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'description' => '<p>Diagenode <b>Tagmentase</b><b> – loaded </b>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 using powerful technologies such as ATAC-seq or ChIPmentation.</p><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">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>
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<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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<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-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>
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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>
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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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<p style="text-align: justify;">Diagenode’s epigenetic reagents include:</p>
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<li style="text-align: justify;"><strong>DNA methylation kits and antibodies</strong> - Validated NGS-compatible kits for MeDIP, MBD pull-down, whole genome bisulfite sequencing, and reduced representation bisulfite sequencing. Official provider for the original clone for 5-mC 33D3.</li>
<li style="text-align: justify;"><strong>ChIP and ChIP-seq kits for industry-leading specificity and sensitivity</strong> - MicroChIP/MicroPlex Kit for ChIP-seq with only 10,000 cells and the iDeal ChIP-seq Kits optimized for both transcription factors and histones. Our kits feature full reagents for ChIP-seq including control primers, control antibodies, magnetics beads, and purification reagents.</li>
<li style="text-align: justify;"><strong>Library preparation kits</strong> tailored for your specific requirements. The MicroPlex Library Preparation Kit simplifies library preparation requiring only 3 simple steps and allowing inputs of only 50 pg. </li>
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'name' => 'High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method',
'authors' => 'Cobb L. et all.',
'description' => '<p><span>Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.</span></p>',
'date' => '2024-03-22',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38517905/',
'doi' => '10.1371/journal.pone.0300865',
'modified' => '2024-03-25 11:15:06',
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'name' => 'On the identification of differentially-active transcription factors from ATAC-seq data',
'authors' => 'Gerbaldo F. et al.',
'description' => '<p><span>ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (chromVAR-limma with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs – in our case NFkB – at the protein level.</span></p>',
'date' => '2024-03-10',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.03.06.583825v2',
'doi' => 'https://doi.org/10.1101/2024.03.06.583825',
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'name' => 'Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity',
'authors' => 'Katsuda T.',
'description' => '<p><span>Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate “reprogramming” by opening new chromatin sites for expression that can attract transcription factors from the starting cell’s enhancers. Here we report that SOX4 is sufficient to initiate hepatobiliary metaplasia in the adult mouse liver, closely mimicking metaplasia initiated by toxic damage to the liver. In lineage-traced cells, we assessed the timing of SOX4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, SOX4 directly binds to and closes hepatocyte regulatory sequences via an overlapping motif with HNF4A, a hepatocyte master regulatory transcription factor. Subsequently, SOX4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.</span></p>',
'date' => '2024-02-26',
'pmid' => 'https://www.nature.com/articles/s41467-024-45939-z',
'doi' => 'https://doi.org/10.1038/s41467-024-45939-z',
'modified' => '2024-02-29 11:59:10',
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'name' => 'The ncBAF complex regulates transcription in AML through H3K27ac sensing by BRD9',
'authors' => 'Klein D.C. et al. ',
