Diagenode rabbit polyclonal antibody against H3K4me3 (Cat. No. C15410003) and the “iDeal ChIPseq” kit (Cat. No. C01010051) on sheared chromatin from 1 million HeLa cells. Rabbit IgG (cat. No. C15410206) was used as a negative IP control. One μg of antibody per ChIP experiment was used for both antibodies. Quantitative PCR was performed with primers specific for the promoters of the active GAPDH and EIF4A2 genes, and for the inactive MYOD1 gene and the Sat2 satellite repeat. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410206-if.jpg" alt="Rabbit IgG validated in Immunofluorescence" /></p>
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<div class="small-8 columns">
<p><small> <strong>Figure 2. Immunofluorescence with the Diagenode rabbit IgG negative control antibody</strong><br />HeLa cells were stained with the Diagenode rabbit polyclonal antibody against H3K4me3 (Cat. No. C15410003) (top) and with DAPI. Rabbit IgG (Cat. No. C15410206) was used as a negative control (bottom). Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me3 or rabbit IgG negative control antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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'info2' => '<p>The negative control IgG from rabbit has been extensively validated in chromatin immunoprecipitation (ChIP). It contains a spectrum of the IgG subclasses present in serum of healthy rabbits. This IgG preparation is intended for use as a negative control in ChIP, MeDIP, IF and other experiments performed with specific antibodies made in rabbit. The negative control IgG from rabbit should be used in parallel with the specific antibody at the same concentration. It is also included in many of our ChIP and MeDIP kits.</p>',
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'meta_title' => 'Rabbit IgG (C15410206) | Diagenode',
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'meta_description' => 'Rabbit IgG - for use as a negative control in ChIP, MeDIP, CUT&Tag IF and other experiments performed with specific antibodies made in rabbit. ',
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'id' => '3158',
'antibody_id' => null,
'name' => '24 UDI for Tagmented libraries - Set I',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/primer-indexes-for-tagmented-libraries_manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>The <strong>24 UDI for tagmented libraries</strong> includes 24 primer pairs for unique dual-indexing allowing the multiplexing of up to <b>24 samples </b>for sequencing on Illumina platforms. These UDI are designed and validated to be used with <a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">μChIPmentation for Histones</a> (Cat. No. C01011011), <a href="https://www.diagenode.com/en/p/chipmentation-kit-for-histones">ChIPmentation Kit for Histones</a> (Cat. No. C01011009), <a href="https://www.diagenode.com/en/p/tag-kit-for-chipmentation-24">TAG Kit for ChIPmentation</a> (Cat. No. C01011030), <a href="https://www.diagenode.com/en/categories/atac-seq">ATAC-seq Kit</a> (Cat. No. C01080002). The 24 UDI for tagmented libraries are compatible with other <b>tagmentation</b><b>-based library preparation </b>protocols, such as <a href="https://www.diagenode.com/en/categories/cutandtag">CUT&Tag</a> technologies.</p>
<p>3 sets of UDI for tagmented libraries are available:</p>
<p><strong>24 UDI for tagmented libraries - Set I</strong><br /> <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set2">24 UDI for tagmented libraries - Set II</a><br /><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set3" target="_blank">24 UDI for tagmented libraries - Set III</a><br /><br /></p>
<p><span>Each set can be used for library multiplexing up to 24. All sets can be used simultaneously for library multiplexing up to 72.</span></p>
<p>Features:</p>
<ul>
<li>Multiplexing: <b>up to 72 samples </b>(using all 3 sets simultaneously)<b><br /></b></li>
<li>Allow for <b>identification of index hopping</b></li>
<li>Compatibility: <b>tagmentation</b><b>-based library preparation protocols</b></li>
</ul>
<script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script>',
'label1' => 'Characteristics',
'info1' => '<p>The <b>24 UDI (Unique dual indexes) for </b><b>tagmented</b><b> libraries – Set I </b>is compatible with any <b>tagmentation</b><b>-based library preparation </b>protocols, such as <strong>ChIPmentation</strong>, <b>ATAC-seq</b> or <b>CUT&Tag</b> technologies.</p>
<p>The <b>24 UDI for </b><b>tagmented</b><b> libraries </b>provides combinations of barcodes where each barcode is uniquely attributed to one sample. This is a great tool to identify mistakes during index sequencing. A phenomenon, known as index hopping, can lead to misattribution of some reads to the wrong sample. This is particularly frequent with the NovaSeq6000, and thus the use of Unique Dual Indexing (UDI) is highly recommended when using this sequencer.</p>
<p></p>
<center><img src="https://www.diagenode.com/img/product/kits/UDI-for-tagmented-fig1.png" /></center>
<p></p>
<p><small><strong>Figure 1. Sequencing profiles of µChIPmentation libraries generated with 24 UDI for Tagmented libraries</strong> Chromatin preparation and immunoprecipitation have been performed on 10.000 cells using the µChIPmentation Kit for Histones (Cat. No. C01011011) and 24 UDI for Tagmented libraries – Set I (Cat. No. Cat. No. C01011034) using K562 cells. The Diagenode antibodies targeting H3K4me3 (Cat. No. C15410003) and rabbit IgG (Cat. No. C15410206) have been used. </small></p>
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'meta_title' => '24 unique dual indexes for tagmented libraries set 1',
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'modified' => '2024-05-15 10:25:12',
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(int) 3 => array(
'id' => '3220',
'antibody_id' => null,
'name' => 'iDeal CUT&Tag kit for Histones <br /> Compatible with histones and some non-histone proteins',
'description' => '<p><a href="https://www.diagenode.com/files/application_notes/AN-iDealCUTandTag.pdf"><img src="https://www.diagenode.com/img/banners/cutandtag-appnote.png" /></a></p>
<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>CUT&Tag-sequencing</strong> (<strong>C</strong>leavage <strong>U</strong>nder <strong>T</strong>argets and <strong>Tag</strong>mentation) is a new alternative method to ChIP-seq combining antibody-targeted controlled cleavage by a protein A-Tn5 fusion with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.</p>
<p><a href="https://www.diagenode.com/files/products/kits/iDeal-CUTandTag-kit-for-histones-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
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<p>The Diagenode’s <strong>iDeal CUT&Tag kit for Histones</strong> provides an optimized protocol for a rapid chromatin profiling on <strong>histone marks</strong> and some <strong>non-histone proteins</strong>. The protocol is optimized for native cells (<strong>10,000-300,000</strong> cells per reaction) and can be completed within 1.5 days. The kit includes all reagents for cell processing, including CoA beads, pA-Tn5 and the DNA purification module. The antibodies (secondary antibodies, control antibodies) as well as primer indexes for multiplexing must be purchased separately.</p>
<p><strong>For a complete CUT&Tag protocol the following items must be purchased:</strong></p>
<ul>
<li><strong>iDeal CUT&Tag kit for Histones</strong> – including all reagents for CUT&Tag workflow (buffers, pA-Tn5, CoA beads, DNA purification)</li>
<li><strong>Antibody package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a></strong> or <strong><a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></strong> - including the secondary antibody, positive and negative control antibodies and primers</li>
<li><strong><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></strong> – for multiplexing up to 72 samples</li>
</ul>
<h3>iDeal CUT&Tag Kit features:</h3>
<ul>
<li><strong>Rapid</strong> and <strong>easy </strong>chromatin profiling assay for <strong>histones </strong>and<strong> some non-histone proteins</strong></li>
<ul style="margin-bottom: 0;">
<li>No chromatin preparation</li>
<li>Easy sample handling due to ConA magnetic beads</li>
<li>Integrated library prep</li>
</ul>
<li><strong>Low cell number</strong>: 10,000-300,000 cells</li>
<li><strong>Accurate amplification</strong> due to intermediate quantification step</li>
<li><strong>High resolution</strong> and <strong>sensitivity</strong></li>
<li><strong>Lower sequencing depth</strong></li>
</ul>
<p>The quality of antibody used in CUT&Tag is one of the crucial factors for assay success. The antibodies with confirmed high specificity will target only the protein of interest, enabling real results. Check out our selection of <strong><a href="https://www.diagenode.com/en/categories/cut-and-tag-antibodies">antibodies validated in CUT&Tag</a>.</strong></p>
<p>Looking for a standalone pA-Tn5? <a href="https://www.diagenode.com/en/products/view/3064">Read more</a>.</p>
<script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script>',
'label1' => 'Method overview',
'info1' => '<p>The iDeal CUT&Tag protocol involves the binding of cells on a solid phase ConA magnetic beads, allowing magnetic handling of the cells for the major steps of the protocol. Bead-bound cells are permeabilized, incubated with primary antibody against a target of interest and secondary antibody. Then, Diagenode’s protein pA-Tn5 Transposase - loaded is bound to the complex. Protein A guides Tn5 transposase on chromatin to the antibody attached to its target. Tn5 transposase is activated by Mg+2 ions to insert the sequencing adaptors into genomic regions of interest. DNA is then purified and the tagmented genomic regions of interest are amplified by PCR using Diagenode’s Primer Indexes for tagmented libraries.</p>
<p></p>
<p><img alt=" pA-Tn5 Antibody package for CUT & Tag" src="https://www.diagenode.com/img/product/kits/workflow-cutandtag.jpg" /></p>',
'label2' => 'Examples of results - histone marks',
'info2' => '<p>Successful CUT&Tag results showing a low background with high region-specific enrichment are presented below. Chromatin profiling has been performed on 50,000 K562 cells, using the Diagenode’s iDeal CUT&Tag kit for Histones (Cat. No. C01070020), the Antibody Package for CUT&Tag anti rabbit (Cat. No. C01070022), the 24 UDI for Tagmented Libraries (Cat.No. C01011034) and H3K4me3 (Cat. No. C15410003), H3K27me3 (Cat. No. C15410069) or H3H9me3 antibodies (Cat. No., C15410193) as indicated. The libraries were sequenced on Illumina’s NovaSeq6000 in 2x50 bp mode.</p>
<p><br /> <img alt="CUT&Tag-sequencing" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1a.png" /> <img alt="CUT&Tag kit for Histones" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1b.png" /> <img alt="Cleavage Under Targets and Tagmentation" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1c.png" /></p>
<p><strong>Figure 1.</strong> Typical library profiles (Agilent Fragment traces) generated by the iDeal CUT&Tag protocol using 50,000 K562 cells and H3K27me3 (top), H3K4me4 (middle) primary antibodies and IgG control (bottom). Sharp peak at around 40 bp is an excess of <strong>free oligonucleotide used for pA-Tn5 loading</strong>.</p>
<p></p>
<p><br /><br /></p>
<div class="row">
<div class="small-4 columns">
<p><img alt="iDeal CUT&Tag kit for Histones" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig2.png" /></p>
</div>
<div class="small-8 columns">
<p><strong>Figure 2.</strong> Enrichments at TSS of the CUT&Tag libraries. The heatmap shows the enrichment around 3kb upstream and downstream of the TSS for H3K4me3. H3K4me3 as an active chromatin mark is associated with active promoters shows a narrow enrichment pattern.</p>
</div>
</div>
<p><br /><br /></p>
<p><br /> <img alt="iDeal CUT&Tag experiments of K562 cells " src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig3.png" /></p>
<p><strong>Figure 3.</strong> Sequencing profiles of the CUT&Tag libraries. Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using 50,000 of K562 cells and H3K4me3 (blue), H3K27me3 (red) or H3K9me3 (green).</p>
<p><br /><br /></p>
<p><br /> <img alt="CUT&Tag experiments using 10,000 K562 cells" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig4.png" /></p>
<p><strong>Figure 4.</strong> Sequencing profiles of the CUT&Tag libraries. Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using 50,000 (blue) or 10,000 (red)) of K562 cells and H3K27me3 antibody.</p>',
'label3' => 'Examples of results - transcription factors',
'info3' => '<p>Diagenode's<strong><span> iDeal CUT&Tag Kit for Histones</span></strong><span>, </span>developed for an efficient chromatin profiling on histone marks, can be used for profiling of <span>some transcription factors and co-factors using a mild fixation as described in the manual. </span></p>
<p><strong><span>Successful CUT&Tag results using CTCF and Suz12 antibodies and iDeal CUT&Tag Kit for Histones. </span></strong></p>
<p></p>
<p><span>Chromatin profiling of <strong>Suz12</strong> has been performed on 50,000 of fixed Mouse ES-E14TG2a cells (kindly provided by Luciano Di Croce, CRG, Spain) accordingly to the protocol of Diagenode’s iDeal CUT&Tag kit for Histones (Cat. No. C01070020). Antibody Package for CUT&Tag anti rabbit (Cat. No. C01070022) and the 24 UDI for Tagmented Libraries (Cat. No. C01011034) were used. The libraries were sized using Fragment Analyzer (Agilent) (triplicates, Figure 1, top). Relative enrichment has been confirmed by qPCR using know positive (T_Bra) and negative (Actb) loci (Figure 1, bottom). Libraries were sequenced on Illumina’s NovaSeq6000 in 2x50 bp mode.</span></p>
<p></p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig1a.jpg" /><br /> <img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig1b.jpg" /></p>
<p><strong>Figure 1.</strong> Typical library profiles (top) and relative enrichment (bottom) generated by the iDeal CUT&Tag protocol using 50,000 ES-E14TG2a cells and Suz12 Antibody and IgG control (bottom). Sharp peak at around 40 bp is an excess of free oligonucleotide used for pA-Tn5 loading which does not interfere with the sequencing.</p>
<p></p>
<p>Pictures of representative loci were taken on Integrative Genome Viewer (IGV) for CTCF demonstrating the presence of high signal at promoter regions.</p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2a.jpg" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2b.jpg" /> <img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2c.jpg" /></p>
<p></p>
<p></p>
<p>Pictures of representative loci were taken on Integrative Genome Viewer (IGV) for SUZ12 and H3K27me3 triplicate samples, showing an overlap between the signal from both proteins, as part of the Polycomb Repressive Complex.</p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci1.jpg" width="100%" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci2.jpg" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci3.jpg" /></p>
<p><strong>Figure 2. IGV snapshots</strong></p>
<p></p>
<p></p>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig3.jpg" /></p>
</div>
<div class="small-8 columns">
<p><strong>Figure 3. Heatmap around the TSS</strong><br /> Heatmap of the CTCF signal around the transcription start sites (TSS) of each gene present in the murine mm10 reference genome.</p>
</div>
</div>
<p></p>
<p></p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig4.jpg" /></p>
<p><strong>Figure 4. CTCF motif</strong><br /> Presence of specific transcription factor binding motifs in the regions identified as CTCF peaks. The top3 motifs are corresponding to the CTCF binding motif.</p>
<p></p>
<p></p>
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<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig5.jpg" /></p>
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<p><strong>Figure 5. CTCF motif density</strong><br /> Location and density of the CTCF binding motif with respect to the center of the identified CTCF peaks.</p>
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<p> </p>
<p>Diagenode <b>Tagmentase</b><b> – loaded </b>is a <strong>hyperactive Tn5 transposase</strong> preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq or ChIPmentation.</p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x-1ml">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for unloaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-20-ul">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul"> (Tn5 transposase) – </a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul">unloaded</a></p>',
'label1' => 'Examples of results',
'info1' => '<p><b>Tagmentase</b><b> (Tn5 transposase) – </b><b>loaded</b> can be used in any application using tagmentation-based library preparation, like for example ChIPmentation, ATAC-seq. Here below we are showing some examples of results.</p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig1.png" width="700" alt="Tn5 transposase Enxzymes" caption="false" /></center>
<p><small><strong>Figure 1. Typical library profile of ATAC-seq library generated with the Tagmentase</strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
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<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig2.png" width="200" alt="Diagenode Tagmentation " caption="false" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 2. Enrichments at TSS of ATAC-seq libraries generated with the Tagmentase</strong><br />ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). Heatmaps around the hg19 TSS were generated using deeptools plotHeatmap functionality.</small></p>
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<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig3.png" alt="Transposase enzymes for ATAC-Seq" caption="false" width="956" height="259" /></center>
<p><small><strong>Figure 3. Sequencing profiles of ATAC-seq libraries generated with the Tagmentase </strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig4.png" width="700" alt="purified Transposase enzymes " caption="false" /></center>
<p><small><strong>Figure 4. Typical library profile of ChIPmentation library generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 1,000,000 K562 cells using the ChIPmentation Kit for Histones (Cat. No. C01011010) in combination with the Diagenode antibody targeting H3K4me3 (Cat. No. C15410003) and with the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig5.png" alt="pA-Tn5 Transposase Enzymes" caption="false" width="956" height="262" /></center>
<p><small><strong>Figure 5. Sequencing profiles of ChIPmentation libraries generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 500.000 to 1,000,000 cells using the <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones </a>(Cat. No. C01011010) in combination with the <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) – loaded </a>(Cat. No. C01070012) on K562 cells. The Diagenode antibodies targeting <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3 </a>(Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-premium-50-mg-18-ml">H3K27ac </a>(Cat. No. C15410196), <a href="https://www.diagenode.com/en/p/h3k36me3-polyclonal-antibody-premium-50-mg">H3K36me3 </a>(Cat. No. C15410192), <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (Cat. No. C15410195) and rabbit <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">IgG </a>(Cat. No. C15410206) have been used.</small></p>
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'info2' => '<p><strong>Tagmentase (Tn5 transposase) - loaded </strong></p>
<div>Protein Molecular weight: 53.3 kDa</div>
<p>Expressed: in Escherichia coli</p>
<p></p>
<p><strong>Product description:</strong> Diagenode Tagmentase – loaded is a hyperactive Tn5 transposase preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments. The Tagmentase is pre-loaded with sequencing adapters compatible with Illumina Nextera platforms, as shown below. The oligos loaded on the Tagmentase are inserted into DNA upon a tagmentation reaction.</p>
<div>Mosaic end_reverse: 5’ [PHO]<span style="text-decoration: underline;">CTGTCTCTTATACACATCT</span> 3’</div>
<div>Mosaic end_Adapter A: 5’ TCGTCGGCAGCGTC<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</div>
<p>Mosaic end_Adapter B: 5’ GTCTCGTGGGCTCGG<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</p>
<p></p>
<div><span style="text-decoration: underline;">Underlined regions</span> correspond to the double-stranded part of the adapter, recognized by the Tagmentase. The final libraries can be amplified using Diagenode Primer indexes for tagmented libraries:</div>
