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<p>A high quality chromatin preparation is very complex and requires a lot of optimization. Chromatin EasyShear Kit – Ultra Low SDS is an optimized solution for efficient chromatin preparation prior to ChIP. The protocol, buffers composition, SDS concentration (<0.1%) is optimized for the preparation of chromatin prior to ChIP on <strong>histones</strong>. The kit has been validated with the Bioruptor ultrasonicator for efficient chromatin shearing, leading to chromatin fragments <strong>suitable for ChIP</strong> with the preserved <strong>epitopes</strong>. The kit is validated for cells and tissues.</p>
<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>',
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<p><strong>Figure 1. Optimal chromatin shearing profile</strong><br /> HeLa cells were fixed with formaldehyde for 8 min and chromatin was prepared according to Diagenode’s Chromatin EasyShear Kit – Ultra Low SDS (Cat. No. C01020010). Samples were sonicated for 5-10-15 cycles of 30” ON/30” OFF as indicated with Bioruptor Pico using 1.5 ml Bioruptor microtubes with caps (Cat. No. C30010016) followed by de-crosslinking and DNA purification. The fragment size was assessed using agarose gel electrophoresis. A 100 bp ladder was loaded as the size standard.</p>
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<p><strong>Figure 2. Chromatin precipitation</strong><br /> Sheared chromatin (obtained with the Chromatin EasyShear Kit – Ultra Low SDS) has been used for immunoprecipitation with H3K4me3 and IgG (negative control) antibodies. Quantitative PCR was performed with positive (GAPDH) and negative (TSH2B) control regions. The Figure 2 shows the recovery expressed as % of input (the relative amount of immunoprecipitated DNA compared to input DNA (panel A) and as enrichment fold of positive locus over negative (panel B).</p>
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<p>Did you use the Chromatin EasyShear Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>
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<p>A high quality chromatin preparation is very complex and requires a lot of optimization. Chromatin EasyShear Kit – Ultra Low SDS is an optimized solution for efficient chromatin preparation prior to ChIP. The protocol, buffers composition, SDS concentration (<0.1%) is optimized for the preparation of chromatin prior to ChIP on <strong>histones</strong>. The kit has been validated with the Bioruptor ultrasonicator for efficient chromatin shearing, leading to chromatin fragments <strong>suitable for ChIP</strong> with the preserved <strong>epitopes</strong>. The kit is validated for cells and tissues.</p>
<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>',
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<p><strong>Figure 1. Optimal chromatin shearing profile</strong><br /> HeLa cells were fixed with formaldehyde for 8 min and chromatin was prepared according to Diagenode’s Chromatin EasyShear Kit – Ultra Low SDS (Cat. No. C01020010). Samples were sonicated for 5-10-15 cycles of 30” ON/30” OFF as indicated with Bioruptor Pico using 1.5 ml Bioruptor microtubes with caps (Cat. No. C30010016) followed by de-crosslinking and DNA purification. The fragment size was assessed using agarose gel electrophoresis. A 100 bp ladder was loaded as the size standard.</p>
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<p><strong>Figure 2. Chromatin precipitation</strong><br /> Sheared chromatin (obtained with the Chromatin EasyShear Kit – Ultra Low SDS) has been used for immunoprecipitation with H3K4me3 and IgG (negative control) antibodies. Quantitative PCR was performed with positive (GAPDH) and negative (TSH2B) control regions. The Figure 2 shows the recovery expressed as % of input (the relative amount of immunoprecipitated DNA compared to input DNA (panel A) and as enrichment fold of positive locus over negative (panel B).</p>
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<li>Human: A549, A673, CD8+ T, Blood vascular endothelial cells, Lymphatic endothelial cells, fibroblasts, K562, MDA-MB231</li>
<li>Mouse: C2C12, primary HSPC, synovial fibroblasts, HeLa-S3, FACS sorted cells from embryonic kidneys, macrophages, mesodermal cells, myoblasts, NPC, salivary glands, spermatids, spermatocytes, skeletal muscle stem cells, stem cells, Th2</li>
<li>Hamster: CHO</li>
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<li>Bee – brain</li>
<li>Daphnia – whole animal</li>
<li>Horse – brain, heart, lamina, liver, lung, skeletal muscles, ovary</li>
<li>Human – Erwing sarcoma tumor samples</li>
<li>Other tissues: compatible, not tested</li>
</ul>
<p>Did you use the Chromatin EasyShear Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>
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<div class="small-12 medium-12 large-12 columns">The most important steps for a successful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, <strong>Diagenode's Bioruptor</strong><sup>®</sup> uses state-of-the-art ultrasound <strong>ACT</strong> (<strong>A</strong>daptive <strong>C</strong>avitation <strong>T</strong>echnology) to efficiently shear chromatin. ACT enables the highest chromatin quality for high IP efficiency and sensitivity for ChIP experiments with gentle yet highly effective shearing forces. Additionally, the Bioruptor<sup>®</sup> provides a precisely controlled temperature environment that preserves chromatin from heat degradation such that protein-DNA complexes are well-preserved for sensitive, unbiased, and accurate ChIP.<br /><br /> <strong>Diagenode's Bioruptor</strong><sup>®</sup> is the instrument of choice for chromatin shearing used for a number of downstream applications such as qPCR and ChIP-seq that require optimally sheared, unbiased chromatin.</div>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/applications/pico_dna_shearing_fig2.png" /></div>
<div class="small-10 medium-10 large-10 columns end small-offset-1"><small> <br /><strong>Panel A, 10 µl volume:</strong> Chromatin samples are sheared for 10, 20 and 30 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.1 ml Bioruptor® Microtubes (Cat. No. B01200041). <strong>Panel B, 100 µl volume:</strong> Chromatin samples are sheared for 10 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.65 ml Bioruptor® Microtubes (Cat. No. WA-005-0500). <strong>Panel C, 300 µl volume:</strong> Chromatin samples are sheared for 5, 10 and 15 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using using 1.5 ml Bioruptor microtubes (Cat. No. C30010016). Prior to de-crosslinking, samples are treated with RNase cocktail mixture at 37°C during 1 hour. The sheared chromatin is then de-crosslinked overnight and phenol/chloroform purified as described in the kit manual. 10 µl of DNA (equivalent of 500, 000 cells) are analyzed on a 2% agarose gel (MW corresponds to the 100 bp DNA molecular weight marker).</small></div>