'description' => '<p><span>The non-canonical BAF complex (ncBAF) subunit BRD9 is essential for acute myeloid leukemia (AML) cell viability but has an unclear role in leukemogenesis. Because BRD9 is required for ncBAF complex assembly through its DUF3512 domain, precise bromodomain inhibition is necessary to parse the role of BRD9 as a transcriptional regulator from that of a scaffolding protein. To understand the role of BRD9 bromodomain function in regulating AML, we selected a panel of five AML cell lines with distinct driver mutations, disease classifications, and genomic aberrations and subjected these cells to short-term BRD9 bromodomain inhibition. We examined the bromodomain-dependent growth of these cell lines, identifying a dependency in AML cell lines but not HEK293T cells. To define a mechanism through which BRD9 maintains AML cell survival, we examined nascent transcription, chromatin accessibility, and ncBAF complex binding genome-wide after bromodomain inhibition. We identified extensive regulation of transcription by BRD9 bromodomain activity, including repression of myeloid maturation factors and tumor suppressor genes, while standard AML chemotherapy targets were repressed by inhibition of the BRD9 bromodomain. BRD9 bromodomain activity maintained accessible chromatin at both gene promoters and gene-distal putative enhancer regions, in a manner that qualitatively correlated with enrichment of BRD9 binding. Furthermore, we identified reduced chromatin accessibility at GATA, ETS, and AP-1 motifs and increased chromatin accessibility at SNAIL-, HIC-, and TP53-recognized motifs after BRD9 inhibition. These data suggest a role for BRD9 in regulating AML cell differentiation through modulation of accessibility at hematopoietic transcription factor binding sites.</span></p>',
'date' => '2023-12-21',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38126767/',
'doi' => '10.1158/2767-9764.CRC-23-0382',
'modified' => '2024-01-02 11:07:14',
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'id' => '4878',
'name' => 'ARID1A governs the silencing of sex-linked transcription during male meiosis in the mouse',
'authors' => 'Menon D.U. et al.',
'description' => '<p><span>We present evidence implicating the BAF (BRG1/BRM Associated Factor) chromatin remodeler in meiotic sex chromosome inactivation (MSCI). By immunofluorescence (IF), the putative BAF DNA binding subunit, ARID1A (AT-rich Interaction Domain 1a), appeared enriched on the male sex chromosomes during diplonema of meiosis I. The germ cell-specific depletion of ARID1A resulted in a pachynema arrest and failure to repress sex-linked genes, indicating a defective MSCI. Consistent with this defect, mutant sex chromosomes displayed an abnormal presence of elongating RNA polymerase II coupled with an overall increase in chromatin accessibility detectable by ATAC-seq. By investigating potential mechanisms underlying these anomalies, we identified a role for ARID1A in promoting the preferential enrichment of the histone variant, H3.3, on the sex chromosomes, a known hallmark of MSCI. Without ARID1A, the sex chromosomes appeared depleted of H3.3 at levels resembling autosomes. Higher resolution analyses by CUT&RUN revealed shifts in sex-linked H3.3 associations from discrete intergenic sites and broader gene-body domains to promoters in response to the loss of ARID1A. Several sex-linked sites displayed ectopic H3.3 occupancy that did not co-localize with DMC1 (DNA Meiotic Recombinase 1). This observation suggests a requirement for ARID1A in DMC1 localization to the asynapsed sex chromatids. We conclude that ARID1A-directed H3.3 localization influences meiotic sex chromosome gene regulation and DNA repair.</span></p>',
'date' => '2023-09-28',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2023.05.25.542290v2.abstract',
'doi' => 'https://doi.org/10.1101/2023.05.25.542290',
'modified' => '2023-11-10 14:53:09',
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'id' => '4825',
'name' => 'Zfp296 knockout enhances chromatin accessibility and induces a uniquestate of pluripotency in embryonic stem cells.',
'authors' => 'Miyazaki S. et al.',
'description' => '<p>The Zfp296 gene encodes a zinc finger-type protein. Its expression is high in mouse embryonic stem cells (ESCs) but rapidly decreases following differentiation. Zfp296-knockout (KO) ESCs grew as flat colonies, which were reverted to rounded colonies by exogenous expression of Zfp296. KO ESCs could not form teratomas when transplanted into mice but could efficiently contribute to germline-competent chimeric mice following blastocyst injection. Transcriptome analysis revealed that Zfp296 deficiency up- and down-regulates a distinct group of genes, among which Dppa3, Otx2, and Pou3f1 were markedly downregulated. Chromatin immunoprecipitation sequencing demonstrated that ZFP296 binding is predominantly seen in the vicinity of the transcription start sites (TSSs) of a number of genes, and ZFP296 was suggested to negatively regulate transcription. Consistently, chromatin accessibility assay clearly showed that ZFP296 binding reduces the accessibility of the TSS regions of target genes. Zfp296-KO ESCs showed increased histone H3K9 di- and trimethylation. Co-immunoprecipitation analyses revealed interaction of ZFP296 with G9a and GLP. These results show that ZFP296 plays essential roles in maintaining the global epigenetic state of ESCs through multiple mechanisms including activation of Dppa3, attenuation of chromatin accessibility, and repression of H3K9 methylation, but that Zfp296-KO ESCs retain a unique state of pluripotency while lacking the teratoma-forming ability.</p>',