<div>24 SI for tagmented libraries, Cat. No. C01011032</div>
<div>24 UDI fortagmented libraries - Set I, Cat. No. C0101134</div>
<div>24 UDI for tagmented libraries - Set II, Cat. No. C0101136</div>
<p>24 UDI for tagmented libraries - Set III, Cat. No. C0101137</p>
<p></p>
<p><strong>Storage conditions: </strong>Store at -20°C. Guaranteed stable for 6 months from date of receipt when stored properly.</p>
<p><strong>Storage buffer:</strong> Supplied in solution containing 50% v/v glycerol.</p>
<p><strong>Properties & Usage: </strong>Tagmentase is dependent on Mg++ for activity. Avoid chelators, such as EDTA/EGTA, in reaction buffers. The enzyme is active at pH 7.5-8 at 37-55°C. SDS, EDTA/EGTA or heating to 65°C will inactivate the enzyme.</p>
<p><strong>Applications:</strong> Tagmentase (Tn5 transposase) – loaded can be used in a variety of applications to construct library for second-generation sequencing. Please note that an additional optimization might be required for custom protocols including the enzyme dose- and time-response experiments.</p>
<div>For ATAC-seq and ChIPmentation, we recommend using Diagenode validated protocols:</div>
<div>ATAC-seq kit, Cat. No. C01080002</div>
<div>ATAC-seq package for tissue, Cat. No. <span>C01080006</span></div>
<div>ChIPmentation Kit for Histones, Cat. No. C01011009</div>
<div>µChIPmentation Kit for Histones, Cat. No. C01011011</div>
<div>TAG Kit for ChIPmentation, Cat. No. C01011030</div>
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<p><strong>CUT&Tag</strong>-sequencing (<strong>C</strong>leavage <strong>U</strong>nder <strong>T</strong>argets and <strong>Tag</strong>mentation) is a new alternative method to ChIP-seq combining antibody-targeted controlled cleavage by a protein A-Tn5 fusion with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. At Diagenode we offer a complete solution for CUT&Tag – our iDeal CUT&Tag for Histones (developped for histone marks and some non-histone proteins), but also stand-alone fusion protein – pA-Tn5 Transposase. Moreover, we have validated our <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a> in <a href="https://www.diagenode.com/en/categories/cut-and-tag-antibodies">CUT&Tag</a> proving their high performance in this assay.</p>
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<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#v5" style="color: #13b29c;"><i class="fa fa-caret-right"></i> How does it work?</a>
<div id="v5" class="content">
<p>The iDeal CUT&Tag protocol involves the binding of cells on a solid phase ConA magnetic beads, allowing magnetic handling of the cells for the major steps of the protocol. Bead-bound cells are permeabilized, incubated with primary antibody against a target of interest and secondary antibody. Then, Diagenode’s protein pA-Tn5 Transposase - loaded is bound to the complex. Protein A guides Tn5 transposase on chromatin to the antibody attached to its target. Tn5 transposase is activated by Mg+2 ions to insert the sequencing adaptors into genomic regions of interest. DNA is then purified and the tagmented genomic regions of interest are amplified by PCR using Diagenode’s Primer Indexes for tagmented libraries.</p>
<img src="https://www.diagenode.com/img/product/kits/workflow-cutandtag.jpg" /></div>
<h2>Products for CUT&Tag assay</h2>
<h3 class="diacol">Complete solutions</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24" target="_blank">iDeal CUT&Tag kit for Histones</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24" target="_blank">Antibody package for CUT&Tag (anti-rabbit)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24" target="_blank">Antibody package for CUT&Tag (anti-mouse)</a></li>
</ul>
<h3 class="diacol">Fusion protein</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/products/view/3064" target="_blank">pA/Tn5 Transposase (loaded)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">pA/Tn5 Transposase (unloaded)</a></li>
</ul>
<h3 class="diacol">CUT&Tag grade antibodies</h3>
<ul class="nobullet">
<li>Antibodies <a href="https://www.diagenode.com/en/applications/cut-and-tag">validated in CUT&Tag</a></li>
<li>Check out our list of <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies" target="_blank">ChIP-seq grade antibodies</a></li>
<li>Read more about the performance of Diagenode antibodies in <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">CUT&Tag</a></li>
</ul>
<h3 class="diacol">Positive & Negative CUT&Tag control</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24" target="_blank">Antibody package for CUT&Tag (anti-rabbit)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24" target="_blank">Antibody package for CUT&Tag (anti-mouse)</a></li>
</ul>
<h3 class="diacol">DNA purification</h3>
<p style="padding-left: 30px;"><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2<br /></a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></p>
<h3 class="diacol">Sequencing indexes</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries" target="_blank">Primer indexes for tagmented libraries</a></li>
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'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a fatal congenital lung disorder strongly associated with genomic alterations in the Forkhead box F1 (FOXF1) gene and its regulatory region. However, little is known about how FOXF1 genomic alterations cause ACD/MPV and what molecular mechanisms are affected by these mutations. Therefore, the effect of ACD/MPV patient-specific mutations in the<span> </span><i>FOXF1</i><span> </span>gene on the molecular function of FOXF1 was studied.</p>
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<p>Epitope-tagged FOXF1 constructs containing one of the ACD/MPV-associated mutations were expressed in mammalian cell lines to study the effect of FOXF1 mutations on protein function. EMSA binding assays and luciferase assays were performed to study the effect on target gene binding and activation. Immunoprecipitation followed by SDS‒PAGE and western blotting were used to study protein‒protein interactions. Protein phosphorylation was studied using phos-tag western blotting.</p>
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<p>An overview of the localization of ACD/MPV-associated FOXF1 mutations revealed that the G91-S101 region was frequently mutated. A three-dimensional model of the forkhead DNA-binding domain of FOXF1 showed that the G91-S101 region consists of an α-helix and is predicted to be important for DNA binding. We showed that FOXF1 missense mutations in this region differentially affect the DNA binding of the FOXF1 protein and influence the transcriptional regulation of target genes depending on the location of the mutation. Furthermore, we showed that some of these mutations can affect the FOXF1 protein at the posttranscriptional level, as shown by altered phosphorylation by MST1 and MST2 kinases.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusion</h3>
<p>Missense mutations in the coding region of the<span> </span><i>FOXF1</i><span> </span>gene alter the molecular function of the FOXF1 protein at multiple levels, such as phosphorylation, DNA binding and target gene activation. These results indicate that FOXF1 molecular pathways may be differentially affected in ACD/MPV patients carrying missense mutations in the DNA-binding domain and may explain the phenotypic heterogeneity of ACD/MPV.</p>',
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'authors' => 'Dias Mirandela M. et al.',
'description' => '<p><span>The PIWI-interacting RNA (piRNA) pathway guides the DNA methylation of young, active transposons during germline development in male mice</span><span>. piRNAs tether the PIWI protein MIWI2 (PIWIL4) to the nascent transposon transcript, resulting in DNA methylation through SPOCD1</span><span>. Transposon methylation requires great precision: every copy needs to be methylated but off-target methylation must be avoided. However, the underlying mechanisms that ensure this precision remain unknown. Here, we show that SPOCD1 interacts directly with SPIN1 (SPINDLIN1), a chromatin reader that primarily binds to H3K4me3-K9me3</span><span>. The prevailing assumption is that all the molecular events required for piRNA-directed DNA methylation occur after the engagement of MIWI2. We find that SPIN1 expression precedes that of both SPOCD1 and MIWI2. Furthermore, we demonstrate that young LINE1 copies, but not old ones, are marked by H3K4me3, H3K9me3 and SPIN1 before the initiation of piRNA-directed DNA methylation. We generated a<span> </span></span><i>Spocd1</i><span><span> </span>separation-of-function allele in the mouse that encodes a SPOCD1 variant that no longer interacts with SPIN1. We found that the interaction between SPOCD1 and SPIN1 is essential for spermatogenesis and piRNA-directed DNA methylation of young LINE1 elements. We propose that piRNA-directed LINE1 DNA methylation requires a developmentally timed two-factor authentication process. The first authentication is the recruitment of SPIN1–SPOCD1 to the young LINE1 promoter, and the second is MIWI2 engagement with the nascent transcript. In summary, independent authentication events underpin the precision of piRNA-directed LINE1 DNA methylation.</span></p>',
'date' => '2024-09-18',
'pmid' => 'https://www.nature.com/articles/s41586-024-07963-3',
'doi' => 'https://doi.org/10.1038/s41586-024-07963-3',
'modified' => '2024-09-23 10:02:22',
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'id' => '4827',
'name' => 'Transcription factor EGR2 controls homing and pathogenicity of T17cells in the central nervous system.',
'authors' => 'Gao Y. et al.',
'description' => '<p>CD4 T helper 17 (T17) cells protect barrier tissues but also trigger autoimmunity. The mechanisms behind these opposing processes remain unclear. Here, we found that the transcription factor EGR2 controlled the transcriptional program of pathogenic T17 cells in the central nervous system (CNS) but not that of protective T17 cells at barrier sites. EGR2 was significantly elevated in myelin-reactive CD4 T cells from patients with multiple sclerosis and mice with autoimmune neuroinflammation. The EGR2 transcriptional program was intricately woven within the T17 cell transcriptional regulatory network and showed high interconnectivity with core T17 cell-specific transcription factors. Mechanistically, EGR2 enhanced T17 cell differentiation and myeloid cell recruitment to the CNS by upregulating pathogenesis-associated genes and myelomonocytic chemokines. T cell-specific deletion of Egr2 attenuated neuroinflammation without compromising the host's ability to control infections. Our study shows that EGR2 regulates tissue-specific and disease-specific functions in pathogenic T17 cells in the CNS.</p>',
'date' => '2023-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37443284',
'doi' => '10.1038/s41590-023-01553-7',
'modified' => '2023-08-01 13:35:13',
'created' => '2023-08-01 15:59:38',
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(int) 3 => array(
'id' => '4671',
'name' => 'The Hdc GC box is critical for Hdc gene transcription andhistamine-mediated anaphylaxis.',
'authors' => 'Li Y. et al.',
'description' => '<p>BACKGROUND: Histamine is a critical mediator of anaphylaxis, a neurotransmitter, and a regulator of gastric acid secretion. Histidine decarboxylase is a rate-limiting enzyme for histamine synthesis. However, in vivo regulation of Hdc, the gene that encodes histidine decarboxylase is poorly understood. OBJECTIVE: We sought to investigate how enhancers regulate Hdc gene transcription and histamine synthesis in resting conditions and in a mouse model of anaphylaxis. METHODS: H3K27 acetylation histone modification and chromatin accessibility were used to identify candidate enhancers; The enhancer activity of candidate enhancers was measured in a reporter gene assay; and the function enhancers were validated using CRISPR deletion. RESULTS: Deletion of the GC box, which binds to zinc finger transcription factors, in the proximal Hdc enhancer, reduced Hdc gene transcription and histamine synthesis in the mouse and human mast cell lines. Mast cells, basophils, brain cells, and stomach cells from GC box-deficient mice transcribed the Hdc gene much less than similar cells from wild-type mice and Hdc GC box-deficient mice failed to develop anaphylaxis. CONCLUSION: Our results demonstrate that the HDC GC box within the proximal enhancer in the mouse and human HDC gene is essential for Hdc gene transcription, histamine synthesis, and histamine-mediated anaphylaxis in vitro and in vivo.</p>',
'date' => '2023-02-01',
'pmid' => 'https://doi.org/10.1016%2Fj.jaci.2023.01.031',
'doi' => '10.1016/j.jaci.2023.01.031',
'modified' => '2023-04-11 10:29:30',
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'id' => '4873',
'name' => 'Retrospective analysis of enhancer activity and transcriptome history.',
'authors' => 'Boers R. et al.',
'description' => '<p>Cell state changes in development and disease are controlled by gene regulatory networks, the dynamics of which are difficult to track in real time. In this study, we used an inducible DCM-RNA polymerase subunit b fusion protein which labels active genes and enhancers with a bacterial methylation mark that does not affect gene transcription and is propagated in S-phase. This DCM-RNA polymerase fusion protein enables transcribed genes and active enhancers to be tagged and then examined at later stages of development or differentiation. We apply this DCM-time machine (DCM-TM) technology to study intestinal homeostasis, revealing rapid and coordinated activation of enhancers and nearby genes during enterocyte differentiation. We provide new insights in absorptive-secretory lineage decision-making in intestinal stem cell (ISC) differentiation and show that ISCs retain a unique chromatin landscape required to maintain ISC identity and delineate future expression of differentiation-associated genes. DCM-TM has wide applicability in tracking cell states, providing new insights in the regulatory networks underlying cell state changes.</p>',
'date' => '2023-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36823354',
'doi' => '10.1038/s41587-023-01683-1',
'modified' => '2023-11-10 09:13:54',
'created' => '2023-09-01 14:23:20',
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'id' => '4627',
'name' => 'Simultaneous profiling of histone modifications and DNA methylation viananopore sequencing.',
'authors' => 'Yue X. et al.',
'description' => '<p>The interplay between histone modifications and DNA methylation drives the establishment and maintenance of the cellular epigenomic landscape, but it remains challenging to investigate the complex relationship between these epigenetic marks across the genome. Here we describe a nanopore-sequencing-based-method, nanoHiMe-seq, for interrogating the genome-wide localization of histone modifications and DNA methylation from single DNA molecules. nanoHiMe-seq leverages a nonspecific methyltransferase to exogenously label adenine bases proximal to antibody-targeted modified nucleosomes in situ. The labelled adenines and the endogenous methylated CpG sites are simultaneously detected on individual nanopore reads using a hidden Markov model, which is implemented in the nanoHiMe software package. We demonstrate the utility, robustness and sensitivity of nanoHiMe-seq by jointly profiling DNA methylation and histone modifications at low coverage depths, concurrently determining phased patterns of DNA methylation and histone modifications, and probing the intrinsic connectivity between these epigenetic marks across the genome.</p>',
'date' => '2022-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36566265',
'doi' => '10.1038/s41467-022-35650-2',
'modified' => '2023-03-28 08:59:26',
'created' => '2023-02-21 09:59:46',
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'id' => '4550',
'name' => 'A SOX2-engineered epigenetic silencer factor represses the glioblastomagenetic program and restrains tumor development.',
'authors' => 'Benedetti V. et al.',
'description' => '<p>Current therapies remain unsatisfactory in preventing the recurrence of glioblastoma multiforme (GBM), which leads to poor patient survival. By rational engineering of the transcription factor SOX2, a key promoter of GBM malignancy, together with the Kruppel-associated box and DNA methyltransferase3A/L catalytic domains, we generated a synthetic repressor named SOX2 epigenetic silencer (SES), which induces the transcriptional silencing of its original targets. By doing so, SES kills both glioma cell lines and patient-derived cancer stem cells in vitro and in vivo. SES expression, through local viral delivery in mouse xenografts, induces strong regression of human tumors and survival rescue. Conversely, SES is not harmful to neurons and glia, also thanks to a minimal promoter that restricts its expression in mitotically active cells, rarely present in the brain parenchyma. Collectively, SES produces a significant silencing of a large fraction of the SOX2 transcriptional network, achieving high levels of efficacy in repressing aggressive brain tumors.</p>',
'date' => '2022-08-01',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/35921410/',
'doi' => '10.1126/sciadv.abn3986',
'modified' => '2023-09-28 11:26:02',
'created' => '2022-11-24 08:49:52',
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(int) 7 => array(
'id' => '4836',
'name' => 'Caffeine intake exerts dual genome-wide effects on hippocampal metabolismand learning-dependent transcription.',
'authors' => 'Paiva I. et al.',
'description' => '<p>Caffeine is the most widely consumed psychoactive substance in the world. Strikingly, the molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal omics techniques. Our results revealed that chronic caffeine exerts concerted pleiotropic effects in the hippocampus at the epigenomic, proteomic, and metabolomic levels. Caffeine lowered metabolism-related processes (e.g., at the level of metabolomics and gene expression) in bulk tissue, while it induced neuron-specific epigenetic changes at synaptic transmission/plasticity-related genes and increased experience-driven transcriptional activity. Altogether, these findings suggest that regular caffeine intake improves the signal-to-noise ratio during information encoding, in part through fine-tuning of metabolic genes, while boosting the salience of information processing during learning in neuronal circuits.</p>',
'date' => '2022-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35536645',
'doi' => '10.1172/JCI149371',
'modified' => '2023-08-01 13:52:29',
'created' => '2023-08-01 15:59:38',
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(int) 8 => array(
'id' => '4263',
'name' => 'ATRX regulates glial identity and the tumor microenvironment inIDH-mutant glioma',
'authors' => 'Babikir, Husam and Wang, Lin and Shamardani, Karin andCatalan, Francisca and Sudhir, Sweta and Aghi, Manish K. andRaleigh, David R. and Phillips, Joanna J. and Diaz, AaronA.',
'description' => '<p>Background Recent single-cell transcriptomic studies report that IDH-mutant gliomas share a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the genetic differences between IDH-mutant glioma subtypes are prognostic, predictive of response to chemotherapy, and correlate with distinct tumor microenvironments. Results To reconcile these findings, we profile 22 human IDH-mutant gliomas using scATAC-seq and scRNA-seq. We determine the cell-type-specific differences in transcription factor expression and associated regulatory grammars between IDH-mutant glioma subtypes. We find that while IDH-mutant gliomas do share a common distribution of cell types, there are significant differences in the expression and targeting of transcription factors that regulate glial identity and cytokine elaboration. We knock out the chromatin remodeler ATRX, which suffers loss-of-function alterations in most IDH-mutant astrocytomas, in an IDH-mutant immunocompetent intracranial murine model. We find that both human ATRX-mutant gliomas and murine ATRX-knockout gliomas are more heavily infiltrated by immunosuppressive monocytic-lineage cells derived from circulation than ATRX-intact gliomas, in an IDH-mutant background. ATRX knockout in murine glioma recapitulates gene expression and open chromatin signatures that are specific to human ATRX-mutant astrocytomas, including drivers of astrocytic lineage and immune-cell chemotaxis. Through single-cell cleavage under targets and tagmentation assays and meta-analysis of public data, we show that ATRX loss leads to a global depletion in CCCTC-binding factor association with DNA, gene dysregulation along associated chromatin loops, and protection from therapy-induced senescence. Conclusions These studies explain how IDH-mutant gliomas from different subtypes maintain distinct phenotypes and tumor microenvironments despite a common lineage hierarchy. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02535-4.</p>',