<div class="small-12 medium-12 large-12 columns"><br /><br /></div>
<div class="small-12 medium-12 large-12 columns">
<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
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<div class="page" title="Page 7">
<table>
<tbody>
<tr valign="middle">
<td></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histone)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-medium-sds-100-million-cells">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p>< 0.1%</p>
</td>
<td style="text-align: center;">
<p>0.2%</p>
</td>
<td style="text-align: center;">
<p>1%</p>
</td>
<td style="text-align: center;">
<p>0.5%</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>No</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>up to 25 g of tissue</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
</table>
<p><em><span style="font-weight: 400;">Table comes from our </span><a href="https://www.diagenode.com/protocols/bioruptor-pico-chromatin-preparation-guide"><span style="font-weight: 400;">Guide for successful chromatin preparation using the Bioruptor® Pico</span></a></em></p>
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'description' => '<p>Optimal detergent concentration is required for best results with chromatin shearing. Diagenode offers four kits with different SDS concentrations that have been pre-optimized for your specific workflow requirements. Our Chromatin EasyShear Kits (previous name: Chromatin Shearing Optimization Kits) together with the Bioruptor combine efficient cell lysis and chromatin shearing leading to consistent results.</p>
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<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>
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<div class="column"><span>• Chromatin EasyShear Kit for Plant</span><span></span>
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<p><span>Learn more about Diagenode <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
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'description' => '<p><span>Ten-Eleven Translocation-2 (</span><em>TET2</em><span>) mutations drive the expansion of mutant hematopoietic stem cells (HSCs) in clonal hematopoiesis (CH). However, the precise mechanisms by which<span> </span></span><em>TET2</em><span><span> </span>mutations confer a competitive advantage to HSCs remain unclear. Here, through an epigenetic drug screen, we discovered that inhibition of disruptor of telomeric silencing 1-like (DOT1L), a H3K79 methyltransferase, selectively reduced the fitness of<span> </span></span><em>Tet2</em><span><span> </span>knockout (</span><em>Tet2</em><sup>KO</sup><span>) hematopoietic stem and progenitor cells (HSPCs). Mechanistically, we found that TET2 deficiency increased H3K79 dimethylation and expression of<span> </span></span><em>Mpl</em><span>, which encodes the thrombopoietin receptor (TPO-R). Correspondingly, TET2 deficiency was associated with a higher proportion of primitive<span> </span></span><em>Mpl</em><span>-expressing (</span><em>Mpl</em><sup>+</sup><span>) cells in the HSC compartment. Importantly, inhibition of<span> </span></span><em>Mpl</em><span><span> </span>expression or the signaling downstream of TPO-R was sufficient to reduce the competitive advantage of murine and human TET2-deficient HSPCs. Our findings demonstrate a critical role for aberrant TPO-R signaling in<span> </span></span><em>TET2</em><span><span> </span>mutation-driven CH and uncover potential therapeutic strategies against this condition.</span></p>',
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'authors' => 'Adamczyk Magdalena et al.',
'description' => '<p>Endometriosis is the cause of infertility. The eutopic endometrium of women with endometriosis showed an aberrant expression pattern of multitude genes. The role of TET1 protein in the pathogenesis of endometriosis and related infertility is not sufficiently known. Further, knowledge on TET1 transcriptional control still remains incomplete. The aim of the study was assessment of TET1 gene expression, DNA methylation and H3K27me3 level of its promoter region in eutopic endometrium of women with endometriosis and infertility. The study included 44 infertile patients with endometriosis (IWE) and 77 infertile (IW) and fertile (FW) patients without endometriosis. The research material was eutopic endometrium. The TET1 mRNA level was analyzed by qPCR. Western blot was used to evaluate the level of TET1 protein. The level of DNA methylation and H3K27me3 level of TET1 gene's promoter region were assessed using HRM and ChIP qPCR, respectively. The level of TET1 expression (TET1 mRNA; TET1 protein level) was lower in IWE during the implantation window (p < 0.001; p = 0.0329). The level of TET1 DNA methylation was higher in the secretory endometrium in mild and advanced IWE (p < 0.004; p < 0.008). H3K27me3 level did not differ between the study groups. The diminished expression of TET1 gene during the secretory phase, may account for the aberrant process of embryonic implantation in infertile endometriosis patients. DNA hypermethylation of TET1 gene is a potential relevant regulator of its expression. H3K27me3 occupancy does not affect the expression of TET1 gene in our study group.</p>',
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<p><span>The first critical step of a successful Chromatin immunoprecipitation (ChIP) experiment is the preparation of sheared chromatin. We therefore suggest to use one of our optimized shearing ChIP kits.</span></p>
<span>• Chromatin EasyShear Kit - Ultra Low SDS <br />• Chromatin EasyShear Kit - Low SDS <br />• Chromatin EasyShear Kit - High SDS </span></div>
<div class="column"><span>• Chromatin EasyShear Kit for Plant</span><span></span>
<p><span></span></p>
<p><span>Our Chromatin EasyShear kits are used in combination with the Bioruptor</span><span>® </span><span>in order to ensure a highly reproducible chromatin shearing and make sure you obtain the right fragment size needed for your experiment. Establish optimal conditions required for shearing cross-linked chromatin (protein-DNA) is usually laborious; the protocol of the Chromatin EasyShear kits is fast, easy-to-use and optimized to get the best results possible. </span></p>
<p><span>Learn more about Diagenode <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
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'description' => '<p>Previous name of the kit: <strong>Chromatin shearing optimization kit – Ultra Low SDS</strong></p>