'date' => '2023-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37488353',
'doi' => '10.1038/s42003-023-05148-8',
'modified' => '2023-08-01 13:30:58',
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'name' => 'YAP/BRD4-controlled ROR1 promotes tumor-initiating cells andhyperproliferation in pancreatic cancer.',
'authors' => 'Yamazaki M. et al.',
'description' => '<p><span>Tumor-initiating cells are major drivers of chemoresistance and attractive targets for cancer therapy, however, their identity in human pancreatic ductal adenocarcinoma (PDAC) and the key molecules underlying their traits remain poorly understood. Here, we show that a cellular subpopulation with partial epithelial-mesenchymal transition (EMT)-like signature marked by high expression of receptor tyrosine kinase-like orphan receptor 1 (ROR1) is the origin of heterogeneous tumor cells in PDAC. We demonstrate that ROR1 depletion suppresses tumor growth, recurrence after chemotherapy, and metastasis. Mechanistically, ROR1 induces the expression of Aurora kinase B (AURKB) by activating E2F through c-Myc to enhance PDAC proliferation. Furthermore, epigenomic analyses reveal that ROR1 is transcriptionally dependent on YAP/BRD4 binding at the enhancer region, and targeting this pathway reduces ROR1 expression and prevents PDAC growth. Collectively, our findings reveal a critical role for ROR1high cells as tumor-initiating cells and the functional importance of ROR1 in PDAC progression, thereby highlighting its therapeutic targetability.</span></p>',
'date' => '2023-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37096681',
'doi' => '10.15252/embj.2022112614',
'modified' => '2023-06-15 10:06:12',
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'name' => 'Analyzing genomic and epigenetic profiles in single cells by hybridtransposase (scGET-seq).',
'authors' => 'Cittaro D. et al.',
'description' => '<p>scGET-seq simultaneously profiles euchromatin and heterochromatin. scGET-seq exploits the concurrent action of transposase Tn5 and its hybrid form TnH, which targets H3K9me3 domains. Here we present a step-by-step protocol to profile single cells by scGET-seq using a 10× Chromium Controller. We describe steps for transposomes preparation and validation. We detail nuclei preparation and transposition, followed by encapsulation, library preparation, sequencing, and data analysis. For complete details on the use and execution of this protocol, please refer to Tedesco et al. (2022) and de Pretis and Cittaro (2022)..</p>',
'date' => '2023-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37000619',
'doi' => '10.1016/j.xpro.2023.102176',
'modified' => '2023-04-17 09:04:55',
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'name' => 'A neurodevelopmental epigenetic programme mediated bySMARCD3-DAB1-Reelin signalling is hijacked to promote medulloblastomametastasis.',
'authors' => 'Zou Han et al.',
'description' => '<p>How abnormal neurodevelopment relates to the tumour aggressiveness of medulloblastoma (MB), the most common type of embryonal tumour, remains elusive. Here we uncover a neurodevelopmental epigenomic programme that is hijacked to induce MB metastatic dissemination. Unsupervised analyses of integrated publicly available datasets with our newly generated data reveal that SMARCD3 (also known as BAF60C) regulates Disabled 1 (DAB1)-mediated Reelin signalling in Purkinje cell migration and MB metastasis by orchestrating cis-regulatory elements at the DAB1 locus. We further identify that a core set of transcription factors, enhancer of zeste homologue 2 (EZH2) and nuclear factor I X (NFIX), coordinates with the cis-regulatory elements at the SMARCD3 locus to form a chromatin hub to control SMARCD3 expression in the developing cerebellum and in metastatic MB. Increased SMARCD3 expression activates Reelin-DAB1-mediated Src kinase signalling, which results in a MB response to Src inhibition. These data deepen our understanding of how neurodevelopmental programming influences disease progression and provide a potential therapeutic option for patients with MB.</p>',
'date' => '2023-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36849558',
'doi' => '10.1038/s41556-023-01093-0',
'modified' => '2023-03-14 09:41:24',
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'name' => 'Physiological reprogramming in vivo mediated by Sox4 pioneer factoractivity',
'authors' => 'Katsuda T. et al.',