'date' => '2021-11-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34763709',
'doi' => '10.1186/s13059-021-02535-4',
'modified' => '2022-05-20 09:50:12',
'created' => '2022-05-19 10:41:50',
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'id' => '4233',
'name' => 'Autocrine Vitamin D-signaling switches off pro-inflammatory programsof Th1 cells',
'authors' => 'Chauss D.et al.',
'description' => '<p>The molecular mechanisms governing orderly shutdown and retraction of CD4+ T helper (Th)1 responses remain poorly understood. Here, we show that complement triggers contraction of Th1 responses by inducing intrinsic expression of the vitamin D (VitD) receptor (VDR) and the VitD-activating enzyme CYP27B1, permitting T cells to both activate and respond to VitD. VitD then initiated transition from pro-inflammatory IFN-γ + Th1 cells to suppressive IL-10+ cells. This process was primed by dynamic changes in the epigenetic landscape of CD4+ T cells, generating super-enhancers and recruiting several transcription factors, notably c-JUN, STAT3 and BACH2, which together with VDR shaped the transcriptional response to VitD. Accordingly, VitD did not induce IL-10 in cells with dysfunctional BACH2 or STAT3. Bronchoalveolar lavage fluid CD4+ T cells of COVID-19 patients were Th1-skewed and showed de-repression of genes down-regulated by VitD, either from lack of substrate (VitD deficiency) and/or abnormal regulation of this system.</p>',
'date' => '2021-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34764490',
'doi' => '10.1038/s41590-021-01080-3',
'modified' => '2022-05-19 16:57:27',
'created' => '2022-05-19 10:41:50',
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<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
</div>
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<div class="row extra-spaced">
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<p><strong><input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/></strong>iDeal CUT&Tag kit for Histones <br /> Compatible with histones and some non-histone proteins個カートに追加。</p>
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<p><strong><input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/></strong>Tagmentase (Tn5 transposase) - loaded個カートに追加。</p>
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<p> </p>
<p>Diagenode <b>Tagmentase</b><b> – loaded </b>is a <strong>hyperactive Tn5 transposase</strong> preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq or ChIPmentation.</p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x-1ml">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for unloaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-20-ul">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul"> (Tn5 transposase) – </a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul">unloaded</a></p>',
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<p><small><strong>Figure 1. Typical library profile of ATAC-seq library generated with the Tagmentase</strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
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<p><small><strong>Figure 2. Enrichments at TSS of ATAC-seq libraries generated with the Tagmentase</strong><br />ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). Heatmaps around the hg19 TSS were generated using deeptools plotHeatmap functionality.</small></p>
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<p><small><strong>Figure 3. Sequencing profiles of ATAC-seq libraries generated with the Tagmentase </strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig4.png" width="700" alt="purified Transposase enzymes " caption="false" /></center>
<p><small><strong>Figure 4. Typical library profile of ChIPmentation library generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 1,000,000 K562 cells using the ChIPmentation Kit for Histones (Cat. No. C01011010) in combination with the Diagenode antibody targeting H3K4me3 (Cat. No. C15410003) and with the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig5.png" alt="pA-Tn5 Transposase Enzymes" caption="false" width="956" height="262" /></center>
<p><small><strong>Figure 5. Sequencing profiles of ChIPmentation libraries generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 500.000 to 1,000,000 cells using the <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones </a>(Cat. No. C01011010) in combination with the <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) – loaded </a>(Cat. No. C01070012) on K562 cells. The Diagenode antibodies targeting <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3 </a>(Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-premium-50-mg-18-ml">H3K27ac </a>(Cat. No. C15410196), <a href="https://www.diagenode.com/en/p/h3k36me3-polyclonal-antibody-premium-50-mg">H3K36me3 </a>(Cat. No. C15410192), <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (Cat. No. C15410195) and rabbit <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">IgG </a>(Cat. No. C15410206) have been used.</small></p>
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<div>Protein Molecular weight: 53.3 kDa</div>
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<p></p>
<p><strong>Product description:</strong> Diagenode Tagmentase – loaded is a hyperactive Tn5 transposase preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments. The Tagmentase is pre-loaded with sequencing adapters compatible with Illumina Nextera platforms, as shown below. The oligos loaded on the Tagmentase are inserted into DNA upon a tagmentation reaction.</p>
<div>Mosaic end_reverse: 5’ [PHO]<span style="text-decoration: underline;">CTGTCTCTTATACACATCT</span> 3’</div>
<div>Mosaic end_Adapter A: 5’ TCGTCGGCAGCGTC<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</div>
<p>Mosaic end_Adapter B: 5’ GTCTCGTGGGCTCGG<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</p>
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<div><span style="text-decoration: underline;">Underlined regions</span> correspond to the double-stranded part of the adapter, recognized by the Tagmentase. The final libraries can be amplified using Diagenode Primer indexes for tagmented libraries:</div>
<div>24 SI for tagmented libraries, Cat. No. C01011032</div>
<div>24 UDI fortagmented libraries - Set I, Cat. No. C0101134</div>
<div>24 UDI for tagmented libraries - Set II, Cat. No. C0101136</div>
<p>24 UDI for tagmented libraries - Set III, Cat. No. C0101137</p>
<p></p>
<p><strong>Storage conditions: </strong>Store at -20°C. Guaranteed stable for 6 months from date of receipt when stored properly.</p>
<p><strong>Storage buffer:</strong> Supplied in solution containing 50% v/v glycerol.</p>
<p><strong>Properties & Usage: </strong>Tagmentase is dependent on Mg++ for activity. Avoid chelators, such as EDTA/EGTA, in reaction buffers. The enzyme is active at pH 7.5-8 at 37-55°C. SDS, EDTA/EGTA or heating to 65°C will inactivate the enzyme.</p>
<p><strong>Applications:</strong> Tagmentase (Tn5 transposase) – loaded can be used in a variety of applications to construct library for second-generation sequencing. Please note that an additional optimization might be required for custom protocols including the enzyme dose- and time-response experiments.</p>
<div>For ATAC-seq and ChIPmentation, we recommend using Diagenode validated protocols:</div>
<div>ATAC-seq kit, Cat. No. C01080002</div>
<div>ATAC-seq package for tissue, Cat. No. <span>C01080006</span></div>
<div>ChIPmentation Kit for Histones, Cat. No. C01011009</div>
<div>µChIPmentation Kit for Histones, Cat. No. C01011011</div>
<div>TAG Kit for ChIPmentation, Cat. No. C01011030</div>
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<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
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<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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'description' => '<p>pA-Tn5トランスポザーゼは、CUT＆Tagアッセイ専用に開発された高活性Tn5トランスポザーゼとプロテインAの融合タンパク質です。 融合タンパク質にはシーケンスアダプターがあらかじめロードされある、便利なプリロードです。</p>
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<p class="lead">CUT＆Tagアッセイに関する推奨製品はこちら</p>
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<li><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a></li>
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<li><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a></li>
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<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="row extra-spaced">
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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'description' => '<p><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24"> <img alt="pA-Tn5 Transposase unloaded" src="https://www.diagenode.com/img/banners/banner-cutruncuttag-small.png" /></a></p>
<p><strong>pA-Tn5 Transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For flexibility, the fusion protein is not pre-loaded with sequencing adapters. Please follow the recommended <a href="https://www.diagenode.com/en/documents/assembly-protocol-patn5-20042020-rms" target="_blank">assembly protocol</a> prior to use in CUT&Tag or similar assays (ACT-seq, CoBATCH, TIP-seq and other).</p>
<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: <a href="https://www.diagenode.com/en/products/view/3064">loaded</a> or unloaded</span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag and similar assays (eg. TIP-seq)<br /></span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> <span>- compatible with histome marks and some transcription factors</span></li>
<li>pA/Tn5 Transposase (<a href="https://www.diagenode.com/en/products/view/3064" target="_blank">loaded </a>or unloaded)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
</ul>',
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase" src="https://www.diagenode.com/img/product/cutandtag/C01070002-fig-a.jpg" width="600" height="265" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">B.<br /><center><img alt="pA-Tn5 Transposase unloaded" src="https://www.diagenode.com/img/product/cutandtag/C01070002-fig-b.jpg" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1: Quality control of pA-Tn5 transposase loaded with sequencing adapters</strong></p>
<p>A: The Fragment Analyzer trace showing the representative cleavage pattern of gDNA. The pA-Tn5 fusion protein (Cat. No. C01070002) loaded with sequencing adapters efficiently digests gDNA to a smear. 500 ng of human genomic DNA were incubated for 7 min at 55°C with 1 μl of pATn5 fusion protein loaded with appropriated adaptors in a tagmentation buffer (40mM Tris-HCl pH7.5, 40mM MgCl2 and 12.5% DMF). The reaction was stopped by adding SDS, cleaned-up and resolved on the Fragment Analyzer to assess the cleavage.</p>
<p>B: Representative screenshot at selected locus obtained using Diagenode pA-Tn5 fusion protein (Cat. No. C01070002) lloaded with sequencing adapters and H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) following CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)).</p>
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<p><small> <strong>Figure 1. ChIP with the Diagenode rabbit IgG negative control antibody</strong><br />ChIP assays were performed using the Diagenode rabbit polyclonal antibody against H3K4me3 (Cat. No. C15410003) and the “iDeal ChIPseq” kit (Cat. No. C01010051) on sheared chromatin from 1 million HeLa cells. Rabbit IgG (cat. No. C15410206) was used as a negative IP control. One μg of antibody per ChIP experiment was used for both antibodies. Quantitative PCR was performed with primers specific for the promoters of the active GAPDH and EIF4A2 genes, and for the inactive MYOD1 gene and the Sat2 satellite repeat. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410206-if.jpg" alt="Rabbit IgG validated in Immunofluorescence" /></p>
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<div class="small-8 columns">
<p><small> <strong>Figure 2. Immunofluorescence with the Diagenode rabbit IgG negative control antibody</strong><br />HeLa cells were stained with the Diagenode rabbit polyclonal antibody against H3K4me3 (Cat. No. C15410003) (top) and with DAPI. Rabbit IgG (Cat. No. C15410206) was used as a negative control (bottom). Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me3 or rabbit IgG negative control antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/primer-indexes-for-tagmented-libraries_manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>The <strong>24 UDI for tagmented libraries</strong> includes 24 primer pairs for unique dual-indexing allowing the multiplexing of up to <b>24 samples </b>for sequencing on Illumina platforms. These UDI are designed and validated to be used with <a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">μChIPmentation for Histones</a> (Cat. No. C01011011), <a href="https://www.diagenode.com/en/p/chipmentation-kit-for-histones">ChIPmentation Kit for Histones</a> (Cat. No. C01011009), <a href="https://www.diagenode.com/en/p/tag-kit-for-chipmentation-24">TAG Kit for ChIPmentation</a> (Cat. No. C01011030), <a href="https://www.diagenode.com/en/categories/atac-seq">ATAC-seq Kit</a> (Cat. No. C01080002). The 24 UDI for tagmented libraries are compatible with other <b>tagmentation</b><b>-based library preparation </b>protocols, such as <a href="https://www.diagenode.com/en/categories/cutandtag">CUT&Tag</a> technologies.</p>
<p>3 sets of UDI for tagmented libraries are available:</p>
<p><strong>24 UDI for tagmented libraries - Set I</strong><br /> <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set2">24 UDI for tagmented libraries - Set II</a><br /><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set3" target="_blank">24 UDI for tagmented libraries - Set III</a><br /><br /></p>
<p><span>Each set can be used for library multiplexing up to 24. All sets can be used simultaneously for library multiplexing up to 72.</span></p>
<p>Features:</p>
<ul>
<li>Multiplexing: <b>up to 72 samples </b>(using all 3 sets simultaneously)<b><br /></b></li>
<li>Allow for <b>identification of index hopping</b></li>
<li>Compatibility: <b>tagmentation</b><b>-based library preparation protocols</b></li>
</ul>
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'info1' => '<p>The <b>24 UDI (Unique dual indexes) for </b><b>tagmented</b><b> libraries – Set I </b>is compatible with any <b>tagmentation</b><b>-based library preparation </b>protocols, such as <strong>ChIPmentation</strong>, <b>ATAC-seq</b> or <b>CUT&Tag</b> technologies.</p>
<p>The <b>24 UDI for </b><b>tagmented</b><b> libraries </b>provides combinations of barcodes where each barcode is uniquely attributed to one sample. This is a great tool to identify mistakes during index sequencing. A phenomenon, known as index hopping, can lead to misattribution of some reads to the wrong sample. This is particularly frequent with the NovaSeq6000, and thus the use of Unique Dual Indexing (UDI) is highly recommended when using this sequencer.</p>
<p></p>
<center><img src="https://www.diagenode.com/img/product/kits/UDI-for-tagmented-fig1.png" /></center>
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<p><small><strong>Figure 1. Sequencing profiles of µChIPmentation libraries generated with 24 UDI for Tagmented libraries</strong> Chromatin preparation and immunoprecipitation have been performed on 10.000 cells using the µChIPmentation Kit for Histones (Cat. No. C01011011) and 24 UDI for Tagmented libraries – Set I (Cat. No. Cat. No. C01011034) using K562 cells. The Diagenode antibodies targeting H3K4me3 (Cat. No. C15410003) and rabbit IgG (Cat. No. C15410206) have been used. </small></p>
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'name' => 'iDeal CUT&Tag kit for Histones <br /> Compatible with histones and some non-histone proteins',
'description' => '<p><a href="https://www.diagenode.com/files/application_notes/AN-iDealCUTandTag.pdf"><img src="https://www.diagenode.com/img/banners/cutandtag-appnote.png" /></a></p>
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<p><strong>CUT&Tag-sequencing</strong> (<strong>C</strong>leavage <strong>U</strong>nder <strong>T</strong>argets and <strong>Tag</strong>mentation) is a new alternative method to ChIP-seq combining antibody-targeted controlled cleavage by a protein A-Tn5 fusion with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.</p>
<p><a href="https://www.diagenode.com/files/products/kits/iDeal-CUTandTag-kit-for-histones-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
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<p>The Diagenode’s <strong>iDeal CUT&Tag kit for Histones</strong> provides an optimized protocol for a rapid chromatin profiling on <strong>histone marks</strong> and some <strong>non-histone proteins</strong>. The protocol is optimized for native cells (<strong>10,000-300,000</strong> cells per reaction) and can be completed within 1.5 days. The kit includes all reagents for cell processing, including CoA beads, pA-Tn5 and the DNA purification module. The antibodies (secondary antibodies, control antibodies) as well as primer indexes for multiplexing must be purchased separately.</p>
<p><strong>For a complete CUT&Tag protocol the following items must be purchased:</strong></p>
<ul>
<li><strong>iDeal CUT&Tag kit for Histones</strong> – including all reagents for CUT&Tag workflow (buffers, pA-Tn5, CoA beads, DNA purification)</li>
<li><strong>Antibody package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a></strong> or <strong><a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></strong> - including the secondary antibody, positive and negative control antibodies and primers</li>
<li><strong><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></strong> – for multiplexing up to 72 samples</li>
</ul>
<h3>iDeal CUT&Tag Kit features:</h3>
<ul>
<li><strong>Rapid</strong> and <strong>easy </strong>chromatin profiling assay for <strong>histones </strong>and<strong> some non-histone proteins</strong></li>
<ul style="margin-bottom: 0;">
<li>No chromatin preparation</li>
<li>Easy sample handling due to ConA magnetic beads</li>
<li>Integrated library prep</li>
</ul>
<li><strong>Low cell number</strong>: 10,000-300,000 cells</li>
<li><strong>Accurate amplification</strong> due to intermediate quantification step</li>
<li><strong>High resolution</strong> and <strong>sensitivity</strong></li>
<li><strong>Lower sequencing depth</strong></li>
</ul>
<p>The quality of antibody used in CUT&Tag is one of the crucial factors for assay success. The antibodies with confirmed high specificity will target only the protein of interest, enabling real results. Check out our selection of <strong><a href="https://www.diagenode.com/en/categories/cut-and-tag-antibodies">antibodies validated in CUT&Tag</a>.</strong></p>
<p>Looking for a standalone pA-Tn5? <a href="https://www.diagenode.com/en/products/view/3064">Read more</a>.</p>
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'info1' => '<p>The iDeal CUT&Tag protocol involves the binding of cells on a solid phase ConA magnetic beads, allowing magnetic handling of the cells for the major steps of the protocol. Bead-bound cells are permeabilized, incubated with primary antibody against a target of interest and secondary antibody. Then, Diagenode’s protein pA-Tn5 Transposase - loaded is bound to the complex. Protein A guides Tn5 transposase on chromatin to the antibody attached to its target. Tn5 transposase is activated by Mg+2 ions to insert the sequencing adaptors into genomic regions of interest. DNA is then purified and the tagmented genomic regions of interest are amplified by PCR using Diagenode’s Primer Indexes for tagmented libraries.</p>
<p></p>
<p><img alt=" pA-Tn5 Antibody package for CUT & Tag" src="https://www.diagenode.com/img/product/kits/workflow-cutandtag.jpg" /></p>',
'label2' => 'Examples of results - histone marks',