<p>A high quality chromatin preparation is very complex and requires a lot of optimization. Chromatin EasyShear Kit – Ultra Low SDS is an optimized solution for efficient chromatin preparation prior to ChIP. The protocol, buffers composition, SDS concentration (<0.1%) is optimized for the preparation of chromatin prior to ChIP on <strong>histones</strong>. The kit has been validated with the Bioruptor ultrasonicator for efficient chromatin shearing, leading to chromatin fragments <strong>suitable for ChIP</strong> with the preserved <strong>epitopes</strong>. The kit is validated for cells and tissues.</p>
<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>',
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<li>Highly optimized protocol for chromatin preparation prior to ChIP on histones SDS concentration optimized for the workflow for histones</li>
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<li>Preserves the epitopes</li>
<li>Validated with the Bioruptor ultrasonicator</li>
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<p><strong>Figure 1. Optimal chromatin shearing profile</strong><br /> HeLa cells were fixed with formaldehyde for 8 min and chromatin was prepared according to Diagenode’s Chromatin EasyShear Kit – Ultra Low SDS (Cat. No. C01020010). Samples were sonicated for 5-10-15 cycles of 30” ON/30” OFF as indicated with Bioruptor Pico using 1.5 ml Bioruptor microtubes with caps (Cat. No. C30010016) followed by de-crosslinking and DNA purification. The fragment size was assessed using agarose gel electrophoresis. A 100 bp ladder was loaded as the size standard.</p>
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<p><strong>Figure 2. Chromatin precipitation</strong><br /> Sheared chromatin (obtained with the Chromatin EasyShear Kit – Ultra Low SDS) has been used for immunoprecipitation with H3K4me3 and IgG (negative control) antibodies. Quantitative PCR was performed with positive (GAPDH) and negative (TSH2B) control regions. The Figure 2 shows the recovery expressed as % of input (the relative amount of immunoprecipitated DNA compared to input DNA (panel A) and as enrichment fold of positive locus over negative (panel B).</p>
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<p><strong>Cell lines</strong>:</p>
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<li>Human: A549, A673, CD8+ T, Blood vascular endothelial cells, Lymphatic endothelial cells, fibroblasts, K562, MDA-MB231</li>
<li>Mouse: C2C12, primary HSPC, synovial fibroblasts, HeLa-S3, FACS sorted cells from embryonic kidneys, macrophages, mesodermal cells, myoblasts, NPC, salivary glands, spermatids, spermatocytes, skeletal muscle stem cells, stem cells, Th2</li>
<li>Hamster: CHO</li>
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<li>Horse – brain, heart, lamina, liver, lung, skeletal muscles, ovary</li>
<li>Human – Erwing sarcoma tumor samples</li>
<li>Other tissues: compatible, not tested</li>
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<p>Did you use the Chromatin EasyShear Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>
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<p>A high quality chromatin preparation is very complex and requires a lot of optimization. Chromatin EasyShear Kit – Ultra Low SDS is an optimized solution for efficient chromatin preparation prior to ChIP. The protocol, buffers composition, SDS concentration (<0.1%) is optimized for the preparation of chromatin prior to ChIP on <strong>histones</strong>. The kit has been validated with the Bioruptor ultrasonicator for efficient chromatin shearing, leading to chromatin fragments <strong>suitable for ChIP</strong> with the preserved <strong>epitopes</strong>. The kit is validated for cells and tissues.</p>
<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>',
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<p><strong>Figure 1. Optimal chromatin shearing profile</strong><br /> HeLa cells were fixed with formaldehyde for 8 min and chromatin was prepared according to Diagenode’s Chromatin EasyShear Kit – Ultra Low SDS (Cat. No. C01020010). Samples were sonicated for 5-10-15 cycles of 30” ON/30” OFF as indicated with Bioruptor Pico using 1.5 ml Bioruptor microtubes with caps (Cat. No. C30010016) followed by de-crosslinking and DNA purification. The fragment size was assessed using agarose gel electrophoresis. A 100 bp ladder was loaded as the size standard.</p>
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<p><strong>Figure 2. Chromatin precipitation</strong><br /> Sheared chromatin (obtained with the Chromatin EasyShear Kit – Ultra Low SDS) has been used for immunoprecipitation with H3K4me3 and IgG (negative control) antibodies. Quantitative PCR was performed with positive (GAPDH) and negative (TSH2B) control regions. The Figure 2 shows the recovery expressed as % of input (the relative amount of immunoprecipitated DNA compared to input DNA (panel A) and as enrichment fold of positive locus over negative (panel B).</p>
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<li>Human – Erwing sarcoma tumor samples</li>
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<div class="small-12 medium-12 large-12 columns">The most important steps for a successful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, <strong>Diagenode's Bioruptor</strong><sup>®</sup> uses state-of-the-art ultrasound <strong>ACT</strong> (<strong>A</strong>daptive <strong>C</strong>avitation <strong>T</strong>echnology) to efficiently shear chromatin. ACT enables the highest chromatin quality for high IP efficiency and sensitivity for ChIP experiments with gentle yet highly effective shearing forces. Additionally, the Bioruptor<sup>®</sup> provides a precisely controlled temperature environment that preserves chromatin from heat degradation such that protein-DNA complexes are well-preserved for sensitive, unbiased, and accurate ChIP.<br /><br /> <strong>Diagenode's Bioruptor</strong><sup>®</sup> is the instrument of choice for chromatin shearing used for a number of downstream applications such as qPCR and ChIP-seq that require optimally sheared, unbiased chromatin.</div>
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<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
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<td></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histone)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-medium-sds-100-million-cells">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p>< 0.1%</p>
</td>
<td style="text-align: center;">
<p>0.2%</p>
</td>
<td style="text-align: center;">
<p>1%</p>
</td>
<td style="text-align: center;">
<p>0.5%</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>No</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>up to 25 g of tissue</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
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<p><em><span style="font-weight: 400;">Table comes from our </span><a href="https://www.diagenode.com/protocols/bioruptor-pico-chromatin-preparation-guide"><span style="font-weight: 400;">Guide for successful chromatin preparation using the Bioruptor® Pico</span></a></em></p>