'description' => '<p>Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate “reprogramming” by opening new chromatin sites for expression that can attract transcription factors from the starting cell’s enhancers. Here we report that Sox4 is sufficient to initiate hepatobiliary metaplasia in the adult liver. In lineage-traced cells, we assessed the timing of Sox4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, Sox4 directly binds to and closes hepatocyte regulatory sequences via a motif it overlaps with Hnf4a, a hepatocyte master regulator. Subsequently, Sox4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.</p>',
'date' => '2023-01-01',
'pmid' => 'https://doi.org/10.1101%2F2023.02.14.528556',
'doi' => '10.1101/2023.02.14.528556',
'modified' => '2023-04-11 10:26:02',
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'name' => 'EBF1 is continuously required for stabilizing local chromatinaccessibility in pro-B cells.',
'authors' => 'Zolotarev Nikolay et al.',
'description' => '<p>The establishment of de novo chromatin accessibility in lymphoid progenitors requires the "pioneering" function of transcription factor (TF) early B cell factor 1 (EBF1), which binds to naïve chromatin and induces accessibility by recruiting the BRG1 chromatin remodeler subunit. However, it remains unclear whether the function of EBF1 is continuously required for stabilizing local chromatin accessibility. To this end, we replaced EBF1 by EBF1-FKBP in pro-B cells, allowing the rapid degradation by adding the degradation TAG13 (dTAG13) dimerizer. EBF1 degradation results in a loss of genome-wide EBF1 occupancy and EBF1-targeted BRG1 binding. Chromatin accessibility was rapidly diminished at EBF1-binding sites with a preference for sites whose occupancy requires the pioneering activity of the C-terminal domain of EBF1. Diminished chromatin accessibility correlated with altered gene expression. Thus, continuous activity of EBF1 is required for the stable maintenance of the transcriptional and epigenetic state of pro-B cells.</p>',
'date' => '2022-11-01',
'pmid' => 'https://doi.org/10.1073%2Fpnas',
'doi' => '10.1073/pnas.2210595119',
'modified' => '2023-03-07 09:07:41',
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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 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>
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<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>
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<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>
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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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<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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<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>
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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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<li style="text-align: justify;"><strong>DNA methylation kits and antibodies</strong> - Validated NGS-compatible kits for MeDIP, MBD pull-down, whole genome bisulfite sequencing, and reduced representation bisulfite sequencing. Official provider for the original clone for 5-mC 33D3.</li>
<li style="text-align: justify;"><strong>ChIP and ChIP-seq kits for industry-leading specificity and sensitivity</strong> - MicroChIP/MicroPlex Kit for ChIP-seq with only 10,000 cells and the iDeal ChIP-seq Kits optimized for both transcription factors and histones. Our kits feature full reagents for ChIP-seq including control primers, control antibodies, magnetics beads, and purification reagents.</li>
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'doi' => '10.1158/2767-9764.CRC-23-0382',
'modified' => '2024-01-02 11:07:14',
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'id' => '4878',
'name' => 'ARID1A governs the silencing of sex-linked transcription during male meiosis in the mouse',
'authors' => 'Menon D.U. et al.',
'description' => '<p><span>We present evidence implicating the BAF (BRG1/BRM Associated Factor) chromatin remodeler in meiotic sex chromosome inactivation (MSCI). By immunofluorescence (IF), the putative BAF DNA binding subunit, ARID1A (AT-rich Interaction Domain 1a), appeared enriched on the male sex chromosomes during diplonema of meiosis I. The germ cell-specific depletion of ARID1A resulted in a pachynema arrest and failure to repress sex-linked genes, indicating a defective MSCI. Consistent with this defect, mutant sex chromosomes displayed an abnormal presence of elongating RNA polymerase II coupled with an overall increase in chromatin accessibility detectable by ATAC-seq. By investigating potential mechanisms underlying these anomalies, we identified a role for ARID1A in promoting the preferential enrichment of the histone variant, H3.3, on the sex chromosomes, a known hallmark of MSCI. Without ARID1A, the sex chromosomes appeared depleted of H3.3 at levels resembling autosomes. Higher resolution analyses by CUT&RUN revealed shifts in sex-linked H3.3 associations from discrete intergenic sites and broader gene-body domains to promoters in response to the loss of ARID1A. Several sex-linked sites displayed ectopic H3.3 occupancy that did not co-localize with DMC1 (DNA Meiotic Recombinase 1). This observation suggests a requirement for ARID1A in DMC1 localization to the asynapsed sex chromatids. We conclude that ARID1A-directed H3.3 localization influences meiotic sex chromosome gene regulation and DNA repair.</span></p>',