'info2' => '<p>Successful CUT&Tag results showing a low background with high region-specific enrichment are presented below. Chromatin profiling has been performed on 50,000 K562 cells, using the Diagenode’s iDeal CUT&Tag kit for Histones (Cat. No. C01070020), the Antibody Package for CUT&Tag anti rabbit (Cat. No. C01070022), the 24 UDI for Tagmented Libraries (Cat.No. C01011034) and H3K4me3 (Cat. No. C15410003), H3K27me3 (Cat. No. C15410069) or H3H9me3 antibodies (Cat. No., C15410193) as indicated. The libraries were sequenced on Illumina’s NovaSeq6000 in 2x50 bp mode.</p>
<p><br /> <img alt="CUT&Tag-sequencing" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1a.png" /> <img alt="CUT&Tag kit for Histones" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1b.png" /> <img alt="Cleavage Under Targets and Tagmentation" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1c.png" /></p>
<p><strong>Figure 1.</strong> Typical library profiles (Agilent Fragment traces) generated by the iDeal CUT&Tag protocol using 50,000 K562 cells and H3K27me3 (top), H3K4me4 (middle) primary antibodies and IgG control (bottom). Sharp peak at around 40 bp is an excess of <strong>free oligonucleotide used for pA-Tn5 loading</strong>.</p>
<p></p>
<p><br /><br /></p>
<div class="row">
<div class="small-4 columns">
<p><img alt="iDeal CUT&Tag kit for Histones" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig2.png" /></p>
</div>
<div class="small-8 columns">
<p><strong>Figure 2.</strong> Enrichments at TSS of the CUT&Tag libraries. The heatmap shows the enrichment around 3kb upstream and downstream of the TSS for H3K4me3. H3K4me3 as an active chromatin mark is associated with active promoters shows a narrow enrichment pattern.</p>
</div>
</div>
<p><br /><br /></p>
<p><br /> <img alt="iDeal CUT&Tag experiments of K562 cells " src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig3.png" /></p>
<p><strong>Figure 3.</strong> Sequencing profiles of the CUT&Tag libraries. Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using 50,000 of K562 cells and H3K4me3 (blue), H3K27me3 (red) or H3K9me3 (green).</p>
<p><br /><br /></p>
<p><br /> <img alt="CUT&Tag experiments using 10,000 K562 cells" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig4.png" /></p>
<p><strong>Figure 4.</strong> Sequencing profiles of the CUT&Tag libraries. Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using 50,000 (blue) or 10,000 (red)) of K562 cells and H3K27me3 antibody.</p>',
'label3' => 'Examples of results - transcription factors',
'info3' => '<p>Diagenode's<strong><span> iDeal CUT&Tag Kit for Histones</span></strong><span>, </span>developed for an efficient chromatin profiling on histone marks, can be used for profiling of <span>some transcription factors and co-factors using a mild fixation as described in the manual. </span></p>
<p><strong><span>Successful CUT&Tag results using CTCF and Suz12 antibodies and iDeal CUT&Tag Kit for Histones. </span></strong></p>
<p></p>
<p><span>Chromatin profiling of <strong>Suz12</strong> has been performed on 50,000 of fixed Mouse ES-E14TG2a cells (kindly provided by Luciano Di Croce, CRG, Spain) accordingly to the protocol of Diagenode’s iDeal CUT&Tag kit for Histones (Cat. No. C01070020). Antibody Package for CUT&Tag anti rabbit (Cat. No. C01070022) and the 24 UDI for Tagmented Libraries (Cat. No. C01011034) were used. The libraries were sized using Fragment Analyzer (Agilent) (triplicates, Figure 1, top). Relative enrichment has been confirmed by qPCR using know positive (T_Bra) and negative (Actb) loci (Figure 1, bottom). Libraries were sequenced on Illumina’s NovaSeq6000 in 2x50 bp mode.</span></p>
<p></p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig1a.jpg" /><br /> <img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig1b.jpg" /></p>
<p><strong>Figure 1.</strong> Typical library profiles (top) and relative enrichment (bottom) generated by the iDeal CUT&Tag protocol using 50,000 ES-E14TG2a cells and Suz12 Antibody and IgG control (bottom). Sharp peak at around 40 bp is an excess of free oligonucleotide used for pA-Tn5 loading which does not interfere with the sequencing.</p>
<p></p>
<p>Pictures of representative loci were taken on Integrative Genome Viewer (IGV) for CTCF demonstrating the presence of high signal at promoter regions.</p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2a.jpg" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2b.jpg" /> <img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2c.jpg" /></p>
<p></p>
<p></p>
<p>Pictures of representative loci were taken on Integrative Genome Viewer (IGV) for SUZ12 and H3K27me3 triplicate samples, showing an overlap between the signal from both proteins, as part of the Polycomb Repressive Complex.</p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci1.jpg" width="100%" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci2.jpg" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci3.jpg" /></p>
<p><strong>Figure 2. IGV snapshots</strong></p>
<p></p>
<p></p>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig3.jpg" /></p>
</div>
<div class="small-8 columns">
<p><strong>Figure 3. Heatmap around the TSS</strong><br /> Heatmap of the CTCF signal around the transcription start sites (TSS) of each gene present in the murine mm10 reference genome.</p>
</div>
</div>
<p></p>
<p></p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig4.jpg" /></p>
<p><strong>Figure 4. CTCF motif</strong><br /> Presence of specific transcription factor binding motifs in the regions identified as CTCF peaks. The top3 motifs are corresponding to the CTCF binding motif.</p>
<p></p>
<p></p>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig5.jpg" /></p>
</div>
<div class="small-6 columns">
<p><strong>Figure 5. CTCF motif density</strong><br /> Location and density of the CTCF binding motif with respect to the center of the identified CTCF peaks.</p>
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<p> </p>
<p>Diagenode <b>Tagmentase</b><b> – loaded </b>is a <strong>hyperactive Tn5 transposase</strong> preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq or ChIPmentation.</p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x-1ml">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for unloaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-20-ul">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul"> (Tn5 transposase) – </a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul">unloaded</a></p>',
'label1' => 'Examples of results',
'info1' => '<p><b>Tagmentase</b><b> (Tn5 transposase) – </b><b>loaded</b> can be used in any application using tagmentation-based library preparation, like for example ChIPmentation, ATAC-seq. Here below we are showing some examples of results.</p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig1.png" width="700" alt="Tn5 transposase Enxzymes" caption="false" /></center>
<p><small><strong>Figure 1. Typical library profile of ATAC-seq library generated with the Tagmentase</strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<div class="row">
<div class="small-8 columns">
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<div class="small-8 columns">
<p><small><strong>Figure 2. Enrichments at TSS of ATAC-seq libraries generated with the Tagmentase</strong><br />ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). Heatmaps around the hg19 TSS were generated using deeptools plotHeatmap functionality.</small></p>
</div>
</div>
</div>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig3.png" alt="Transposase enzymes for ATAC-Seq" caption="false" width="956" height="259" /></center>
<p><small><strong>Figure 3. Sequencing profiles of ATAC-seq libraries generated with the Tagmentase </strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig4.png" width="700" alt="purified Transposase enzymes " caption="false" /></center>
<p><small><strong>Figure 4. Typical library profile of ChIPmentation library generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 1,000,000 K562 cells using the ChIPmentation Kit for Histones (Cat. No. C01011010) in combination with the Diagenode antibody targeting H3K4me3 (Cat. No. C15410003) and with the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig5.png" alt="pA-Tn5 Transposase Enzymes" caption="false" width="956" height="262" /></center>
<p><small><strong>Figure 5. Sequencing profiles of ChIPmentation libraries generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 500.000 to 1,000,000 cells using the <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones </a>(Cat. No. C01011010) in combination with the <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) – loaded </a>(Cat. No. C01070012) on K562 cells. The Diagenode antibodies targeting <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3 </a>(Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-premium-50-mg-18-ml">H3K27ac </a>(Cat. No. C15410196), <a href="https://www.diagenode.com/en/p/h3k36me3-polyclonal-antibody-premium-50-mg">H3K36me3 </a>(Cat. No. C15410192), <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (Cat. No. C15410195) and rabbit <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">IgG </a>(Cat. No. C15410206) have been used.</small></p>
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<div>Protein Molecular weight: 53.3 kDa</div>
<p>Expressed: in Escherichia coli</p>
<p></p>
<p><strong>Product description:</strong> Diagenode Tagmentase – loaded is a hyperactive Tn5 transposase preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments. The Tagmentase is pre-loaded with sequencing adapters compatible with Illumina Nextera platforms, as shown below. The oligos loaded on the Tagmentase are inserted into DNA upon a tagmentation reaction.</p>
<div>Mosaic end_reverse: 5’ [PHO]<span style="text-decoration: underline;">CTGTCTCTTATACACATCT</span> 3’</div>
<div>Mosaic end_Adapter A: 5’ TCGTCGGCAGCGTC<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</div>
<p>Mosaic end_Adapter B: 5’ GTCTCGTGGGCTCGG<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</p>
<p></p>
<div><span style="text-decoration: underline;">Underlined regions</span> correspond to the double-stranded part of the adapter, recognized by the Tagmentase. The final libraries can be amplified using Diagenode Primer indexes for tagmented libraries:</div>
<div>24 SI for tagmented libraries, Cat. No. C01011032</div>
<div>24 UDI fortagmented libraries - Set I, Cat. No. C0101134</div>
<div>24 UDI for tagmented libraries - Set II, Cat. No. C0101136</div>
<p>24 UDI for tagmented libraries - Set III, Cat. No. C0101137</p>
<p></p>
<p><strong>Storage conditions: </strong>Store at -20°C. Guaranteed stable for 6 months from date of receipt when stored properly.</p>
<p><strong>Storage buffer:</strong> Supplied in solution containing 50% v/v glycerol.</p>
<p><strong>Properties & Usage: </strong>Tagmentase is dependent on Mg++ for activity. Avoid chelators, such as EDTA/EGTA, in reaction buffers. The enzyme is active at pH 7.5-8 at 37-55°C. SDS, EDTA/EGTA or heating to 65°C will inactivate the enzyme.</p>
<p><strong>Applications:</strong> Tagmentase (Tn5 transposase) – loaded can be used in a variety of applications to construct library for second-generation sequencing. Please note that an additional optimization might be required for custom protocols including the enzyme dose- and time-response experiments.</p>
<div>For ATAC-seq and ChIPmentation, we recommend using Diagenode validated protocols:</div>
<div>ATAC-seq kit, Cat. No. C01080002</div>
<div>ATAC-seq package for tissue, Cat. No. <span>C01080006</span></div>
<div>ChIPmentation Kit for Histones, Cat. No. C01011009</div>
<div>µChIPmentation Kit for Histones, Cat. No. C01011011</div>
<div>TAG Kit for ChIPmentation, Cat. No. C01011030</div>
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<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>CUT&Tag</strong>-sequencing (<strong>C</strong>leavage <strong>U</strong>nder <strong>T</strong>argets and <strong>Tag</strong>mentation) is a new alternative method to ChIP-seq combining antibody-targeted controlled cleavage by a protein A-Tn5 fusion with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. At Diagenode we offer a complete solution for CUT&Tag – our iDeal CUT&Tag for Histones (developped for histone marks and some non-histone proteins), but also stand-alone fusion protein – pA-Tn5 Transposase. Moreover, we have validated our <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a> in <a href="https://www.diagenode.com/en/categories/cut-and-tag-antibodies">CUT&Tag</a> proving their high performance in this assay.</p>
<br /> <a href="https://www.diagenode.com/files/application_notes/AN-iDealCUTandTag.pdf"><img src="https://www.diagenode.com/img/banners/cutandtag-appnote.png" /></a><br /><br /></div>
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<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#v5" style="color: #13b29c;"><i class="fa fa-caret-right"></i> How does it work?</a>
<div id="v5" class="content">
<p>The iDeal CUT&Tag protocol involves the binding of cells on a solid phase ConA magnetic beads, allowing magnetic handling of the cells for the major steps of the protocol. Bead-bound cells are permeabilized, incubated with primary antibody against a target of interest and secondary antibody. Then, Diagenode’s protein pA-Tn5 Transposase - loaded is bound to the complex. Protein A guides Tn5 transposase on chromatin to the antibody attached to its target. Tn5 transposase is activated by Mg+2 ions to insert the sequencing adaptors into genomic regions of interest. DNA is then purified and the tagmented genomic regions of interest are amplified by PCR using Diagenode’s Primer Indexes for tagmented libraries.</p>
<img src="https://www.diagenode.com/img/product/kits/workflow-cutandtag.jpg" /></div>
<h2>Products for CUT&Tag assay</h2>
<h3 class="diacol">Complete solutions</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24" target="_blank">iDeal CUT&Tag kit for Histones</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24" target="_blank">Antibody package for CUT&Tag (anti-rabbit)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24" target="_blank">Antibody package for CUT&Tag (anti-mouse)</a></li>
</ul>
<h3 class="diacol">Fusion protein</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/products/view/3064" target="_blank">pA/Tn5 Transposase (loaded)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">pA/Tn5 Transposase (unloaded)</a></li>
</ul>
<h3 class="diacol">CUT&Tag grade antibodies</h3>
<ul class="nobullet">
<li>Antibodies <a href="https://www.diagenode.com/en/applications/cut-and-tag">validated in CUT&Tag</a></li>
<li>Check out our list of <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies" target="_blank">ChIP-seq grade antibodies</a></li>
<li>Read more about the performance of Diagenode antibodies in <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">CUT&Tag</a></li>
</ul>
<h3 class="diacol">Positive & Negative CUT&Tag control</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24" target="_blank">Antibody package for CUT&Tag (anti-rabbit)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24" target="_blank">Antibody package for CUT&Tag (anti-mouse)</a></li>
</ul>
<h3 class="diacol">DNA purification</h3>
<p style="padding-left: 30px;"><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2<br /></a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></p>
<h3 class="diacol">Sequencing indexes</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries" target="_blank">Primer indexes for tagmented libraries</a></li>
</ul>
</li>
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'name' => 'The molecular consequences of FOXF1 missense mutations associated with alveolar capillary dysplasia with misalignment of pulmonary veins',
'authors' => 'G. G. Edel et al.',
'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a fatal congenital lung disorder strongly associated with genomic alterations in the Forkhead box F1 (FOXF1) gene and its regulatory region. However, little is known about how FOXF1 genomic alterations cause ACD/MPV and what molecular mechanisms are affected by these mutations. Therefore, the effect of ACD/MPV patient-specific mutations in the<span> </span><i>FOXF1</i><span> </span>gene on the molecular function of FOXF1 was studied.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Methods</h3>
<p>Epitope-tagged FOXF1 constructs containing one of the ACD/MPV-associated mutations were expressed in mammalian cell lines to study the effect of FOXF1 mutations on protein function. EMSA binding assays and luciferase assays were performed to study the effect on target gene binding and activation. Immunoprecipitation followed by SDS‒PAGE and western blotting were used to study protein‒protein interactions. Protein phosphorylation was studied using phos-tag western blotting.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>An overview of the localization of ACD/MPV-associated FOXF1 mutations revealed that the G91-S101 region was frequently mutated. A three-dimensional model of the forkhead DNA-binding domain of FOXF1 showed that the G91-S101 region consists of an α-helix and is predicted to be important for DNA binding. We showed that FOXF1 missense mutations in this region differentially affect the DNA binding of the FOXF1 protein and influence the transcriptional regulation of target genes depending on the location of the mutation. Furthermore, we showed that some of these mutations can affect the FOXF1 protein at the posttranscriptional level, as shown by altered phosphorylation by MST1 and MST2 kinases.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusion</h3>
<p>Missense mutations in the coding region of the<span> </span><i>FOXF1</i><span> </span>gene alter the molecular function of the FOXF1 protein at multiple levels, such as phosphorylation, DNA binding and target gene activation. These results indicate that FOXF1 molecular pathways may be differentially affected in ACD/MPV patients carrying missense mutations in the DNA-binding domain and may explain the phenotypic heterogeneity of ACD/MPV.</p>',
'date' => '2024-11-04',
'pmid' => 'https://link.springer.com/article/10.1186/s12929-024-01088-5',
'doi' => 'https://doi.org/10.1186/s12929-024-01088-5',
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'name' => 'Two-factor authentication underpins the precision of the piRNA pathway',
'authors' => 'Dias Mirandela M. et al.',
'description' => '<p><span>The PIWI-interacting RNA (piRNA) pathway guides the DNA methylation of young, active transposons during germline development in male mice</span><span>. piRNAs tether the PIWI protein MIWI2 (PIWIL4) to the nascent transposon transcript, resulting in DNA methylation through SPOCD1</span><span>. Transposon methylation requires great precision: every copy needs to be methylated but off-target methylation must be avoided. However, the underlying mechanisms that ensure this precision remain unknown. Here, we show that SPOCD1 interacts directly with SPIN1 (SPINDLIN1), a chromatin reader that primarily binds to H3K4me3-K9me3</span><span>. The prevailing assumption is that all the molecular events required for piRNA-directed DNA methylation occur after the engagement of MIWI2. We find that SPIN1 expression precedes that of both SPOCD1 and MIWI2. Furthermore, we demonstrate that young LINE1 copies, but not old ones, are marked by H3K4me3, H3K9me3 and SPIN1 before the initiation of piRNA-directed DNA methylation. We generated a<span> </span></span><i>Spocd1</i><span><span> </span>separation-of-function allele in the mouse that encodes a SPOCD1 variant that no longer interacts with SPIN1. We found that the interaction between SPOCD1 and SPIN1 is essential for spermatogenesis and piRNA-directed DNA methylation of young LINE1 elements. We propose that piRNA-directed LINE1 DNA methylation requires a developmentally timed two-factor authentication process. The first authentication is the recruitment of SPIN1–SPOCD1 to the young LINE1 promoter, and the second is MIWI2 engagement with the nascent transcript. In summary, independent authentication events underpin the precision of piRNA-directed LINE1 DNA methylation.</span></p>',
'date' => '2024-09-18',
'pmid' => 'https://www.nature.com/articles/s41586-024-07963-3',
'doi' => 'https://doi.org/10.1038/s41586-024-07963-3',
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'name' => 'Transcription factor EGR2 controls homing and pathogenicity of T17cells in the central nervous system.',
'authors' => 'Gao Y. et al.',