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<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>
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<p><span>The first critical step of a successful Chromatin immunoprecipitation (ChIP) experiment is the preparation of sheared chromatin. We therefore suggest to use one of our optimized shearing ChIP kits.</span></p>
<span>• Chromatin EasyShear Kit - Ultra Low SDS <br />• Chromatin EasyShear Kit - Low SDS <br />• Chromatin EasyShear Kit - High SDS </span></div>
<div class="column"><span>• Chromatin EasyShear Kit for Plant</span><span></span>
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<p><span>Our Chromatin EasyShear kits are used in combination with the Bioruptor</span><span>® </span><span>in order to ensure a highly reproducible chromatin shearing and make sure you obtain the right fragment size needed for your experiment. Establish optimal conditions required for shearing cross-linked chromatin (protein-DNA) is usually laborious; the protocol of the Chromatin EasyShear kits is fast, easy-to-use and optimized to get the best results possible. </span></p>
<p><span>Learn more about Diagenode <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
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'description' => '<p><span>Ten-Eleven Translocation-2 (</span><em>TET2</em><span>) mutations drive the expansion of mutant hematopoietic stem cells (HSCs) in clonal hematopoiesis (CH). However, the precise mechanisms by which<span> </span></span><em>TET2</em><span><span> </span>mutations confer a competitive advantage to HSCs remain unclear. Here, through an epigenetic drug screen, we discovered that inhibition of disruptor of telomeric silencing 1-like (DOT1L), a H3K79 methyltransferase, selectively reduced the fitness of<span> </span></span><em>Tet2</em><span><span> </span>knockout (</span><em>Tet2</em><sup>KO</sup><span>) hematopoietic stem and progenitor cells (HSPCs). Mechanistically, we found that TET2 deficiency increased H3K79 dimethylation and expression of<span> </span></span><em>Mpl</em><span>, which encodes the thrombopoietin receptor (TPO-R). Correspondingly, TET2 deficiency was associated with a higher proportion of primitive<span> </span></span><em>Mpl</em><span>-expressing (</span><em>Mpl</em><sup>+</sup><span>) cells in the HSC compartment. Importantly, inhibition of<span> </span></span><em>Mpl</em><span><span> </span>expression or the signaling downstream of TPO-R was sufficient to reduce the competitive advantage of murine and human TET2-deficient HSPCs. Our findings demonstrate a critical role for aberrant TPO-R signaling in<span> </span></span><em>TET2</em><span><span> </span>mutation-driven CH and uncover potential therapeutic strategies against this condition.</span></p>',
'date' => '2024-03-25',
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'name' => 'Assessment of TET1 gene expression, DNA methylation and H3K27me3level of its promoter region in eutopic endometrium of women withendometriosis and infertility.',
'authors' => 'Adamczyk Magdalena et al.',
'description' => '<p>Endometriosis is the cause of infertility. The eutopic endometrium of women with endometriosis showed an aberrant expression pattern of multitude genes. The role of TET1 protein in the pathogenesis of endometriosis and related infertility is not sufficiently known. Further, knowledge on TET1 transcriptional control still remains incomplete. The aim of the study was assessment of TET1 gene expression, DNA methylation and H3K27me3 level of its promoter region in eutopic endometrium of women with endometriosis and infertility. The study included 44 infertile patients with endometriosis (IWE) and 77 infertile (IW) and fertile (FW) patients without endometriosis. The research material was eutopic endometrium. The TET1 mRNA level was analyzed by qPCR. Western blot was used to evaluate the level of TET1 protein. The level of DNA methylation and H3K27me3 level of TET1 gene's promoter region were assessed using HRM and ChIP qPCR, respectively. The level of TET1 expression (TET1 mRNA; TET1 protein level) was lower in IWE during the implantation window (p < 0.001; p = 0.0329). The level of TET1 DNA methylation was higher in the secretory endometrium in mild and advanced IWE (p < 0.004; p < 0.008). H3K27me3 level did not differ between the study groups. The diminished expression of TET1 gene during the secretory phase, may account for the aberrant process of embryonic implantation in infertile endometriosis patients. DNA hypermethylation of TET1 gene is a potential relevant regulator of its expression. H3K27me3 occupancy does not affect the expression of TET1 gene in our study group.</p>',
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<p><span>The first critical step of a successful Chromatin immunoprecipitation (ChIP) experiment is the preparation of sheared chromatin. We therefore suggest to use one of our optimized shearing ChIP kits.</span></p>
<span>• Chromatin EasyShear Kit - Ultra Low SDS <br />• Chromatin EasyShear Kit - Low SDS <br />• Chromatin EasyShear Kit - High SDS </span></div>
<div class="column"><span>• Chromatin EasyShear Kit for Plant</span><span></span>
<p><span></span></p>
<p><span>Our Chromatin EasyShear kits are used in combination with the Bioruptor</span><span>® </span><span>in order to ensure a highly reproducible chromatin shearing and make sure you obtain the right fragment size needed for your experiment. Establish optimal conditions required for shearing cross-linked chromatin (protein-DNA) is usually laborious; the protocol of the Chromatin EasyShear kits is fast, easy-to-use and optimized to get the best results possible. </span></p>
<p><span>Learn more about Diagenode <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
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'description' => '<p>Tumor suppressors can exert pro-proliferation functions in specific contexts. In the beta human papillomavirus type 38 (HPV38) experimental model, the viral proteins E6 and E7 promote accumulation of a wild-type (WT) p53 form in human keratinocytes (HKs), promoting cellular proliferation. Inactivation of p53 by different means strongly decreases the proliferation of HPV38 E6/E7 HKs. This p53 form is phosphorylated at S392 by the double-stranded RNA-dependent protein kinase PKR, which is highly activated by HPV38. PKR-mediated S392 p53 phosphorylation promotes the formation of a p53/DNMT1 complex, which inhibits expression of integrin alpha 1 (ITGA1), a repressor of epidermal growth factor receptor (EGFR) signaling. Ectopic expression of ITGA1 in HPV38 E6/E7 HKs promotes EGFR degradation, inhibition of cellular proliferation, and cellular death. Itga1 expression was also inhibited in the skin of HPV38 transgenic mice that have an elevated susceptibility to UV-induced skin carcinogenesis. In summary, these findings reveal the existence of a specific WT p53 form that displays pro-proliferation properties.</p>',