'date' => '2023-09-28',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2023.05.25.542290v2.abstract',
'doi' => 'https://doi.org/10.1101/2023.05.25.542290',
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'name' => 'Zfp296 knockout enhances chromatin accessibility and induces a uniquestate of pluripotency in embryonic stem cells.',
'authors' => 'Miyazaki S. et al.',
'description' => '<p>The Zfp296 gene encodes a zinc finger-type protein. Its expression is high in mouse embryonic stem cells (ESCs) but rapidly decreases following differentiation. Zfp296-knockout (KO) ESCs grew as flat colonies, which were reverted to rounded colonies by exogenous expression of Zfp296. KO ESCs could not form teratomas when transplanted into mice but could efficiently contribute to germline-competent chimeric mice following blastocyst injection. Transcriptome analysis revealed that Zfp296 deficiency up- and down-regulates a distinct group of genes, among which Dppa3, Otx2, and Pou3f1 were markedly downregulated. Chromatin immunoprecipitation sequencing demonstrated that ZFP296 binding is predominantly seen in the vicinity of the transcription start sites (TSSs) of a number of genes, and ZFP296 was suggested to negatively regulate transcription. Consistently, chromatin accessibility assay clearly showed that ZFP296 binding reduces the accessibility of the TSS regions of target genes. Zfp296-KO ESCs showed increased histone H3K9 di- and trimethylation. Co-immunoprecipitation analyses revealed interaction of ZFP296 with G9a and GLP. These results show that ZFP296 plays essential roles in maintaining the global epigenetic state of ESCs through multiple mechanisms including activation of Dppa3, attenuation of chromatin accessibility, and repression of H3K9 methylation, but that Zfp296-KO ESCs retain a unique state of pluripotency while lacking the teratoma-forming ability.</p>',
'date' => '2023-07-01',
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'description' => '<p><span>Tumor-initiating cells are major drivers of chemoresistance and attractive targets for cancer therapy, however, their identity in human pancreatic ductal adenocarcinoma (PDAC) and the key molecules underlying their traits remain poorly understood. Here, we show that a cellular subpopulation with partial epithelial-mesenchymal transition (EMT)-like signature marked by high expression of receptor tyrosine kinase-like orphan receptor 1 (ROR1) is the origin of heterogeneous tumor cells in PDAC. We demonstrate that ROR1 depletion suppresses tumor growth, recurrence after chemotherapy, and metastasis. Mechanistically, ROR1 induces the expression of Aurora kinase B (AURKB) by activating E2F through c-Myc to enhance PDAC proliferation. Furthermore, epigenomic analyses reveal that ROR1 is transcriptionally dependent on YAP/BRD4 binding at the enhancer region, and targeting this pathway reduces ROR1 expression and prevents PDAC growth. Collectively, our findings reveal a critical role for ROR1high cells as tumor-initiating cells and the functional importance of ROR1 in PDAC progression, thereby highlighting its therapeutic targetability.</span></p>',
'date' => '2023-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37096681',
'doi' => '10.15252/embj.2022112614',
'modified' => '2023-06-15 10:06:12',
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'name' => 'Analyzing genomic and epigenetic profiles in single cells by hybridtransposase (scGET-seq).',
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'description' => '<p>scGET-seq simultaneously profiles euchromatin and heterochromatin. scGET-seq exploits the concurrent action of transposase Tn5 and its hybrid form TnH, which targets H3K9me3 domains. Here we present a step-by-step protocol to profile single cells by scGET-seq using a 10× Chromium Controller. We describe steps for transposomes preparation and validation. We detail nuclei preparation and transposition, followed by encapsulation, library preparation, sequencing, and data analysis. For complete details on the use and execution of this protocol, please refer to Tedesco et al. (2022) and de Pretis and Cittaro (2022)..</p>',
'date' => '2023-03-01',
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'doi' => '10.1016/j.xpro.2023.102176',