'description' => '<p>CD4 T helper 17 (T17) cells protect barrier tissues but also trigger autoimmunity. The mechanisms behind these opposing processes remain unclear. Here, we found that the transcription factor EGR2 controlled the transcriptional program of pathogenic T17 cells in the central nervous system (CNS) but not that of protective T17 cells at barrier sites. EGR2 was significantly elevated in myelin-reactive CD4 T cells from patients with multiple sclerosis and mice with autoimmune neuroinflammation. The EGR2 transcriptional program was intricately woven within the T17 cell transcriptional regulatory network and showed high interconnectivity with core T17 cell-specific transcription factors. Mechanistically, EGR2 enhanced T17 cell differentiation and myeloid cell recruitment to the CNS by upregulating pathogenesis-associated genes and myelomonocytic chemokines. T cell-specific deletion of Egr2 attenuated neuroinflammation without compromising the host's ability to control infections. Our study shows that EGR2 regulates tissue-specific and disease-specific functions in pathogenic T17 cells in the CNS.</p>',
'date' => '2023-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37443284',
'doi' => '10.1038/s41590-023-01553-7',
'modified' => '2023-08-01 13:35:13',
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'name' => 'The Hdc GC box is critical for Hdc gene transcription andhistamine-mediated anaphylaxis.',
'authors' => 'Li Y. et al.',
'description' => '<p>BACKGROUND: Histamine is a critical mediator of anaphylaxis, a neurotransmitter, and a regulator of gastric acid secretion. Histidine decarboxylase is a rate-limiting enzyme for histamine synthesis. However, in vivo regulation of Hdc, the gene that encodes histidine decarboxylase is poorly understood. OBJECTIVE: We sought to investigate how enhancers regulate Hdc gene transcription and histamine synthesis in resting conditions and in a mouse model of anaphylaxis. METHODS: H3K27 acetylation histone modification and chromatin accessibility were used to identify candidate enhancers; The enhancer activity of candidate enhancers was measured in a reporter gene assay; and the function enhancers were validated using CRISPR deletion. RESULTS: Deletion of the GC box, which binds to zinc finger transcription factors, in the proximal Hdc enhancer, reduced Hdc gene transcription and histamine synthesis in the mouse and human mast cell lines. Mast cells, basophils, brain cells, and stomach cells from GC box-deficient mice transcribed the Hdc gene much less than similar cells from wild-type mice and Hdc GC box-deficient mice failed to develop anaphylaxis. CONCLUSION: Our results demonstrate that the HDC GC box within the proximal enhancer in the mouse and human HDC gene is essential for Hdc gene transcription, histamine synthesis, and histamine-mediated anaphylaxis in vitro and in vivo.</p>',
'date' => '2023-02-01',
'pmid' => 'https://doi.org/10.1016%2Fj.jaci.2023.01.031',
'doi' => '10.1016/j.jaci.2023.01.031',
'modified' => '2023-04-11 10:29:30',
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'description' => '<p>Cell state changes in development and disease are controlled by gene regulatory networks, the dynamics of which are difficult to track in real time. In this study, we used an inducible DCM-RNA polymerase subunit b fusion protein which labels active genes and enhancers with a bacterial methylation mark that does not affect gene transcription and is propagated in S-phase. This DCM-RNA polymerase fusion protein enables transcribed genes and active enhancers to be tagged and then examined at later stages of development or differentiation. We apply this DCM-time machine (DCM-TM) technology to study intestinal homeostasis, revealing rapid and coordinated activation of enhancers and nearby genes during enterocyte differentiation. We provide new insights in absorptive-secretory lineage decision-making in intestinal stem cell (ISC) differentiation and show that ISCs retain a unique chromatin landscape required to maintain ISC identity and delineate future expression of differentiation-associated genes. DCM-TM has wide applicability in tracking cell states, providing new insights in the regulatory networks underlying cell state changes.</p>',
'date' => '2023-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36823354',
'doi' => '10.1038/s41587-023-01683-1',
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'name' => 'Simultaneous profiling of histone modifications and DNA methylation viananopore sequencing.',
'authors' => 'Yue X. et al.',
'description' => '<p>The interplay between histone modifications and DNA methylation drives the establishment and maintenance of the cellular epigenomic landscape, but it remains challenging to investigate the complex relationship between these epigenetic marks across the genome. Here we describe a nanopore-sequencing-based-method, nanoHiMe-seq, for interrogating the genome-wide localization of histone modifications and DNA methylation from single DNA molecules. nanoHiMe-seq leverages a nonspecific methyltransferase to exogenously label adenine bases proximal to antibody-targeted modified nucleosomes in situ. The labelled adenines and the endogenous methylated CpG sites are simultaneously detected on individual nanopore reads using a hidden Markov model, which is implemented in the nanoHiMe software package. We demonstrate the utility, robustness and sensitivity of nanoHiMe-seq by jointly profiling DNA methylation and histone modifications at low coverage depths, concurrently determining phased patterns of DNA methylation and histone modifications, and probing the intrinsic connectivity between these epigenetic marks across the genome.</p>',
'date' => '2022-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36566265',
'doi' => '10.1038/s41467-022-35650-2',
'modified' => '2023-03-28 08:59:26',
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'name' => 'A SOX2-engineered epigenetic silencer factor represses the glioblastomagenetic program and restrains tumor development.',
'authors' => 'Benedetti V. et al.',
'description' => '<p>Current therapies remain unsatisfactory in preventing the recurrence of glioblastoma multiforme (GBM), which leads to poor patient survival. By rational engineering of the transcription factor SOX2, a key promoter of GBM malignancy, together with the Kruppel-associated box and DNA methyltransferase3A/L catalytic domains, we generated a synthetic repressor named SOX2 epigenetic silencer (SES), which induces the transcriptional silencing of its original targets. By doing so, SES kills both glioma cell lines and patient-derived cancer stem cells in vitro and in vivo. SES expression, through local viral delivery in mouse xenografts, induces strong regression of human tumors and survival rescue. Conversely, SES is not harmful to neurons and glia, also thanks to a minimal promoter that restricts its expression in mitotically active cells, rarely present in the brain parenchyma. Collectively, SES produces a significant silencing of a large fraction of the SOX2 transcriptional network, achieving high levels of efficacy in repressing aggressive brain tumors.</p>',
'date' => '2022-08-01',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/35921410/',
'doi' => '10.1126/sciadv.abn3986',
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'name' => 'Caffeine intake exerts dual genome-wide effects on hippocampal metabolismand learning-dependent transcription.',
'authors' => 'Paiva I. et al.',
'description' => '<p>Caffeine is the most widely consumed psychoactive substance in the world. Strikingly, the molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal omics techniques. Our results revealed that chronic caffeine exerts concerted pleiotropic effects in the hippocampus at the epigenomic, proteomic, and metabolomic levels. Caffeine lowered metabolism-related processes (e.g., at the level of metabolomics and gene expression) in bulk tissue, while it induced neuron-specific epigenetic changes at synaptic transmission/plasticity-related genes and increased experience-driven transcriptional activity. Altogether, these findings suggest that regular caffeine intake improves the signal-to-noise ratio during information encoding, in part through fine-tuning of metabolic genes, while boosting the salience of information processing during learning in neuronal circuits.</p>',
'date' => '2022-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35536645',
'doi' => '10.1172/JCI149371',
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'name' => 'ATRX regulates glial identity and the tumor microenvironment inIDH-mutant glioma',
'authors' => 'Babikir, Husam and Wang, Lin and Shamardani, Karin andCatalan, Francisca and Sudhir, Sweta and Aghi, Manish K. andRaleigh, David R. and Phillips, Joanna J. and Diaz, AaronA.',
'description' => '<p>Background Recent single-cell transcriptomic studies report that IDH-mutant gliomas share a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the genetic differences between IDH-mutant glioma subtypes are prognostic, predictive of response to chemotherapy, and correlate with distinct tumor microenvironments. Results To reconcile these findings, we profile 22 human IDH-mutant gliomas using scATAC-seq and scRNA-seq. We determine the cell-type-specific differences in transcription factor expression and associated regulatory grammars between IDH-mutant glioma subtypes. We find that while IDH-mutant gliomas do share a common distribution of cell types, there are significant differences in the expression and targeting of transcription factors that regulate glial identity and cytokine elaboration. We knock out the chromatin remodeler ATRX, which suffers loss-of-function alterations in most IDH-mutant astrocytomas, in an IDH-mutant immunocompetent intracranial murine model. We find that both human ATRX-mutant gliomas and murine ATRX-knockout gliomas are more heavily infiltrated by immunosuppressive monocytic-lineage cells derived from circulation than ATRX-intact gliomas, in an IDH-mutant background. ATRX knockout in murine glioma recapitulates gene expression and open chromatin signatures that are specific to human ATRX-mutant astrocytomas, including drivers of astrocytic lineage and immune-cell chemotaxis. Through single-cell cleavage under targets and tagmentation assays and meta-analysis of public data, we show that ATRX loss leads to a global depletion in CCCTC-binding factor association with DNA, gene dysregulation along associated chromatin loops, and protection from therapy-induced senescence. Conclusions These studies explain how IDH-mutant gliomas from different subtypes maintain distinct phenotypes and tumor microenvironments despite a common lineage hierarchy. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02535-4.</p>',
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<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
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<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
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<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
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<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<p> </p>
<p>Diagenode <b>Tagmentase</b><b> – loaded </b>is a <strong>hyperactive Tn5 transposase</strong> preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq or ChIPmentation.</p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x-1ml">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for unloaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-20-ul">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul"> (Tn5 transposase) – </a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul">unloaded</a></p>',
'label1' => 'Examples of results',
'info1' => '<p><b>Tagmentase</b><b> (Tn5 transposase) – </b><b>loaded</b> can be used in any application using tagmentation-based library preparation, like for example ChIPmentation, ATAC-seq. Here below we are showing some examples of results.</p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig1.png" width="700" alt="Tn5 transposase Enxzymes" caption="false" /></center>
<p><small><strong>Figure 1. Typical library profile of ATAC-seq library generated with the Tagmentase</strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<div class="row">
<div class="small-8 columns">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig2.png" width="200" alt="Diagenode Tagmentation " caption="false" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 2. Enrichments at TSS of ATAC-seq libraries generated with the Tagmentase</strong><br />ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). Heatmaps around the hg19 TSS were generated using deeptools plotHeatmap functionality.</small></p>
</div>
</div>
</div>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig3.png" alt="Transposase enzymes for ATAC-Seq" caption="false" width="956" height="259" /></center>
<p><small><strong>Figure 3. Sequencing profiles of ATAC-seq libraries generated with the Tagmentase </strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig4.png" width="700" alt="purified Transposase enzymes " caption="false" /></center>
<p><small><strong>Figure 4. Typical library profile of ChIPmentation library generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 1,000,000 K562 cells using the ChIPmentation Kit for Histones (Cat. No. C01011010) in combination with the Diagenode antibody targeting H3K4me3 (Cat. No. C15410003) and with the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig5.png" alt="pA-Tn5 Transposase Enzymes" caption="false" width="956" height="262" /></center>
<p><small><strong>Figure 5. Sequencing profiles of ChIPmentation libraries generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 500.000 to 1,000,000 cells using the <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones </a>(Cat. No. C01011010) in combination with the <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) – loaded </a>(Cat. No. C01070012) on K562 cells. The Diagenode antibodies targeting <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3 </a>(Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-premium-50-mg-18-ml">H3K27ac </a>(Cat. No. C15410196), <a href="https://www.diagenode.com/en/p/h3k36me3-polyclonal-antibody-premium-50-mg">H3K36me3 </a>(Cat. No. C15410192), <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (Cat. No. C15410195) and rabbit <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">IgG </a>(Cat. No. C15410206) have been used.</small></p>
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<div>Protein Molecular weight: 53.3 kDa</div>
<p>Expressed: in Escherichia coli</p>
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<p><strong>Product description:</strong> Diagenode Tagmentase – loaded is a hyperactive Tn5 transposase preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments. The Tagmentase is pre-loaded with sequencing adapters compatible with Illumina Nextera platforms, as shown below. The oligos loaded on the Tagmentase are inserted into DNA upon a tagmentation reaction.</p>
<div>Mosaic end_reverse: 5’ [PHO]<span style="text-decoration: underline;">CTGTCTCTTATACACATCT</span> 3’</div>
<div>Mosaic end_Adapter A: 5’ TCGTCGGCAGCGTC<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</div>
<p>Mosaic end_Adapter B: 5’ GTCTCGTGGGCTCGG<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</p>
<p></p>
<div><span style="text-decoration: underline;">Underlined regions</span> correspond to the double-stranded part of the adapter, recognized by the Tagmentase. The final libraries can be amplified using Diagenode Primer indexes for tagmented libraries:</div>
<div>24 SI for tagmented libraries, Cat. No. C01011032</div>
<div>24 UDI fortagmented libraries - Set I, Cat. No. C0101134</div>
<div>24 UDI for tagmented libraries - Set II, Cat. No. C0101136</div>
<p>24 UDI for tagmented libraries - Set III, Cat. No. C0101137</p>
<p></p>
<p><strong>Storage conditions: </strong>Store at -20°C. Guaranteed stable for 6 months from date of receipt when stored properly.</p>
<p><strong>Storage buffer:</strong> Supplied in solution containing 50% v/v glycerol.</p>
<p><strong>Properties & Usage: </strong>Tagmentase is dependent on Mg++ for activity. Avoid chelators, such as EDTA/EGTA, in reaction buffers. The enzyme is active at pH 7.5-8 at 37-55°C. SDS, EDTA/EGTA or heating to 65°C will inactivate the enzyme.</p>
<p><strong>Applications:</strong> Tagmentase (Tn5 transposase) – loaded can be used in a variety of applications to construct library for second-generation sequencing. Please note that an additional optimization might be required for custom protocols including the enzyme dose- and time-response experiments.</p>
<div>For ATAC-seq and ChIPmentation, we recommend using Diagenode validated protocols:</div>
<div>ATAC-seq kit, Cat. No. C01080002</div>
<div>ATAC-seq package for tissue, Cat. No. <span>C01080006</span></div>
<div>ChIPmentation Kit for Histones, Cat. No. C01011009</div>
<div>µChIPmentation Kit for Histones, Cat. No. C01011011</div>
<div>TAG Kit for ChIPmentation, Cat. No. C01011030</div>
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<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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'description' => '<p>The molecular mechanisms governing orderly shutdown and retraction of CD4+ T helper (Th)1 responses remain poorly understood. Here, we show that complement triggers contraction of Th1 responses by inducing intrinsic expression of the vitamin D (VitD) receptor (VDR) and the VitD-activating enzyme CYP27B1, permitting T cells to both activate and respond to VitD. VitD then initiated transition from pro-inflammatory IFN-γ + Th1 cells to suppressive IL-10+ cells. This process was primed by dynamic changes in the epigenetic landscape of CD4+ T cells, generating super-enhancers and recruiting several transcription factors, notably c-JUN, STAT3 and BACH2, which together with VDR shaped the transcriptional response to VitD. Accordingly, VitD did not induce IL-10 in cells with dysfunctional BACH2 or STAT3. Bronchoalveolar lavage fluid CD4+ T cells of COVID-19 patients were Th1-skewed and showed de-repression of genes down-regulated by VitD, either from lack of substrate (VitD deficiency) and/or abnormal regulation of this system.</p>',
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'name' => 'pA-Tn5 Transposase - loaded',
'description' => '<p>pA-Tn5トランスポザーゼは、CUT＆Tagアッセイ専用に開発された高活性Tn5トランスポザーゼとプロテインAの融合タンパク質です。 融合タンパク質にはシーケンスアダプターがあらかじめロードされある、便利なプリロードです。</p>
<p>目的のタンパク質のみをターゲットとすることが重要であるため、CUT＆Tagアッセイの成功には非常に特異的な抗体が不可欠です。 厳密な検証基準を満たしている特異性が検証されているDiagenode ChIP-seqグレードの抗体は、CUT＆Tagアッセイでの高いパフォーマンスを保証します。</p>
<p class="lead">CUT＆Tagアッセイに関する推奨製品はこちら</p>
<ul>
<li>pA/Tn5 Transposase (loaded or unloaded)</li>
<li><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a></li>
<li>Negative CUT&Tag control <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">Rabbit IgG</a></li>
<li>Sequencing indexes <a href="https://www.diagenode.com/en/p/24-si-for-chipmentation">24 Single indexes</a></li>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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'description' => '<p>pA-Tn5トランスポザーゼは、CUT＆Tagアッセイ専用に開発された高活性Tn5トランスポザーゼとプロテインAの融合タンパク質です。 融合タンパク質にはシーケンスアダプターがあらかじめロードされある、便利なプリロードです。</p>
<p>目的のタンパク質のみをターゲットとすることが重要であるため、CUT＆Tagアッセイの成功には非常に特異的な抗体が不可欠です。 厳密な検証基準を満たしている特異性が検証されているDiagenode ChIP-seqグレードの抗体は、CUT＆Tagアッセイでの高いパフォーマンスを保証します。</p>
<p class="lead">CUT＆Tagアッセイに関する推奨製品はこちら</p>
<ul>
<li>pA/Tn5 Transposase (loaded or unloaded)</li>
<li><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a></li>
<li>Negative CUT&Tag control <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">Rabbit IgG</a></li>
<li>Sequencing indexes <a href="https://www.diagenode.com/en/p/24-si-for-chipmentation">24 Single indexes</a></li>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
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<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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'slug' => 'pa-tn5-transposase-loaded',
'meta_title' => 'pA-Tn5 Transposase (loaded) developed for the CUT&Tag assay | Diagenode.com',
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'meta_description' => 'Diagenode pA-Tn5 Transposase (loaded) is a fusion protein of hyperactive Tn5 transposase and protein A developed for the CUT&Tag assay. For convenience, the fusion protein is pre-loaded with sequencing adapters.',
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'name' => 'pA-Tn5 Transposase - unloaded',
'description' => '<p><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24"> <img alt="pA-Tn5 Transposase unloaded" src="https://www.diagenode.com/img/banners/banner-cutruncuttag-small.png" /></a></p>