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'description' => '<p>Previous name of the kit: <strong>Chromatin shearing optimization kit – Ultra Low SDS</strong></p>
<p>A high quality chromatin preparation is very complex and requires a lot of optimization. Chromatin EasyShear Kit – Ultra Low SDS is an optimized solution for efficient chromatin preparation prior to ChIP. The protocol, buffers composition, SDS concentration (<0.1%) is optimized for the preparation of chromatin prior to ChIP on <strong>histones</strong>. The kit has been validated with the Bioruptor ultrasonicator for efficient chromatin shearing, leading to chromatin fragments <strong>suitable for ChIP</strong> with the preserved <strong>epitopes</strong>. The kit is validated for cells and tissues.</p>
<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>',
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<p><strong>Figure 1. Optimal chromatin shearing profile</strong><br /> HeLa cells were fixed with formaldehyde for 8 min and chromatin was prepared according to Diagenode’s Chromatin EasyShear Kit – Ultra Low SDS (Cat. No. C01020010). Samples were sonicated for 5-10-15 cycles of 30” ON/30” OFF as indicated with Bioruptor Pico using 1.5 ml Bioruptor microtubes with caps (Cat. No. C30010016) followed by de-crosslinking and DNA purification. The fragment size was assessed using agarose gel electrophoresis. A 100 bp ladder was loaded as the size standard.</p>
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<p><strong>Figure 2. Chromatin precipitation</strong><br /> Sheared chromatin (obtained with the Chromatin EasyShear Kit – Ultra Low SDS) has been used for immunoprecipitation with H3K4me3 and IgG (negative control) antibodies. Quantitative PCR was performed with positive (GAPDH) and negative (TSH2B) control regions. The Figure 2 shows the recovery expressed as % of input (the relative amount of immunoprecipitated DNA compared to input DNA (panel A) and as enrichment fold of positive locus over negative (panel B).</p>
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<p>Did you use the Chromatin EasyShear Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>
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'description' => '<p>Previous name of the kit: <strong>Chromatin shearing optimization kit – Ultra Low SDS</strong></p>
<p>A high quality chromatin preparation is very complex and requires a lot of optimization. Chromatin EasyShear Kit – Ultra Low SDS is an optimized solution for efficient chromatin preparation prior to ChIP. The protocol, buffers composition, SDS concentration (<0.1%) is optimized for the preparation of chromatin prior to ChIP on <strong>histones</strong>. The kit has been validated with the Bioruptor ultrasonicator for efficient chromatin shearing, leading to chromatin fragments <strong>suitable for ChIP</strong> with the preserved <strong>epitopes</strong>. The kit is validated for cells and tissues.</p>
<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>',
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<p><strong>Figure 1. Optimal chromatin shearing profile</strong><br /> HeLa cells were fixed with formaldehyde for 8 min and chromatin was prepared according to Diagenode’s Chromatin EasyShear Kit – Ultra Low SDS (Cat. No. C01020010). Samples were sonicated for 5-10-15 cycles of 30” ON/30” OFF as indicated with Bioruptor Pico using 1.5 ml Bioruptor microtubes with caps (Cat. No. C30010016) followed by de-crosslinking and DNA purification. The fragment size was assessed using agarose gel electrophoresis. A 100 bp ladder was loaded as the size standard.</p>
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<p><strong>Figure 2. Chromatin precipitation</strong><br /> Sheared chromatin (obtained with the Chromatin EasyShear Kit – Ultra Low SDS) has been used for immunoprecipitation with H3K4me3 and IgG (negative control) antibodies. Quantitative PCR was performed with positive (GAPDH) and negative (TSH2B) control regions. The Figure 2 shows the recovery expressed as % of input (the relative amount of immunoprecipitated DNA compared to input DNA (panel A) and as enrichment fold of positive locus over negative (panel B).</p>
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<p><strong>Cell lines</strong>:</p>
<ul>
<li>Human: A549, A673, CD8+ T, Blood vascular endothelial cells, Lymphatic endothelial cells, fibroblasts, K562, MDA-MB231</li>
<li>Mouse: C2C12, primary HSPC, synovial fibroblasts, HeLa-S3, FACS sorted cells from embryonic kidneys, macrophages, mesodermal cells, myoblasts, NPC, salivary glands, spermatids, spermatocytes, skeletal muscle stem cells, stem cells, Th2</li>
<li>Hamster: CHO</li>
<li>Other cell lines/speices: compatible, not tested</li>
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<p><strong>Tissue</strong>:</p>
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<li>Bee – brain</li>
<li>Daphnia – whole animal</li>
<li>Horse – brain, heart, lamina, liver, lung, skeletal muscles, ovary</li>
<li>Human – Erwing sarcoma tumor samples</li>
<li>Other tissues: compatible, not tested</li>
</ul>
<p>Did you use the Chromatin EasyShear Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>
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<div class="small-12 medium-12 large-12 columns">The most important steps for a successful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, <strong>Diagenode's Bioruptor</strong><sup>®</sup> uses state-of-the-art ultrasound <strong>ACT</strong> (<strong>A</strong>daptive <strong>C</strong>avitation <strong>T</strong>echnology) to efficiently shear chromatin. ACT enables the highest chromatin quality for high IP efficiency and sensitivity for ChIP experiments with gentle yet highly effective shearing forces. Additionally, the Bioruptor<sup>®</sup> provides a precisely controlled temperature environment that preserves chromatin from heat degradation such that protein-DNA complexes are well-preserved for sensitive, unbiased, and accurate ChIP.<br /><br /> <strong>Diagenode's Bioruptor</strong><sup>®</sup> is the instrument of choice for chromatin shearing used for a number of downstream applications such as qPCR and ChIP-seq that require optimally sheared, unbiased chromatin.</div>
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<div class="small-10 medium-10 large-10 columns end small-offset-1"><small> <br /><strong>Panel A, 10 µl volume:</strong> Chromatin samples are sheared for 10, 20 and 30 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.1 ml Bioruptor® Microtubes (Cat. No. B01200041). <strong>Panel B, 100 µl volume:</strong> Chromatin samples are sheared for 10 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.65 ml Bioruptor® Microtubes (Cat. No. WA-005-0500). <strong>Panel C, 300 µl volume:</strong> Chromatin samples are sheared for 5, 10 and 15 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using using 1.5 ml Bioruptor microtubes (Cat. No. C30010016). Prior to de-crosslinking, samples are treated with RNase cocktail mixture at 37°C during 1 hour. The sheared chromatin is then de-crosslinked overnight and phenol/chloroform purified as described in the kit manual. 10 µl of DNA (equivalent of 500, 000 cells) are analyzed on a 2% agarose gel (MW corresponds to the 100 bp DNA molecular weight marker).</small></div>