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'name' => 'A neurodevelopmental epigenetic programme mediated bySMARCD3-DAB1-Reelin signalling is hijacked to promote medulloblastomametastasis.',
'authors' => 'Zou Han et al.',
'description' => '<p>How abnormal neurodevelopment relates to the tumour aggressiveness of medulloblastoma (MB), the most common type of embryonal tumour, remains elusive. Here we uncover a neurodevelopmental epigenomic programme that is hijacked to induce MB metastatic dissemination. Unsupervised analyses of integrated publicly available datasets with our newly generated data reveal that SMARCD3 (also known as BAF60C) regulates Disabled 1 (DAB1)-mediated Reelin signalling in Purkinje cell migration and MB metastasis by orchestrating cis-regulatory elements at the DAB1 locus. We further identify that a core set of transcription factors, enhancer of zeste homologue 2 (EZH2) and nuclear factor I X (NFIX), coordinates with the cis-regulatory elements at the SMARCD3 locus to form a chromatin hub to control SMARCD3 expression in the developing cerebellum and in metastatic MB. Increased SMARCD3 expression activates Reelin-DAB1-mediated Src kinase signalling, which results in a MB response to Src inhibition. These data deepen our understanding of how neurodevelopmental programming influences disease progression and provide a potential therapeutic option for patients with MB.</p>',
'date' => '2023-02-01',
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'doi' => '10.1038/s41556-023-01093-0',
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'name' => 'Physiological reprogramming in vivo mediated by Sox4 pioneer factoractivity',
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'description' => '<p>Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate “reprogramming” by opening new chromatin sites for expression that can attract transcription factors from the starting cell’s enhancers. Here we report that Sox4 is sufficient to initiate hepatobiliary metaplasia in the adult liver. In lineage-traced cells, we assessed the timing of Sox4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, Sox4 directly binds to and closes hepatocyte regulatory sequences via a motif it overlaps with Hnf4a, a hepatocyte master regulator. Subsequently, Sox4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.</p>',
'date' => '2023-01-01',
'pmid' => 'https://doi.org/10.1101%2F2023.02.14.528556',
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'name' => 'EBF1 is continuously required for stabilizing local chromatinaccessibility in pro-B cells.',
'authors' => 'Zolotarev Nikolay et al.',
'description' => '<p>The establishment of de novo chromatin accessibility in lymphoid progenitors requires the "pioneering" function of transcription factor (TF) early B cell factor 1 (EBF1), which binds to naïve chromatin and induces accessibility by recruiting the BRG1 chromatin remodeler subunit. However, it remains unclear whether the function of EBF1 is continuously required for stabilizing local chromatin accessibility. To this end, we replaced EBF1 by EBF1-FKBP in pro-B cells, allowing the rapid degradation by adding the degradation TAG13 (dTAG13) dimerizer. EBF1 degradation results in a loss of genome-wide EBF1 occupancy and EBF1-targeted BRG1 binding. Chromatin accessibility was rapidly diminished at EBF1-binding sites with a preference for sites whose occupancy requires the pioneering activity of the C-terminal domain of EBF1. Diminished chromatin accessibility correlated with altered gene expression. Thus, continuous activity of EBF1 is required for the stable maintenance of the transcriptional and epigenetic state of pro-B cells.</p>',
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'description' => '<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>
<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>
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<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>
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<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>
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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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<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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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
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<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>
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<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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<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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<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