<p><strong>pA-Tn5 Transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For flexibility, the fusion protein is not pre-loaded with sequencing adapters. Please follow the recommended <a href="https://www.diagenode.com/en/documents/assembly-protocol-patn5-20042020-rms" target="_blank">assembly protocol</a> prior to use in CUT&Tag or similar assays (ACT-seq, CoBATCH, TIP-seq and other).</p>
<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: <a href="https://www.diagenode.com/en/products/view/3064">loaded</a> or unloaded</span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag and similar assays (eg. TIP-seq)<br /></span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> <span>- compatible with histome marks and some transcription factors</span></li>
<li>pA/Tn5 Transposase (<a href="https://www.diagenode.com/en/products/view/3064" target="_blank">loaded </a>or unloaded)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase" src="https://www.diagenode.com/img/product/cutandtag/C01070002-fig-a.jpg" width="600" height="265" /></center></div>
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<div class="small-12 medium-12 large-12 columns">B.<br /><center><img alt="pA-Tn5 Transposase unloaded" src="https://www.diagenode.com/img/product/cutandtag/C01070002-fig-b.jpg" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1: Quality control of pA-Tn5 transposase loaded with sequencing adapters</strong></p>
<p>A: The Fragment Analyzer trace showing the representative cleavage pattern of gDNA. The pA-Tn5 fusion protein (Cat. No. C01070002) loaded with sequencing adapters efficiently digests gDNA to a smear. 500 ng of human genomic DNA were incubated for 7 min at 55°C with 1 μl of pATn5 fusion protein loaded with appropriated adaptors in a tagmentation buffer (40mM Tris-HCl pH7.5, 40mM MgCl2 and 12.5% DMF). The reaction was stopped by adding SDS, cleaned-up and resolved on the Fragment Analyzer to assess the cleavage.</p>
<p>B: Representative screenshot at selected locus obtained using Diagenode pA-Tn5 fusion protein (Cat. No. C01070002) lloaded with sequencing adapters and H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) following CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)).</p>
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<p><span><span style="left: 94.4882px; top: 499.039px; font-size: 15px; font-family: sans-serif; transform: scaleX(1.00223);">The negative Ctrl IgG is intended for use </span><span style="left: 94.4882px; top: 519.039px; font-size: 15px; font-family: sans-serif; transform: scaleX(1.02185);">as a negative control in ChIP, CUT&Tag, MeDIP, IF and other experiments performed with specific antibodies made in rabbit.</span></span></p>',
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<p><small> <strong>Figure 1. ChIP with the Diagenode rabbit IgG negative control antibody</strong><br />ChIP assays were performed using the Diagenode rabbit polyclonal antibody against H3K4me3 (Cat. No. C15410003) and the “iDeal ChIPseq” kit (Cat. No. C01010051) on sheared chromatin from 1 million HeLa cells. Rabbit IgG (cat. No. C15410206) was used as a negative IP control. One μg of antibody per ChIP experiment was used for both antibodies. Quantitative PCR was performed with primers specific for the promoters of the active GAPDH and EIF4A2 genes, and for the inactive MYOD1 gene and the Sat2 satellite repeat. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
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<p><small> <strong>Figure 2. Immunofluorescence with the Diagenode rabbit IgG negative control antibody</strong><br />HeLa cells were stained with the Diagenode rabbit polyclonal antibody against H3K4me3 (Cat. No. C15410003) (top) and with DAPI. Rabbit IgG (Cat. No. C15410206) was used as a negative control (bottom). Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me3 or rabbit IgG negative control antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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<p>The <strong>24 UDI for tagmented libraries</strong> includes 24 primer pairs for unique dual-indexing allowing the multiplexing of up to <b>24 samples </b>for sequencing on Illumina platforms. These UDI are designed and validated to be used with <a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">μChIPmentation for Histones</a> (Cat. No. C01011011), <a href="https://www.diagenode.com/en/p/chipmentation-kit-for-histones">ChIPmentation Kit for Histones</a> (Cat. No. C01011009), <a href="https://www.diagenode.com/en/p/tag-kit-for-chipmentation-24">TAG Kit for ChIPmentation</a> (Cat. No. C01011030), <a href="https://www.diagenode.com/en/categories/atac-seq">ATAC-seq Kit</a> (Cat. No. C01080002). The 24 UDI for tagmented libraries are compatible with other <b>tagmentation</b><b>-based library preparation </b>protocols, such as <a href="https://www.diagenode.com/en/categories/cutandtag">CUT&Tag</a> technologies.</p>
<p>3 sets of UDI for tagmented libraries are available:</p>
<p><strong>24 UDI for tagmented libraries - Set I</strong><br /> <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set2">24 UDI for tagmented libraries - Set II</a><br /><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set3" target="_blank">24 UDI for tagmented libraries - Set III</a><br /><br /></p>
<p><span>Each set can be used for library multiplexing up to 24. All sets can be used simultaneously for library multiplexing up to 72.</span></p>
<p>Features:</p>
<ul>
<li>Multiplexing: <b>up to 72 samples </b>(using all 3 sets simultaneously)<b><br /></b></li>
<li>Allow for <b>identification of index hopping</b></li>
<li>Compatibility: <b>tagmentation</b><b>-based library preparation protocols</b></li>
</ul>
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<p>The <b>24 UDI for </b><b>tagmented</b><b> libraries </b>provides combinations of barcodes where each barcode is uniquely attributed to one sample. This is a great tool to identify mistakes during index sequencing. A phenomenon, known as index hopping, can lead to misattribution of some reads to the wrong sample. This is particularly frequent with the NovaSeq6000, and thus the use of Unique Dual Indexing (UDI) is highly recommended when using this sequencer.</p>
<p></p>
<center><img src="https://www.diagenode.com/img/product/kits/UDI-for-tagmented-fig1.png" /></center>
<p></p>
<p><small><strong>Figure 1. Sequencing profiles of µChIPmentation libraries generated with 24 UDI for Tagmented libraries</strong> Chromatin preparation and immunoprecipitation have been performed on 10.000 cells using the µChIPmentation Kit for Histones (Cat. No. C01011011) and 24 UDI for Tagmented libraries – Set I (Cat. No. Cat. No. C01011034) using K562 cells. The Diagenode antibodies targeting H3K4me3 (Cat. No. C15410003) and rabbit IgG (Cat. No. C15410206) have been used. </small></p>
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'name' => 'iDeal CUT&Tag kit for Histones <br /> Compatible with histones and some non-histone proteins',
'description' => '<p><a href="https://www.diagenode.com/files/application_notes/AN-iDealCUTandTag.pdf"><img src="https://www.diagenode.com/img/banners/cutandtag-appnote.png" /></a></p>
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<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>CUT&Tag-sequencing</strong> (<strong>C</strong>leavage <strong>U</strong>nder <strong>T</strong>argets and <strong>Tag</strong>mentation) is a new alternative method to ChIP-seq combining antibody-targeted controlled cleavage by a protein A-Tn5 fusion with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.</p>
<p><a href="https://www.diagenode.com/files/products/kits/iDeal-CUTandTag-kit-for-histones-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
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<p>The Diagenode’s <strong>iDeal CUT&Tag kit for Histones</strong> provides an optimized protocol for a rapid chromatin profiling on <strong>histone marks</strong> and some <strong>non-histone proteins</strong>. The protocol is optimized for native cells (<strong>10,000-300,000</strong> cells per reaction) and can be completed within 1.5 days. The kit includes all reagents for cell processing, including CoA beads, pA-Tn5 and the DNA purification module. The antibodies (secondary antibodies, control antibodies) as well as primer indexes for multiplexing must be purchased separately.</p>
<p><strong>For a complete CUT&Tag protocol the following items must be purchased:</strong></p>
<ul>
<li><strong>iDeal CUT&Tag kit for Histones</strong> – including all reagents for CUT&Tag workflow (buffers, pA-Tn5, CoA beads, DNA purification)</li>
<li><strong>Antibody package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a></strong> or <strong><a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></strong> - including the secondary antibody, positive and negative control antibodies and primers</li>
<li><strong><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></strong> – for multiplexing up to 72 samples</li>
</ul>
<h3>iDeal CUT&Tag Kit features:</h3>
<ul>
<li><strong>Rapid</strong> and <strong>easy </strong>chromatin profiling assay for <strong>histones </strong>and<strong> some non-histone proteins</strong></li>
<ul style="margin-bottom: 0;">
<li>No chromatin preparation</li>
<li>Easy sample handling due to ConA magnetic beads</li>
<li>Integrated library prep</li>
</ul>
<li><strong>Low cell number</strong>: 10,000-300,000 cells</li>
<li><strong>Accurate amplification</strong> due to intermediate quantification step</li>
<li><strong>High resolution</strong> and <strong>sensitivity</strong></li>
<li><strong>Lower sequencing depth</strong></li>
</ul>
<p>The quality of antibody used in CUT&Tag is one of the crucial factors for assay success. The antibodies with confirmed high specificity will target only the protein of interest, enabling real results. Check out our selection of <strong><a href="https://www.diagenode.com/en/categories/cut-and-tag-antibodies">antibodies validated in CUT&Tag</a>.</strong></p>
<p>Looking for a standalone pA-Tn5? <a href="https://www.diagenode.com/en/products/view/3064">Read more</a>.</p>
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'info1' => '<p>The iDeal CUT&Tag protocol involves the binding of cells on a solid phase ConA magnetic beads, allowing magnetic handling of the cells for the major steps of the protocol. Bead-bound cells are permeabilized, incubated with primary antibody against a target of interest and secondary antibody. Then, Diagenode’s protein pA-Tn5 Transposase - loaded is bound to the complex. Protein A guides Tn5 transposase on chromatin to the antibody attached to its target. Tn5 transposase is activated by Mg+2 ions to insert the sequencing adaptors into genomic regions of interest. DNA is then purified and the tagmented genomic regions of interest are amplified by PCR using Diagenode’s Primer Indexes for tagmented libraries.</p>
<p></p>
<p><img alt=" pA-Tn5 Antibody package for CUT & Tag" src="https://www.diagenode.com/img/product/kits/workflow-cutandtag.jpg" /></p>',
'label2' => 'Examples of results - histone marks',
'info2' => '<p>Successful CUT&Tag results showing a low background with high region-specific enrichment are presented below. Chromatin profiling has been performed on 50,000 K562 cells, using the Diagenode’s iDeal CUT&Tag kit for Histones (Cat. No. C01070020), the Antibody Package for CUT&Tag anti rabbit (Cat. No. C01070022), the 24 UDI for Tagmented Libraries (Cat.No. C01011034) and H3K4me3 (Cat. No. C15410003), H3K27me3 (Cat. No. C15410069) or H3H9me3 antibodies (Cat. No., C15410193) as indicated. The libraries were sequenced on Illumina’s NovaSeq6000 in 2x50 bp mode.</p>
<p><br /> <img alt="CUT&Tag-sequencing" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1a.png" /> <img alt="CUT&Tag kit for Histones" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1b.png" /> <img alt="Cleavage Under Targets and Tagmentation" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig1c.png" /></p>
<p><strong>Figure 1.</strong> Typical library profiles (Agilent Fragment traces) generated by the iDeal CUT&Tag protocol using 50,000 K562 cells and H3K27me3 (top), H3K4me4 (middle) primary antibodies and IgG control (bottom). Sharp peak at around 40 bp is an excess of <strong>free oligonucleotide used for pA-Tn5 loading</strong>.</p>
<p></p>
<p><br /><br /></p>
<div class="row">
<div class="small-4 columns">
<p><img alt="iDeal CUT&Tag kit for Histones" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig2.png" /></p>
</div>
<div class="small-8 columns">
<p><strong>Figure 2.</strong> Enrichments at TSS of the CUT&Tag libraries. The heatmap shows the enrichment around 3kb upstream and downstream of the TSS for H3K4me3. H3K4me3 as an active chromatin mark is associated with active promoters shows a narrow enrichment pattern.</p>
</div>
</div>
<p><br /><br /></p>
<p><br /> <img alt="iDeal CUT&Tag experiments of K562 cells " src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig3.png" /></p>
<p><strong>Figure 3.</strong> Sequencing profiles of the CUT&Tag libraries. Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using 50,000 of K562 cells and H3K4me3 (blue), H3K27me3 (red) or H3K9me3 (green).</p>
<p><br /><br /></p>
<p><br /> <img alt="CUT&Tag experiments using 10,000 K562 cells" src="https://www.diagenode.com/img/product/cutandtag/C01070020-cuttag-fig4.png" /></p>
<p><strong>Figure 4.</strong> Sequencing profiles of the CUT&Tag libraries. Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using 50,000 (blue) or 10,000 (red)) of K562 cells and H3K27me3 antibody.</p>',
'label3' => 'Examples of results - transcription factors',
'info3' => '<p>Diagenode's<strong><span> iDeal CUT&Tag Kit for Histones</span></strong><span>, </span>developed for an efficient chromatin profiling on histone marks, can be used for profiling of <span>some transcription factors and co-factors using a mild fixation as described in the manual. </span></p>
<p><strong><span>Successful CUT&Tag results using CTCF and Suz12 antibodies and iDeal CUT&Tag Kit for Histones. </span></strong></p>
<p></p>
<p><span>Chromatin profiling of <strong>Suz12</strong> has been performed on 50,000 of fixed Mouse ES-E14TG2a cells (kindly provided by Luciano Di Croce, CRG, Spain) accordingly to the protocol of Diagenode’s iDeal CUT&Tag kit for Histones (Cat. No. C01070020). Antibody Package for CUT&Tag anti rabbit (Cat. No. C01070022) and the 24 UDI for Tagmented Libraries (Cat. No. C01011034) were used. The libraries were sized using Fragment Analyzer (Agilent) (triplicates, Figure 1, top). Relative enrichment has been confirmed by qPCR using know positive (T_Bra) and negative (Actb) loci (Figure 1, bottom). Libraries were sequenced on Illumina’s NovaSeq6000 in 2x50 bp mode.</span></p>
<p></p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig1a.jpg" /><br /> <img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig1b.jpg" /></p>
<p><strong>Figure 1.</strong> Typical library profiles (top) and relative enrichment (bottom) generated by the iDeal CUT&Tag protocol using 50,000 ES-E14TG2a cells and Suz12 Antibody and IgG control (bottom). Sharp peak at around 40 bp is an excess of free oligonucleotide used for pA-Tn5 loading which does not interfere with the sequencing.</p>
<p></p>
<p>Pictures of representative loci were taken on Integrative Genome Viewer (IGV) for CTCF demonstrating the presence of high signal at promoter regions.</p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2a.jpg" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2b.jpg" /> <img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-Fig2c.jpg" /></p>
<p></p>
<p></p>
<p>Pictures of representative loci were taken on Integrative Genome Viewer (IGV) for SUZ12 and H3K27me3 triplicate samples, showing an overlap between the signal from both proteins, as part of the Polycomb Repressive Complex.</p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci1.jpg" width="100%" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci2.jpg" /><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig2-loci3.jpg" /></p>
<p><strong>Figure 2. IGV snapshots</strong></p>
<p></p>
<p></p>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig3.jpg" /></p>
</div>
<div class="small-8 columns">
<p><strong>Figure 3. Heatmap around the TSS</strong><br /> Heatmap of the CTCF signal around the transcription start sites (TSS) of each gene present in the murine mm10 reference genome.</p>
</div>
</div>
<p></p>
<p></p>
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig4.jpg" /></p>
<p><strong>Figure 4. CTCF motif</strong><br /> Presence of specific transcription factor binding motifs in the regions identified as CTCF peaks. The top3 motifs are corresponding to the CTCF binding motif.</p>
<p></p>
<p></p>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/cutandtag/C01070020-TF-fig5.jpg" /></p>
</div>
<div class="small-6 columns">
<p><strong>Figure 5. CTCF motif density</strong><br /> Location and density of the CTCF binding motif with respect to the center of the identified CTCF peaks.</p>
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<p> </p>
<p>Diagenode <b>Tagmentase</b><b> – loaded </b>is a <strong>hyperactive Tn5 transposase</strong> preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq or ChIPmentation.</p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x-1ml">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for unloaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-20-ul">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul"> (Tn5 transposase) – </a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul">unloaded</a></p>',
'label1' => 'Examples of results',
'info1' => '<p><b>Tagmentase</b><b> (Tn5 transposase) – </b><b>loaded</b> can be used in any application using tagmentation-based library preparation, like for example ChIPmentation, ATAC-seq. Here below we are showing some examples of results.</p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig1.png" width="700" alt="Tn5 transposase Enxzymes" caption="false" /></center>
<p><small><strong>Figure 1. Typical library profile of ATAC-seq library generated with the Tagmentase</strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<div class="row">
<div class="small-8 columns">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig2.png" width="200" alt="Diagenode Tagmentation " caption="false" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 2. Enrichments at TSS of ATAC-seq libraries generated with the Tagmentase</strong><br />ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). Heatmaps around the hg19 TSS were generated using deeptools plotHeatmap functionality.</small></p>
</div>
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<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig3.png" alt="Transposase enzymes for ATAC-Seq" caption="false" width="956" height="259" /></center>
<p><small><strong>Figure 3. Sequencing profiles of ATAC-seq libraries generated with the Tagmentase </strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig4.png" width="700" alt="purified Transposase enzymes " caption="false" /></center>
<p><small><strong>Figure 4. Typical library profile of ChIPmentation library generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 1,000,000 K562 cells using the ChIPmentation Kit for Histones (Cat. No. C01011010) in combination with the Diagenode antibody targeting H3K4me3 (Cat. No. C15410003) and with the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig5.png" alt="pA-Tn5 Transposase Enzymes" caption="false" width="956" height="262" /></center>
<p><small><strong>Figure 5. Sequencing profiles of ChIPmentation libraries generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 500.000 to 1,000,000 cells using the <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones </a>(Cat. No. C01011010) in combination with the <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) – loaded </a>(Cat. No. C01070012) on K562 cells. The Diagenode antibodies targeting <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3 </a>(Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-premium-50-mg-18-ml">H3K27ac </a>(Cat. No. C15410196), <a href="https://www.diagenode.com/en/p/h3k36me3-polyclonal-antibody-premium-50-mg">H3K36me3 </a>(Cat. No. C15410192), <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (Cat. No. C15410195) and rabbit <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">IgG </a>(Cat. No. C15410206) have been used.</small></p>