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<div class="small-12 medium-12 large-12 columns">
<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
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<td></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histone)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-medium-sds-100-million-cells">Chromatin Shearing Kit (for Plant)</a></strong></td>
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<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p>< 0.1%</p>
</td>
<td style="text-align: center;">
<p>0.2%</p>
</td>
<td style="text-align: center;">
<p>1%</p>
</td>
<td style="text-align: center;">
<p>0.5%</p>
</td>
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<td>
<p><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p>Yes</p>
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<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>No</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>up to 25 g of tissue</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit</a></p>
</td>
</tr>
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<p><em><span style="font-weight: 400;">Table comes from our </span><a href="https://www.diagenode.com/protocols/bioruptor-pico-chromatin-preparation-guide"><span style="font-weight: 400;">Guide for successful chromatin preparation using the Bioruptor® Pico</span></a></em></p>
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'description' => '<p>Optimal detergent concentration is required for best results with chromatin shearing. Diagenode offers four kits with different SDS concentrations that have been pre-optimized for your specific workflow requirements. Our Chromatin EasyShear Kits (previous name: Chromatin Shearing Optimization Kits) together with the Bioruptor combine efficient cell lysis and chromatin shearing leading to consistent results.</p>
<p>The Chromatin EasyShear Kits are recommended for:</p>
<ul>
<li>The optimization of the chromatin shearing and/or chromatin preparation prior to any ChIP protocol</li>
<li>The optimization of the chromatin shearing of a new cell line/new sample type prior to ChIP using Diagenode’s ChIP kits</li>
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<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>
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<p><span>The first critical step of a successful Chromatin immunoprecipitation (ChIP) experiment is the preparation of sheared chromatin. We therefore suggest to use one of our optimized shearing ChIP kits.</span></p>
<span>• Chromatin EasyShear Kit - Ultra Low SDS <br />• Chromatin EasyShear Kit - Low SDS <br />• Chromatin EasyShear Kit - High SDS </span></div>
<div class="column"><span>• Chromatin EasyShear Kit for Plant</span><span></span>
<p><span></span></p>
<p><span>Our Chromatin EasyShear kits are used in combination with the Bioruptor</span><span>® </span><span>in order to ensure a highly reproducible chromatin shearing and make sure you obtain the right fragment size needed for your experiment. Establish optimal conditions required for shearing cross-linked chromatin (protein-DNA) is usually laborious; the protocol of the Chromatin EasyShear kits is fast, easy-to-use and optimized to get the best results possible. </span></p>
<p><span>Learn more about Diagenode <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
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'authors' => 'Chan S. et al.',
'description' => '<p><span>Ten-Eleven Translocation-2 (</span><em>TET2</em><span>) mutations drive the expansion of mutant hematopoietic stem cells (HSCs) in clonal hematopoiesis (CH). However, the precise mechanisms by which<span> </span></span><em>TET2</em><span><span> </span>mutations confer a competitive advantage to HSCs remain unclear. Here, through an epigenetic drug screen, we discovered that inhibition of disruptor of telomeric silencing 1-like (DOT1L), a H3K79 methyltransferase, selectively reduced the fitness of<span> </span></span><em>Tet2</em><span><span> </span>knockout (</span><em>Tet2</em><sup>KO</sup><span>) hematopoietic stem and progenitor cells (HSPCs). Mechanistically, we found that TET2 deficiency increased H3K79 dimethylation and expression of<span> </span></span><em>Mpl</em><span>, which encodes the thrombopoietin receptor (TPO-R). Correspondingly, TET2 deficiency was associated with a higher proportion of primitive<span> </span></span><em>Mpl</em><span>-expressing (</span><em>Mpl</em><sup>+</sup><span>) cells in the HSC compartment. Importantly, inhibition of<span> </span></span><em>Mpl</em><span><span> </span>expression or the signaling downstream of TPO-R was sufficient to reduce the competitive advantage of murine and human TET2-deficient HSPCs. Our findings demonstrate a critical role for aberrant TPO-R signaling in<span> </span></span><em>TET2</em><span><span> </span>mutation-driven CH and uncover potential therapeutic strategies against this condition.</span></p>',
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'authors' => 'Adamczyk Magdalena et al.',
'description' => '<p>Endometriosis is the cause of infertility. The eutopic endometrium of women with endometriosis showed an aberrant expression pattern of multitude genes. The role of TET1 protein in the pathogenesis of endometriosis and related infertility is not sufficiently known. Further, knowledge on TET1 transcriptional control still remains incomplete. The aim of the study was assessment of TET1 gene expression, DNA methylation and H3K27me3 level of its promoter region in eutopic endometrium of women with endometriosis and infertility. The study included 44 infertile patients with endometriosis (IWE) and 77 infertile (IW) and fertile (FW) patients without endometriosis. The research material was eutopic endometrium. The TET1 mRNA level was analyzed by qPCR. Western blot was used to evaluate the level of TET1 protein. The level of DNA methylation and H3K27me3 level of TET1 gene's promoter region were assessed using HRM and ChIP qPCR, respectively. The level of TET1 expression (TET1 mRNA; TET1 protein level) was lower in IWE during the implantation window (p < 0.001; p = 0.0329). The level of TET1 DNA methylation was higher in the secretory endometrium in mild and advanced IWE (p < 0.004; p < 0.008). H3K27me3 level did not differ between the study groups. The diminished expression of TET1 gene during the secretory phase, may account for the aberrant process of embryonic implantation in infertile endometriosis patients. DNA hypermethylation of TET1 gene is a potential relevant regulator of its expression. H3K27me3 occupancy does not affect the expression of TET1 gene in our study group.</p>',