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<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>
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<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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<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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<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>
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'description' => '<p>Diagenode <b>Tagmentase</b><b> – loaded </b>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 using powerful technologies such as ATAC-seq or ChIPmentation.</p><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">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 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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<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig4.png" width="700" alt="purified Transposase enzymes " caption="false" /></center>
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<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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<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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<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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<p style="text-align: justify;">Diagenode’s epigenetic reagents include:</p>
<ul>
<li style="text-align: justify;"><strong>DNA methylation kits and antibodies</strong> - Validated NGS-compatible kits for MeDIP, MBD pull-down, whole genome bisulfite sequencing, and reduced representation bisulfite sequencing. Official provider for the original clone for 5-mC 33D3.</li>
<li style="text-align: justify;"><strong>ChIP and ChIP-seq kits for industry-leading specificity and sensitivity</strong> - MicroChIP/MicroPlex Kit for ChIP-seq with only 10,000 cells and the iDeal ChIP-seq Kits optimized for both transcription factors and histones. Our kits feature full reagents for ChIP-seq including control primers, control antibodies, magnetics beads, and purification reagents.</li>
<li style="text-align: justify;"><strong>Library preparation kits</strong> tailored for your specific requirements. The MicroPlex Library Preparation Kit simplifies library preparation requiring only 3 simple steps and allowing inputs of only 50 pg. </li>
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'name' => 'High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method',
'authors' => 'Cobb L. et all.',
'description' => '<p><span>Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.</span></p>',
'date' => '2024-03-22',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38517905/',
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'name' => 'On the identification of differentially-active transcription factors from ATAC-seq data',
'authors' => 'Gerbaldo F. et al.',
'description' => '<p><span>ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (chromVAR-limma with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs – in our case NFkB – at the protein level.</span></p>',
'date' => '2024-03-10',
'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.03.06.583825v2',
'doi' => 'https://doi.org/10.1101/2024.03.06.583825',
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'name' => 'Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity',
'authors' => 'Katsuda T.',
'description' => '<p><span>Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate “reprogramming” by opening new chromatin sites for expression that can attract transcription factors from the starting cell’s enhancers. Here we report that SOX4 is sufficient to initiate hepatobiliary metaplasia in the adult mouse liver, closely mimicking metaplasia initiated by toxic damage to the liver. In lineage-traced cells, we assessed the timing of SOX4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, SOX4 directly binds to and closes hepatocyte regulatory sequences via an overlapping motif with HNF4A, a hepatocyte master regulatory transcription factor. Subsequently, SOX4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.</span></p>',
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'doi' => 'https://doi.org/10.1038/s41467-024-45939-z',
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'name' => 'The ncBAF complex regulates transcription in AML through H3K27ac sensing by BRD9',