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'info2' => '<p><strong>Tagmentase (Tn5 transposase) - loaded </strong></p>
<div>Protein Molecular weight: 53.3 kDa</div>
<p>Expressed: in Escherichia coli</p>
<p></p>
<p><strong>Product description:</strong> Diagenode Tagmentase – loaded is a hyperactive Tn5 transposase preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments. The Tagmentase is pre-loaded with sequencing adapters compatible with Illumina Nextera platforms, as shown below. The oligos loaded on the Tagmentase are inserted into DNA upon a tagmentation reaction.</p>
<div>Mosaic end_reverse: 5’ [PHO]<span style="text-decoration: underline;">CTGTCTCTTATACACATCT</span> 3’</div>
<div>Mosaic end_Adapter A: 5’ TCGTCGGCAGCGTC<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</div>
<p>Mosaic end_Adapter B: 5’ GTCTCGTGGGCTCGG<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</p>
<p></p>
<div><span style="text-decoration: underline;">Underlined regions</span> correspond to the double-stranded part of the adapter, recognized by the Tagmentase. The final libraries can be amplified using Diagenode Primer indexes for tagmented libraries:</div>
<div>24 SI for tagmented libraries, Cat. No. C01011032</div>
<div>24 UDI fortagmented libraries - Set I, Cat. No. C0101134</div>
<div>24 UDI for tagmented libraries - Set II, Cat. No. C0101136</div>
<p>24 UDI for tagmented libraries - Set III, Cat. No. C0101137</p>
<p></p>
<p><strong>Storage conditions: </strong>Store at -20°C. Guaranteed stable for 6 months from date of receipt when stored properly.</p>
<p><strong>Storage buffer:</strong> Supplied in solution containing 50% v/v glycerol.</p>
<p><strong>Properties & Usage: </strong>Tagmentase is dependent on Mg++ for activity. Avoid chelators, such as EDTA/EGTA, in reaction buffers. The enzyme is active at pH 7.5-8 at 37-55°C. SDS, EDTA/EGTA or heating to 65°C will inactivate the enzyme.</p>
<p><strong>Applications:</strong> Tagmentase (Tn5 transposase) – loaded can be used in a variety of applications to construct library for second-generation sequencing. Please note that an additional optimization might be required for custom protocols including the enzyme dose- and time-response experiments.</p>
<div>For ATAC-seq and ChIPmentation, we recommend using Diagenode validated protocols:</div>
<div>ATAC-seq kit, Cat. No. C01080002</div>
<div>ATAC-seq package for tissue, Cat. No. <span>C01080006</span></div>
<div>ChIPmentation Kit for Histones, Cat. No. C01011009</div>
<div>µChIPmentation Kit for Histones, Cat. No. C01011011</div>
<div>TAG Kit for ChIPmentation, Cat. No. C01011030</div>
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<p><strong>CUT&Tag</strong>-sequencing (<strong>C</strong>leavage <strong>U</strong>nder <strong>T</strong>argets and <strong>Tag</strong>mentation) is a new alternative method to ChIP-seq combining antibody-targeted controlled cleavage by a protein A-Tn5 fusion with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. At Diagenode we offer a complete solution for CUT&Tag – our iDeal CUT&Tag for Histones (developped for histone marks and some non-histone proteins), but also stand-alone fusion protein – pA-Tn5 Transposase. Moreover, we have validated our <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade antibodies</a> in <a href="https://www.diagenode.com/en/categories/cut-and-tag-antibodies">CUT&Tag</a> proving their high performance in this assay.</p>
<br /> <a href="https://www.diagenode.com/files/application_notes/AN-iDealCUTandTag.pdf"><img src="https://www.diagenode.com/img/banners/cutandtag-appnote.png" /></a><br /><br /></div>
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<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#v5" style="color: #13b29c;"><i class="fa fa-caret-right"></i> How does it work?</a>
<div id="v5" class="content">
<p>The iDeal CUT&Tag protocol involves the binding of cells on a solid phase ConA magnetic beads, allowing magnetic handling of the cells for the major steps of the protocol. Bead-bound cells are permeabilized, incubated with primary antibody against a target of interest and secondary antibody. Then, Diagenode’s protein pA-Tn5 Transposase - loaded is bound to the complex. Protein A guides Tn5 transposase on chromatin to the antibody attached to its target. Tn5 transposase is activated by Mg+2 ions to insert the sequencing adaptors into genomic regions of interest. DNA is then purified and the tagmented genomic regions of interest are amplified by PCR using Diagenode’s Primer Indexes for tagmented libraries.</p>
<img src="https://www.diagenode.com/img/product/kits/workflow-cutandtag.jpg" /></div>
<h2>Products for CUT&Tag assay</h2>
<h3 class="diacol">Complete solutions</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24" target="_blank">iDeal CUT&Tag kit for Histones</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24" target="_blank">Antibody package for CUT&Tag (anti-rabbit)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24" target="_blank">Antibody package for CUT&Tag (anti-mouse)</a></li>
</ul>
<h3 class="diacol">Fusion protein</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/products/view/3064" target="_blank">pA/Tn5 Transposase (loaded)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">pA/Tn5 Transposase (unloaded)</a></li>
</ul>
<h3 class="diacol">CUT&Tag grade antibodies</h3>
<ul class="nobullet">
<li>Antibodies <a href="https://www.diagenode.com/en/applications/cut-and-tag">validated in CUT&Tag</a></li>
<li>Check out our list of <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies" target="_blank">ChIP-seq grade antibodies</a></li>
<li>Read more about the performance of Diagenode antibodies in <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">CUT&Tag</a></li>
</ul>
<h3 class="diacol">Positive & Negative CUT&Tag control</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24" target="_blank">Antibody package for CUT&Tag (anti-rabbit)</a></li>
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24" target="_blank">Antibody package for CUT&Tag (anti-mouse)</a></li>
</ul>
<h3 class="diacol">DNA purification</h3>
<p style="padding-left: 30px;"><a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2<br /></a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></p>
<h3 class="diacol">Sequencing indexes</h3>
<ul class="nobullet">
<li><i class="fa fa-arrow-circle-right"></i> <a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries" target="_blank">Primer indexes for tagmented libraries</a></li>
</ul>
</li>
</ul>',
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'description' => '<p>pA-Tn5 Transposase is a fusion protein of hyperactive Tn5 transposase and protein A developed for the CUT&Tag assay. For ease of use, the fusion protein is pre-loaded with sequencing adapters suitable for single or dual indexing in single or paired-end Illumina platforms. The adaptors contain 19-mer Tn5 mosaic ends and the sequences for PCR amplification with barcoded i7/i5.</p>',
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'name' => 'The molecular consequences of FOXF1 missense mutations associated with alveolar capillary dysplasia with misalignment of pulmonary veins',
'authors' => 'G. G. Edel et al.',
'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a fatal congenital lung disorder strongly associated with genomic alterations in the Forkhead box F1 (FOXF1) gene and its regulatory region. However, little is known about how FOXF1 genomic alterations cause ACD/MPV and what molecular mechanisms are affected by these mutations. Therefore, the effect of ACD/MPV patient-specific mutations in the<span> </span><i>FOXF1</i><span> </span>gene on the molecular function of FOXF1 was studied.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Methods</h3>
<p>Epitope-tagged FOXF1 constructs containing one of the ACD/MPV-associated mutations were expressed in mammalian cell lines to study the effect of FOXF1 mutations on protein function. EMSA binding assays and luciferase assays were performed to study the effect on target gene binding and activation. Immunoprecipitation followed by SDS‒PAGE and western blotting were used to study protein‒protein interactions. Protein phosphorylation was studied using phos-tag western blotting.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>An overview of the localization of ACD/MPV-associated FOXF1 mutations revealed that the G91-S101 region was frequently mutated. A three-dimensional model of the forkhead DNA-binding domain of FOXF1 showed that the G91-S101 region consists of an α-helix and is predicted to be important for DNA binding. We showed that FOXF1 missense mutations in this region differentially affect the DNA binding of the FOXF1 protein and influence the transcriptional regulation of target genes depending on the location of the mutation. Furthermore, we showed that some of these mutations can affect the FOXF1 protein at the posttranscriptional level, as shown by altered phosphorylation by MST1 and MST2 kinases.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusion</h3>
<p>Missense mutations in the coding region of the<span> </span><i>FOXF1</i><span> </span>gene alter the molecular function of the FOXF1 protein at multiple levels, such as phosphorylation, DNA binding and target gene activation. These results indicate that FOXF1 molecular pathways may be differentially affected in ACD/MPV patients carrying missense mutations in the DNA-binding domain and may explain the phenotypic heterogeneity of ACD/MPV.</p>',
'date' => '2024-11-04',
'pmid' => 'https://link.springer.com/article/10.1186/s12929-024-01088-5',
'doi' => 'https://doi.org/10.1186/s12929-024-01088-5',
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'id' => '4972',
'name' => 'Two-factor authentication underpins the precision of the piRNA pathway',
'authors' => 'Dias Mirandela M. et al.',
'description' => '<p><span>The PIWI-interacting RNA (piRNA) pathway guides the DNA methylation of young, active transposons during germline development in male mice</span><span>. piRNAs tether the PIWI protein MIWI2 (PIWIL4) to the nascent transposon transcript, resulting in DNA methylation through SPOCD1</span><span>. Transposon methylation requires great precision: every copy needs to be methylated but off-target methylation must be avoided. However, the underlying mechanisms that ensure this precision remain unknown. Here, we show that SPOCD1 interacts directly with SPIN1 (SPINDLIN1), a chromatin reader that primarily binds to H3K4me3-K9me3</span><span>. The prevailing assumption is that all the molecular events required for piRNA-directed DNA methylation occur after the engagement of MIWI2. We find that SPIN1 expression precedes that of both SPOCD1 and MIWI2. Furthermore, we demonstrate that young LINE1 copies, but not old ones, are marked by H3K4me3, H3K9me3 and SPIN1 before the initiation of piRNA-directed DNA methylation. We generated a<span> </span></span><i>Spocd1</i><span><span> </span>separation-of-function allele in the mouse that encodes a SPOCD1 variant that no longer interacts with SPIN1. We found that the interaction between SPOCD1 and SPIN1 is essential for spermatogenesis and piRNA-directed DNA methylation of young LINE1 elements. We propose that piRNA-directed LINE1 DNA methylation requires a developmentally timed two-factor authentication process. The first authentication is the recruitment of SPIN1–SPOCD1 to the young LINE1 promoter, and the second is MIWI2 engagement with the nascent transcript. In summary, independent authentication events underpin the precision of piRNA-directed LINE1 DNA methylation.</span></p>',
'date' => '2024-09-18',
'pmid' => 'https://www.nature.com/articles/s41586-024-07963-3',
'doi' => 'https://doi.org/10.1038/s41586-024-07963-3',
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'name' => 'Transcription factor EGR2 controls homing and pathogenicity of T17cells in the central nervous system.',
'authors' => 'Gao Y. et al.',
'description' => '<p>CD4 T helper 17 (T17) cells protect barrier tissues but also trigger autoimmunity. The mechanisms behind these opposing processes remain unclear. Here, we found that the transcription factor EGR2 controlled the transcriptional program of pathogenic T17 cells in the central nervous system (CNS) but not that of protective T17 cells at barrier sites. EGR2 was significantly elevated in myelin-reactive CD4 T cells from patients with multiple sclerosis and mice with autoimmune neuroinflammation. The EGR2 transcriptional program was intricately woven within the T17 cell transcriptional regulatory network and showed high interconnectivity with core T17 cell-specific transcription factors. Mechanistically, EGR2 enhanced T17 cell differentiation and myeloid cell recruitment to the CNS by upregulating pathogenesis-associated genes and myelomonocytic chemokines. T cell-specific deletion of Egr2 attenuated neuroinflammation without compromising the host's ability to control infections. Our study shows that EGR2 regulates tissue-specific and disease-specific functions in pathogenic T17 cells in the CNS.</p>',
'date' => '2023-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37443284',
'doi' => '10.1038/s41590-023-01553-7',
'modified' => '2023-08-01 13:35:13',
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'name' => 'The Hdc GC box is critical for Hdc gene transcription andhistamine-mediated anaphylaxis.',
'authors' => 'Li Y. et al.',
'description' => '<p>BACKGROUND: Histamine is a critical mediator of anaphylaxis, a neurotransmitter, and a regulator of gastric acid secretion. Histidine decarboxylase is a rate-limiting enzyme for histamine synthesis. However, in vivo regulation of Hdc, the gene that encodes histidine decarboxylase is poorly understood. OBJECTIVE: We sought to investigate how enhancers regulate Hdc gene transcription and histamine synthesis in resting conditions and in a mouse model of anaphylaxis. METHODS: H3K27 acetylation histone modification and chromatin accessibility were used to identify candidate enhancers; The enhancer activity of candidate enhancers was measured in a reporter gene assay; and the function enhancers were validated using CRISPR deletion. RESULTS: Deletion of the GC box, which binds to zinc finger transcription factors, in the proximal Hdc enhancer, reduced Hdc gene transcription and histamine synthesis in the mouse and human mast cell lines. Mast cells, basophils, brain cells, and stomach cells from GC box-deficient mice transcribed the Hdc gene much less than similar cells from wild-type mice and Hdc GC box-deficient mice failed to develop anaphylaxis. CONCLUSION: Our results demonstrate that the HDC GC box within the proximal enhancer in the mouse and human HDC gene is essential for Hdc gene transcription, histamine synthesis, and histamine-mediated anaphylaxis in vitro and in vivo.</p>',
'date' => '2023-02-01',
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'name' => 'Retrospective analysis of enhancer activity and transcriptome history.',
'authors' => 'Boers R. et al.',
'description' => '<p>Cell state changes in development and disease are controlled by gene regulatory networks, the dynamics of which are difficult to track in real time. In this study, we used an inducible DCM-RNA polymerase subunit b fusion protein which labels active genes and enhancers with a bacterial methylation mark that does not affect gene transcription and is propagated in S-phase. This DCM-RNA polymerase fusion protein enables transcribed genes and active enhancers to be tagged and then examined at later stages of development or differentiation. We apply this DCM-time machine (DCM-TM) technology to study intestinal homeostasis, revealing rapid and coordinated activation of enhancers and nearby genes during enterocyte differentiation. We provide new insights in absorptive-secretory lineage decision-making in intestinal stem cell (ISC) differentiation and show that ISCs retain a unique chromatin landscape required to maintain ISC identity and delineate future expression of differentiation-associated genes. DCM-TM has wide applicability in tracking cell states, providing new insights in the regulatory networks underlying cell state changes.</p>',
'date' => '2023-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36823354',
'doi' => '10.1038/s41587-023-01683-1',
'modified' => '2023-11-10 09:13:54',
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'id' => '4627',
'name' => 'Simultaneous profiling of histone modifications and DNA methylation viananopore sequencing.',
'authors' => 'Yue X. et al.',
'description' => '<p>The interplay between histone modifications and DNA methylation drives the establishment and maintenance of the cellular epigenomic landscape, but it remains challenging to investigate the complex relationship between these epigenetic marks across the genome. Here we describe a nanopore-sequencing-based-method, nanoHiMe-seq, for interrogating the genome-wide localization of histone modifications and DNA methylation from single DNA molecules. nanoHiMe-seq leverages a nonspecific methyltransferase to exogenously label adenine bases proximal to antibody-targeted modified nucleosomes in situ. The labelled adenines and the endogenous methylated CpG sites are simultaneously detected on individual nanopore reads using a hidden Markov model, which is implemented in the nanoHiMe software package. We demonstrate the utility, robustness and sensitivity of nanoHiMe-seq by jointly profiling DNA methylation and histone modifications at low coverage depths, concurrently determining phased patterns of DNA methylation and histone modifications, and probing the intrinsic connectivity between these epigenetic marks across the genome.</p>',
'date' => '2022-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36566265',
'doi' => '10.1038/s41467-022-35650-2',
'modified' => '2023-03-28 08:59:26',
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'name' => 'A SOX2-engineered epigenetic silencer factor represses the glioblastomagenetic program and restrains tumor development.',
'authors' => 'Benedetti V. et al.',
'description' => '<p>Current therapies remain unsatisfactory in preventing the recurrence of glioblastoma multiforme (GBM), which leads to poor patient survival. By rational engineering of the transcription factor SOX2, a key promoter of GBM malignancy, together with the Kruppel-associated box and DNA methyltransferase3A/L catalytic domains, we generated a synthetic repressor named SOX2 epigenetic silencer (SES), which induces the transcriptional silencing of its original targets. By doing so, SES kills both glioma cell lines and patient-derived cancer stem cells in vitro and in vivo. SES expression, through local viral delivery in mouse xenografts, induces strong regression of human tumors and survival rescue. Conversely, SES is not harmful to neurons and glia, also thanks to a minimal promoter that restricts its expression in mitotically active cells, rarely present in the brain parenchyma. Collectively, SES produces a significant silencing of a large fraction of the SOX2 transcriptional network, achieving high levels of efficacy in repressing aggressive brain tumors.</p>',
'date' => '2022-08-01',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/35921410/',
'doi' => '10.1126/sciadv.abn3986',
'modified' => '2023-09-28 11:26:02',
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'id' => '4836',
'name' => 'Caffeine intake exerts dual genome-wide effects on hippocampal metabolismand learning-dependent transcription.',
'authors' => 'Paiva I. et al.',
'description' => '<p>Caffeine is the most widely consumed psychoactive substance in the world. Strikingly, the molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal omics techniques. Our results revealed that chronic caffeine exerts concerted pleiotropic effects in the hippocampus at the epigenomic, proteomic, and metabolomic levels. Caffeine lowered metabolism-related processes (e.g., at the level of metabolomics and gene expression) in bulk tissue, while it induced neuron-specific epigenetic changes at synaptic transmission/plasticity-related genes and increased experience-driven transcriptional activity. Altogether, these findings suggest that regular caffeine intake improves the signal-to-noise ratio during information encoding, in part through fine-tuning of metabolic genes, while boosting the salience of information processing during learning in neuronal circuits.</p>',
'date' => '2022-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35536645',
'doi' => '10.1172/JCI149371',
'modified' => '2023-08-01 13:52:29',