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<p><span>The first critical step of a successful Chromatin immunoprecipitation (ChIP) experiment is the preparation of sheared chromatin. We therefore suggest to use one of our optimized shearing ChIP kits.</span></p>
<span>• Chromatin EasyShear Kit - Ultra Low SDS <br />• Chromatin EasyShear Kit - Low SDS <br />• Chromatin EasyShear Kit - High SDS </span></div>
<div class="column"><span>• Chromatin EasyShear Kit for Plant</span><span></span>
<p><span></span></p>
<p><span>Our Chromatin EasyShear kits are used in combination with the Bioruptor</span><span>® </span><span>in order to ensure a highly reproducible chromatin shearing and make sure you obtain the right fragment size needed for your experiment. Establish optimal conditions required for shearing cross-linked chromatin (protein-DNA) is usually laborious; the protocol of the Chromatin EasyShear kits is fast, easy-to-use and optimized to get the best results possible. </span></p>
<p><span>Learn more about Diagenode <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
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<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>',
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<p>Did you use the Chromatin EasyShear Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>
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<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>',
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<p><strong>Cell lines</strong>:</p>
<ul>
<li>Human: A549, A673, CD8+ T, Blood vascular endothelial cells, Lymphatic endothelial cells, fibroblasts, K562, MDA-MB231</li>
<li>Mouse: C2C12, primary HSPC, synovial fibroblasts, HeLa-S3, FACS sorted cells from embryonic kidneys, macrophages, mesodermal cells, myoblasts, NPC, salivary glands, spermatids, spermatocytes, skeletal muscle stem cells, stem cells, Th2</li>
<li>Hamster: CHO</li>
<li>Other cell lines/speices: compatible, not tested</li>
</ul>
<p><strong>Tissue</strong>:</p>
<ul>
<li>Bee – brain</li>
<li>Daphnia – whole animal</li>
<li>Horse – brain, heart, lamina, liver, lung, skeletal muscles, ovary</li>
<li>Human – Erwing sarcoma tumor samples</li>
<li>Other tissues: compatible, not tested</li>
</ul>
<p>Did you use the Chromatin EasyShear Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>
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<div class="small-12 medium-12 large-12 columns">The most important steps for a successful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, <strong>Diagenode's Bioruptor</strong><sup>®</sup> uses state-of-the-art ultrasound <strong>ACT</strong> (<strong>A</strong>daptive <strong>C</strong>avitation <strong>T</strong>echnology) to efficiently shear chromatin. ACT enables the highest chromatin quality for high IP efficiency and sensitivity for ChIP experiments with gentle yet highly effective shearing forces. Additionally, the Bioruptor<sup>®</sup> provides a precisely controlled temperature environment that preserves chromatin from heat degradation such that protein-DNA complexes are well-preserved for sensitive, unbiased, and accurate ChIP.<br /><br /> <strong>Diagenode's Bioruptor</strong><sup>®</sup> is the instrument of choice for chromatin shearing used for a number of downstream applications such as qPCR and ChIP-seq that require optimally sheared, unbiased chromatin.</div>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/applications/pico_dna_shearing_fig2.png" /></div>
<div class="small-10 medium-10 large-10 columns end small-offset-1"><small> <br /><strong>Panel A, 10 µl volume:</strong> Chromatin samples are sheared for 10, 20 and 30 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.1 ml Bioruptor® Microtubes (Cat. No. B01200041). <strong>Panel B, 100 µl volume:</strong> Chromatin samples are sheared for 10 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using 0.65 ml Bioruptor® Microtubes (Cat. No. WA-005-0500). <strong>Panel C, 300 µl volume:</strong> Chromatin samples are sheared for 5, 10 and 15 cycles of 30 sec ON/30 sec OFF with the Bioruptor® Pico using using 1.5 ml Bioruptor microtubes (Cat. No. C30010016). Prior to de-crosslinking, samples are treated with RNase cocktail mixture at 37°C during 1 hour. The sheared chromatin is then de-crosslinked overnight and phenol/chloroform purified as described in the kit manual. 10 µl of DNA (equivalent of 500, 000 cells) are analyzed on a 2% agarose gel (MW corresponds to the 100 bp DNA molecular weight marker).</small></div>
<div class="small-12 medium-12 large-12 columns"><br /><br /></div>
<div class="small-12 medium-12 large-12 columns">
<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
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<tr valign="middle">
<td></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histone)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center;"><strong><a href="https://www.diagenode.com/p/chromatin-shearing-optimization-kit-medium-sds-100-million-cells">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center;">
<p>< 0.1%</p>
</td>
<td style="text-align: center;">
<p>0.2%</p>
</td>
<td style="text-align: center;">
<p>1%</p>
</td>
<td style="text-align: center;">
<p>0.5%</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
<td style="text-align: center;">
<p>No</p>
</td>
<td style="text-align: center;">
<p>Yes</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>100 million cells</p>
</td>
<td style="text-align: center;">
<p>up to 25 g of tissue</p>
</td>
</tr>
<tr valign="middle" style="background-color: #fff;">
<td>
<p><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center;">
<p><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
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<p><em><span style="font-weight: 400;">Table comes from our </span><a href="https://www.diagenode.com/protocols/bioruptor-pico-chromatin-preparation-guide"><span style="font-weight: 400;">Guide for successful chromatin preparation using the Bioruptor® Pico</span></a></em></p>
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<li>The optimization of the chromatin shearing and/or chromatin preparation prior to any ChIP protocol</li>
<li>The optimization of the chromatin shearing of a new cell line/new sample type prior to ChIP using Diagenode’s ChIP kits</li>
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<p>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</p>
<p>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></p>
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<p><span>The first critical step of a successful Chromatin immunoprecipitation (ChIP) experiment is the preparation of sheared chromatin. We therefore suggest to use one of our optimized shearing ChIP kits.</span></p>
<span>• Chromatin EasyShear Kit - Ultra Low SDS <br />• Chromatin EasyShear Kit - Low SDS <br />• Chromatin EasyShear Kit - High SDS </span></div>
<div class="column"><span>• Chromatin EasyShear Kit for Plant</span><span></span>
<p><span></span></p>
<p><span>Our Chromatin EasyShear kits are used in combination with the Bioruptor</span><span>® </span><span>in order to ensure a highly reproducible chromatin shearing and make sure you obtain the right fragment size needed for your experiment. Establish optimal conditions required for shearing cross-linked chromatin (protein-DNA) is usually laborious; the protocol of the Chromatin EasyShear kits is fast, easy-to-use and optimized to get the best results possible. </span></p>
<p><span>Learn more about Diagenode <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
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'authors' => 'Chan S. et al.',
'description' => '<p><span>Ten-Eleven Translocation-2 (</span><em>TET2</em><span>) mutations drive the expansion of mutant hematopoietic stem cells (HSCs) in clonal hematopoiesis (CH). However, the precise mechanisms by which<span> </span></span><em>TET2</em><span><span> </span>mutations confer a competitive advantage to HSCs remain unclear. Here, through an epigenetic drug screen, we discovered that inhibition of disruptor of telomeric silencing 1-like (DOT1L), a H3K79 methyltransferase, selectively reduced the fitness of<span> </span></span><em>Tet2</em><span><span> </span>knockout (</span><em>Tet2</em><sup>KO</sup><span>) hematopoietic stem and progenitor cells (HSPCs). Mechanistically, we found that TET2 deficiency increased H3K79 dimethylation and expression of<span> </span></span><em>Mpl</em><span>, which encodes the thrombopoietin receptor (TPO-R). Correspondingly, TET2 deficiency was associated with a higher proportion of primitive<span> </span></span><em>Mpl</em><span>-expressing (</span><em>Mpl</em><sup>+</sup><span>) cells in the HSC compartment. Importantly, inhibition of<span> </span></span><em>Mpl</em><span><span> </span>expression or the signaling downstream of TPO-R was sufficient to reduce the competitive advantage of murine and human TET2-deficient HSPCs. Our findings demonstrate a critical role for aberrant TPO-R signaling in<span> </span></span><em>TET2</em><span><span> </span>mutation-driven CH and uncover potential therapeutic strategies against this condition.</span></p>',
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'authors' => 'Adamczyk Magdalena et al.',
'description' => '<p>Endometriosis is the cause of infertility. The eutopic endometrium of women with endometriosis showed an aberrant expression pattern of multitude genes. The role of TET1 protein in the pathogenesis of endometriosis and related infertility is not sufficiently known. Further, knowledge on TET1 transcriptional control still remains incomplete. The aim of the study was assessment of TET1 gene expression, DNA methylation and H3K27me3 level of its promoter region in eutopic endometrium of women with endometriosis and infertility. The study included 44 infertile patients with endometriosis (IWE) and 77 infertile (IW) and fertile (FW) patients without endometriosis. The research material was eutopic endometrium. The TET1 mRNA level was analyzed by qPCR. Western blot was used to evaluate the level of TET1 protein. The level of DNA methylation and H3K27me3 level of TET1 gene's promoter region were assessed using HRM and ChIP qPCR, respectively. The level of TET1 expression (TET1 mRNA; TET1 protein level) was lower in IWE during the implantation window (p < 0.001; p = 0.0329). The level of TET1 DNA methylation was higher in the secretory endometrium in mild and advanced IWE (p < 0.004; p < 0.008). H3K27me3 level did not differ between the study groups. The diminished expression of TET1 gene during the secretory phase, may account for the aberrant process of embryonic implantation in infertile endometriosis patients. DNA hypermethylation of TET1 gene is a potential relevant regulator of its expression. H3K27me3 occupancy does not affect the expression of TET1 gene in our study group.</p>',
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<p><span>The first critical step of a successful Chromatin immunoprecipitation (ChIP) experiment is the preparation of sheared chromatin. We therefore suggest to use one of our optimized shearing ChIP kits.</span></p>
<span>• Chromatin EasyShear Kit - Ultra Low SDS <br />• Chromatin EasyShear Kit - Low SDS <br />• Chromatin EasyShear Kit - High SDS </span></div>
<div class="column"><span>• Chromatin EasyShear Kit for Plant</span><span></span>
<p><span></span></p>
<p><span>Our Chromatin EasyShear kits are used in combination with the Bioruptor</span><span>® </span><span>in order to ensure a highly reproducible chromatin shearing and make sure you obtain the right fragment size needed for your experiment. Establish optimal conditions required for shearing cross-linked chromatin (protein-DNA) is usually laborious; the protocol of the Chromatin EasyShear kits is fast, easy-to-use and optimized to get the best results possible. </span></p>
<p><span>Learn more about Diagenode <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
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'authors' => 'Romero-Medina, MC and Venuti, A and Melita, G and Robitaille, A andCeraolo, MG and Pacini, L and Sirand, C and Viarisio, D and Taverniti, Vand Gupta, P and Scalise, M and Indiveri, C and Accardi, R and Tommasino, M',
'description' => '<p>Tumor suppressors can exert pro-proliferation functions in specific contexts. In the beta human papillomavirus type 38 (HPV38) experimental model, the viral proteins E6 and E7 promote accumulation of a wild-type (WT) p53 form in human keratinocytes (HKs), promoting cellular proliferation. Inactivation of p53 by different means strongly decreases the proliferation of HPV38 E6/E7 HKs. This p53 form is phosphorylated at S392 by the double-stranded RNA-dependent protein kinase PKR, which is highly activated by HPV38. PKR-mediated S392 p53 phosphorylation promotes the formation of a p53/DNMT1 complex, which inhibits expression of integrin alpha 1 (ITGA1), a repressor of epidermal growth factor receptor (EGFR) signaling. Ectopic expression of ITGA1 in HPV38 E6/E7 HKs promotes EGFR degradation, inhibition of cellular proliferation, and cellular death. Itga1 expression was also inhibited in the skin of HPV38 transgenic mice that have an elevated susceptibility to UV-induced skin carcinogenesis. In summary, these findings reveal the existence of a specific WT p53 form that displays pro-proliferation properties.</p>',
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