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'id' => '4263',
'name' => 'ATRX regulates glial identity and the tumor microenvironment inIDH-mutant glioma',
'authors' => 'Babikir, Husam and Wang, Lin and Shamardani, Karin andCatalan, Francisca and Sudhir, Sweta and Aghi, Manish K. andRaleigh, David R. and Phillips, Joanna J. and Diaz, AaronA.',
'description' => '<p>Background Recent single-cell transcriptomic studies report that IDH-mutant gliomas share a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the genetic differences between IDH-mutant glioma subtypes are prognostic, predictive of response to chemotherapy, and correlate with distinct tumor microenvironments. Results To reconcile these findings, we profile 22 human IDH-mutant gliomas using scATAC-seq and scRNA-seq. We determine the cell-type-specific differences in transcription factor expression and associated regulatory grammars between IDH-mutant glioma subtypes. We find that while IDH-mutant gliomas do share a common distribution of cell types, there are significant differences in the expression and targeting of transcription factors that regulate glial identity and cytokine elaboration. We knock out the chromatin remodeler ATRX, which suffers loss-of-function alterations in most IDH-mutant astrocytomas, in an IDH-mutant immunocompetent intracranial murine model. We find that both human ATRX-mutant gliomas and murine ATRX-knockout gliomas are more heavily infiltrated by immunosuppressive monocytic-lineage cells derived from circulation than ATRX-intact gliomas, in an IDH-mutant background. ATRX knockout in murine glioma recapitulates gene expression and open chromatin signatures that are specific to human ATRX-mutant astrocytomas, including drivers of astrocytic lineage and immune-cell chemotaxis. Through single-cell cleavage under targets and tagmentation assays and meta-analysis of public data, we show that ATRX loss leads to a global depletion in CCCTC-binding factor association with DNA, gene dysregulation along associated chromatin loops, and protection from therapy-induced senescence. Conclusions These studies explain how IDH-mutant gliomas from different subtypes maintain distinct phenotypes and tumor microenvironments despite a common lineage hierarchy. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02535-4.</p>',
'date' => '2021-11-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34763709',
'doi' => '10.1186/s13059-021-02535-4',
'modified' => '2022-05-20 09:50:12',
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'name' => 'Autocrine Vitamin D-signaling switches off pro-inflammatory programsof Th1 cells',
'authors' => 'Chauss D.et al.',
'description' => '<p>The molecular mechanisms governing orderly shutdown and retraction of CD4+ T helper (Th)1 responses remain poorly understood. Here, we show that complement triggers contraction of Th1 responses by inducing intrinsic expression of the vitamin D (VitD) receptor (VDR) and the VitD-activating enzyme CYP27B1, permitting T cells to both activate and respond to VitD. VitD then initiated transition from pro-inflammatory IFN-γ + Th1 cells to suppressive IL-10+ cells. This process was primed by dynamic changes in the epigenetic landscape of CD4+ T cells, generating super-enhancers and recruiting several transcription factors, notably c-JUN, STAT3 and BACH2, which together with VDR shaped the transcriptional response to VitD. Accordingly, VitD did not induce IL-10 in cells with dysfunctional BACH2 or STAT3. Bronchoalveolar lavage fluid CD4+ T cells of COVID-19 patients were Th1-skewed and showed de-repression of genes down-regulated by VitD, either from lack of substrate (VitD deficiency) and/or abnormal regulation of this system.</p>',
'date' => '2021-10-01',
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'modified' => '2022-05-19 16:57:27',
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'meta_title' => 'pA-Tn5 Transposase (loaded) developed for the CUT&Tag assay | Diagenode.com',
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'meta_description' => 'Diagenode pA-Tn5 Transposase (loaded) is a fusion protein of hyperactive Tn5 transposase and protein A developed for the CUT&Tag assay. For convenience, the fusion protein is pre-loaded with sequencing adapters.',
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<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
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<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
</div>
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<div class="row extra-spaced">
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
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<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
</ul>',
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<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
</div>
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'description' => '<p>We are really happy to use the loaded pA-Tn5 for CUT&Tag. Easy to use and reproductible for samples with a starting low number of cells. Besides, Diagenode has a great customer service and technical support which are really responsive.</p>',
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<p><strong><input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/></strong>pA-Tn5 Transposase - unloaded個カートに追加。</p>
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<a href="/jp/p/rabbit-igg-250-ug-250-ul"><img src="/img/product/antibodies/antibody.png" alt="Mouse IgG" class="th"/></a> </div>
<div class="small-12 columns">
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<span class="success label" style="">C15410206</span>
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<p><strong><input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/></strong>Tagmentase (Tn5 transposase) - loaded個カートに追加。</p>
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<p> </p>
<p>Diagenode <b>Tagmentase</b><b> – loaded </b>is a <strong>hyperactive Tn5 transposase</strong> preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq or ChIPmentation.</p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x-1ml">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for unloaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-20-ul">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul"> (Tn5 transposase) – </a><a href="https://www.diagenode.com/en/p/tagmentase-20-ul">unloaded</a></p>',
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<p><small><strong>Figure 1. Typical library profile of ATAC-seq library generated with the Tagmentase</strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
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<p><small><strong>Figure 2. Enrichments at TSS of ATAC-seq libraries generated with the Tagmentase</strong><br />ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043). Heatmaps around the hg19 TSS were generated using deeptools plotHeatmap functionality.</small></p>
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<p><small><strong>Figure 3. Sequencing profiles of ATAC-seq libraries generated with the Tagmentase </strong><br /> ATAC-seq has been performed on 50,000 nuclei from K562 cells, in triplicates, using the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012) and Tagmentation Buffer (2x) (Cat. No. C01019043).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig4.png" width="700" alt="purified Transposase enzymes " caption="false" /></center>
<p><small><strong>Figure 4. Typical library profile of ChIPmentation library generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 1,000,000 K562 cells using the ChIPmentation Kit for Histones (Cat. No. C01011010) in combination with the Diagenode antibody targeting H3K4me3 (Cat. No. C15410003) and with the Tagmentase (Tn5 transposase) – loaded (Cat. No. C01070012). The library profile has been generated on a Fragment Analyzer (Agilent).</small></p>
<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig5.png" alt="pA-Tn5 Transposase Enzymes" caption="false" width="956" height="262" /></center>
<p><small><strong>Figure 5. Sequencing profiles of ChIPmentation libraries generated with the Tagmentase</strong><br /> Chromatin preparation and immunoprecipitation have been performed on 500.000 to 1,000,000 cells using the <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones </a>(Cat. No. C01011010) in combination with the <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) – loaded </a>(Cat. No. C01070012) on K562 cells. The Diagenode antibodies targeting <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3 </a>(Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-premium-50-mg-18-ml">H3K27ac </a>(Cat. No. C15410196), <a href="https://www.diagenode.com/en/p/h3k36me3-polyclonal-antibody-premium-50-mg">H3K36me3 </a>(Cat. No. C15410192), <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (Cat. No. C15410195) and rabbit <a href="https://www.diagenode.com/en/p/rabbit-igg-250-ug-250-ul">IgG </a>(Cat. No. C15410206) have been used.</small></p>
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<div>Protein Molecular weight: 53.3 kDa</div>
<p>Expressed: in Escherichia coli</p>
<p></p>
<p><strong>Product description:</strong> Diagenode Tagmentase – loaded is a hyperactive Tn5 transposase preloaded with Illumina-compatible sequencing adapters. Its ability to cut DNA and insert the sequencing adapters in one step makes it the perfect companion for Next-Generation Sequencing experiments. The Tagmentase is pre-loaded with sequencing adapters compatible with Illumina Nextera platforms, as shown below. The oligos loaded on the Tagmentase are inserted into DNA upon a tagmentation reaction.</p>
<div>Mosaic end_reverse: 5’ [PHO]<span style="text-decoration: underline;">CTGTCTCTTATACACATCT</span> 3’</div>
<div>Mosaic end_Adapter A: 5’ TCGTCGGCAGCGTC<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</div>
<p>Mosaic end_Adapter B: 5’ GTCTCGTGGGCTCGG<span style="text-decoration: underline;">AGATGTGTATAAGAGACAG</span> 3’</p>
<p></p>
<div><span style="text-decoration: underline;">Underlined regions</span> correspond to the double-stranded part of the adapter, recognized by the Tagmentase. The final libraries can be amplified using Diagenode Primer indexes for tagmented libraries:</div>
<div>24 SI for tagmented libraries, Cat. No. C01011032</div>
<div>24 UDI fortagmented libraries - Set I, Cat. No. C0101134</div>
<div>24 UDI for tagmented libraries - Set II, Cat. No. C0101136</div>
<p>24 UDI for tagmented libraries - Set III, Cat. No. C0101137</p>
<p></p>
<p><strong>Storage conditions: </strong>Store at -20°C. Guaranteed stable for 6 months from date of receipt when stored properly.</p>
<p><strong>Storage buffer:</strong> Supplied in solution containing 50% v/v glycerol.</p>
<p><strong>Properties & Usage: </strong>Tagmentase is dependent on Mg++ for activity. Avoid chelators, such as EDTA/EGTA, in reaction buffers. The enzyme is active at pH 7.5-8 at 37-55°C. SDS, EDTA/EGTA or heating to 65°C will inactivate the enzyme.</p>
<p><strong>Applications:</strong> Tagmentase (Tn5 transposase) – loaded can be used in a variety of applications to construct library for second-generation sequencing. Please note that an additional optimization might be required for custom protocols including the enzyme dose- and time-response experiments.</p>
<div>For ATAC-seq and ChIPmentation, we recommend using Diagenode validated protocols:</div>
<div>ATAC-seq kit, Cat. No. C01080002</div>
<div>ATAC-seq package for tissue, Cat. No. <span>C01080006</span></div>
<div>ChIPmentation Kit for Histones, Cat. No. C01011009</div>
<div>µChIPmentation Kit for Histones, Cat. No. C01011011</div>
<div>TAG Kit for ChIPmentation, Cat. No. C01011030</div>
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<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>pA-Tn5 transposase</strong> is a fusion protein of hyperactive Tn5 transposase and protein A developed for the <strong>CUT&Tag assay</strong>. For convenience, the fusion protein is pre-loaded with sequencing adapters. Diagenode pA-Tn5 transposase is compatible with CUT&Tag and other antibody-tethered Tn5 based methods, like ACT-seq and CoBATCH.</p>
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<p><strong>pA-Tn5 Transposase</strong></p>
<ul style="list-style-type: circle;">
<li>High enrichment and specificity of the signal around the TSS</li>
<li>No contamination<span style="font-weight: 400;"> with </span><i><span style="font-weight: 400;">E. coli</span></i><span style="font-weight: 400;"> DNA</span></li>
<li><span style="font-weight: 400;">Flexible versions: loaded or <a href="https://www.diagenode.com/en/p/pa-tn5-transposase-unloaded">unloaded</a><br /></span></li>
<li><span style="font-weight: 400;">Excellent for CUT&Tag </span></li>
</ul>
<p>As it is crucial to target only the protein of interest, a highly specific antibody is critical for the success of the CUT&Tag assay. All Diagenode ChIP-seq grade antibodies are validated for specificity using strict validation criteria to assure <a href="https://www.diagenode.com/en/pages/cut-and-tag" target="_blank">high performance in CUT&Tag</a>.</p>
<p class="lead"><strong>Check out all products recommended for CUT&Tag assay</strong>:</p>
<ul class="nobullet" style="list-style-type: circle;">
<li><a href="https://www.diagenode.com/en/p/ideal-cut-and-tag-kit-for-histones-24">iDeal CUT&Tag kit for Histones</a> - compatible with histome marks and some transcription factors</li>
<li>pA/Tn5 Transposase (loaded or <a href="https://www.diagenode.com/en/products/view/3065" target="_blank">unloaded</a>)</li>
<li><a href="https://www.diagenode.com/en/applications/cut-and-tag">CUT&Tag grade</a> and <a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies">ChIP-seq grade</a> antibodies</li>
<li>Negative & positive CUT&Tag controls: <span>Antibody Package for CUT&Tag: <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antirabbit-24">anti-rabbit</a> and <a href="https://www.diagenode.com/en/p/antibody-package-cut-and-tag-antimouse-24">anti-mouse</a></span></li>
<li>DNA purification: <a href="https://www.diagenode.com/en/p/ipure-kit-v2-x24">IPure kit v2</a> or <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP DiaPure columns</a></li>
<li>Sequencing indexes: <a href="https://www.diagenode.com/en/p/24-si-for-tagmented-libraries">single indexes</a> and <a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">UDI</a></li>
</ul>',
'label1' => 'Validation Data',
'info1' => '<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">A.<br /><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-a.png" width="800" height="374" /></center><br /> B.<br /><center><img alt="pA-Tn5 Transposase loaded H3K9me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-b.png" width="800" height="374" /></center><br /> C.<br /><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation" src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-1-c.png" width="800" height="374" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1.</strong> Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (A), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">H3K9me3</a> (B) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (C) data obtained using Diagenode pA-Tn5 fusion protein (C01070001) and CUT&Tag protocol (Kaya-Okur, H.S., Nat Commun 10, 1930 (2019)) at selected loci. CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), H3K27me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>) and H3K9me3 polyclonal ChIP-seq grade antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-premium-50-mg">C15410193</a>).</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K27me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-a.png" /></center></div>
<div class="small-12 medium-6 large-6 columns"><center><img alt="pA-Tn5 Transposase loaded H3K4me3 Validation " src="https://www.diagenode.com/img/product/cutandtag/pa-tn5-loaded-fig-2-b.png" /></center></div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2.</strong> CUT&Tag profiles show typical enrichments specific for a given histone mark. Representative screenshots for <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">H3K27me3</a> (red) and <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (green) are shown at selected loci. H3K27me3, which marks inactive regions (red), does not show enrichment over open chromatin regions, marked by H3K4me3 (green). CUT&Tag was performed using 50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody (Cat. No. <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.<a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">C15410195</a>).</p>
</div>
</div>',
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'format' => '100 µl (200 rxns)',
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'online' => true,
'master' => false,
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'slug' => 'pa-tn5-transposase-loaded-100',
'meta_title' => 'pA-Tn5 Transposase (loaded) developed for the CUT&Tag assay | Diagenode.com',
'meta_keywords' => '',
'meta_description' => 'Diagenode pA-Tn5 Transposase (loaded) is a fusion protein of hyperactive Tn5 transposase and protein A developed for the CUT&Tag assay. For convenience, the fusion protein is pre-loaded with sequencing adapters.',
'modified' => '2024-08-29 10:35:51',
'created' => '2024-08-29 10:31:56',
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'id' => '429',
'product_id' => '3239',
'group_id' => '274'
)
)
$label = '<img src="/img/banners/banner-customizer-back.png" alt=""/>'
$document = array(
'id' => '1078',
'name' => 'pA-TN5 transposase (loaded) datasheet',
'description' => '<p>pA-Tn5 Transposase is a fusion protein of hyperactive Tn5 transposase and protein A developed for the CUT&Tag assay. For ease of use, the fusion protein is pre-loaded with sequencing adapters suitable for single or dual indexing in single or paired-end Illumina platforms. The adaptors contain 19-mer Tn5 mosaic ends and the sequences for PCR amplification with barcoded i7/i5.</p>',
'image_id' => null,
'type' => 'Datasheet',
'url' => 'files/products/cutandtag/C01070001-pa-tn5-transposase-loaded.pdf',
'slug' => 'c01070001-pa-tn5-transposase-loaded-tds',
'meta_keywords' => '',
'meta_description' => '',
'modified' => '2020-04-28 16:49:59',
'created' => '2020-04-28 16:43:37',
'ProductsDocument' => array(
'id' => '2874',
'product_id' => '3064',
'document_id' => '1078'
)
)
$sds = array(
'id' => '204',
'name' => 'pA-Tn5 Transposase - loaded SDS ES es',
'language' => 'es',
'url' => 'files/SDS/pA-Tn5_Transposase/SDS-C01070001-pA-Tn5_Transposase_-_loaded-ES-es-GHS_1_0.pdf',
'countries' => 'ES',
'modified' => '2020-06-08 16:03:25',
'created' => '2020-06-08 16:03:25',
'ProductsSafetySheet' => array(
'id' => '391',
'product_id' => '3064',
'safety_sheet_id' => '204'
)
)
$publication = array(
'id' => '4233',
'name' => 'Autocrine Vitamin D-signaling switches off pro-inflammatory programsof Th1 cells',
'authors' => 'Chauss D.et al.',
'description' => '<p>The molecular mechanisms governing orderly shutdown and retraction of CD4+ T helper (Th)1 responses remain poorly understood. Here, we show that complement triggers contraction of Th1 responses by inducing intrinsic expression of the vitamin D (VitD) receptor (VDR) and the VitD-activating enzyme CYP27B1, permitting T cells to both activate and respond to VitD. VitD then initiated transition from pro-inflammatory IFN-γ + Th1 cells to suppressive IL-10+ cells. This process was primed by dynamic changes in the epigenetic landscape of CD4+ T cells, generating super-enhancers and recruiting several transcription factors, notably c-JUN, STAT3 and BACH2, which together with VDR shaped the transcriptional response to VitD. Accordingly, VitD did not induce IL-10 in cells with dysfunctional BACH2 or STAT3. Bronchoalveolar lavage fluid CD4+ T cells of COVID-19 patients were Th1-skewed and showed de-repression of genes down-regulated by VitD, either from lack of substrate (VitD deficiency) and/or abnormal regulation of this system.</p>',
'date' => '2021-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34764490',
'doi' => '10.1038/s41590-021-01080-3',
'modified' => '2022-05-19 16:57:27',
'created' => '2022-05-19 10:41:50',
'ProductsPublication' => array(
'id' => '5629',
'product_id' => '3064',
'publication_id' => '4233'
)
)
$externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/34764490" target="_blank"><i class="fa fa-external-link"></i></a>'include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118
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