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'description' => '<p><span>The non-canonical BAF complex (ncBAF) subunit BRD9 is essential for acute myeloid leukemia (AML) cell viability but has an unclear role in leukemogenesis. Because BRD9 is required for ncBAF complex assembly through its DUF3512 domain, precise bromodomain inhibition is necessary to parse the role of BRD9 as a transcriptional regulator from that of a scaffolding protein. To understand the role of BRD9 bromodomain function in regulating AML, we selected a panel of five AML cell lines with distinct driver mutations, disease classifications, and genomic aberrations and subjected these cells to short-term BRD9 bromodomain inhibition. We examined the bromodomain-dependent growth of these cell lines, identifying a dependency in AML cell lines but not HEK293T cells. To define a mechanism through which BRD9 maintains AML cell survival, we examined nascent transcription, chromatin accessibility, and ncBAF complex binding genome-wide after bromodomain inhibition. We identified extensive regulation of transcription by BRD9 bromodomain activity, including repression of myeloid maturation factors and tumor suppressor genes, while standard AML chemotherapy targets were repressed by inhibition of the BRD9 bromodomain. BRD9 bromodomain activity maintained accessible chromatin at both gene promoters and gene-distal putative enhancer regions, in a manner that qualitatively correlated with enrichment of BRD9 binding. Furthermore, we identified reduced chromatin accessibility at GATA, ETS, and AP-1 motifs and increased chromatin accessibility at SNAIL-, HIC-, and TP53-recognized motifs after BRD9 inhibition. These data suggest a role for BRD9 in regulating AML cell differentiation through modulation of accessibility at hematopoietic transcription factor binding sites.</span></p>',
'date' => '2023-12-21',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38126767/',
'doi' => '10.1158/2767-9764.CRC-23-0382',
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'name' => 'ARID1A governs the silencing of sex-linked transcription during male meiosis in the mouse',
'authors' => 'Menon D.U. et al.',
'description' => '<p><span>We present evidence implicating the BAF (BRG1/BRM Associated Factor) chromatin remodeler in meiotic sex chromosome inactivation (MSCI). By immunofluorescence (IF), the putative BAF DNA binding subunit, ARID1A (AT-rich Interaction Domain 1a), appeared enriched on the male sex chromosomes during diplonema of meiosis I. The germ cell-specific depletion of ARID1A resulted in a pachynema arrest and failure to repress sex-linked genes, indicating a defective MSCI. Consistent with this defect, mutant sex chromosomes displayed an abnormal presence of elongating RNA polymerase II coupled with an overall increase in chromatin accessibility detectable by ATAC-seq. By investigating potential mechanisms underlying these anomalies, we identified a role for ARID1A in promoting the preferential enrichment of the histone variant, H3.3, on the sex chromosomes, a known hallmark of MSCI. Without ARID1A, the sex chromosomes appeared depleted of H3.3 at levels resembling autosomes. Higher resolution analyses by CUT&RUN revealed shifts in sex-linked H3.3 associations from discrete intergenic sites and broader gene-body domains to promoters in response to the loss of ARID1A. Several sex-linked sites displayed ectopic H3.3 occupancy that did not co-localize with DMC1 (DNA Meiotic Recombinase 1). This observation suggests a requirement for ARID1A in DMC1 localization to the asynapsed sex chromatids. We conclude that ARID1A-directed H3.3 localization influences meiotic sex chromosome gene regulation and DNA repair.</span></p>',
'date' => '2023-09-28',
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'doi' => 'https://doi.org/10.1101/2023.05.25.542290',
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'name' => 'Zfp296 knockout enhances chromatin accessibility and induces a uniquestate of pluripotency in embryonic stem cells.',
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'description' => '<p>The Zfp296 gene encodes a zinc finger-type protein. Its expression is high in mouse embryonic stem cells (ESCs) but rapidly decreases following differentiation. Zfp296-knockout (KO) ESCs grew as flat colonies, which were reverted to rounded colonies by exogenous expression of Zfp296. KO ESCs could not form teratomas when transplanted into mice but could efficiently contribute to germline-competent chimeric mice following blastocyst injection. Transcriptome analysis revealed that Zfp296 deficiency up- and down-regulates a distinct group of genes, among which Dppa3, Otx2, and Pou3f1 were markedly downregulated. Chromatin immunoprecipitation sequencing demonstrated that ZFP296 binding is predominantly seen in the vicinity of the transcription start sites (TSSs) of a number of genes, and ZFP296 was suggested to negatively regulate transcription. Consistently, chromatin accessibility assay clearly showed that ZFP296 binding reduces the accessibility of the TSS regions of target genes. Zfp296-KO ESCs showed increased histone H3K9 di- and trimethylation. Co-immunoprecipitation analyses revealed interaction of ZFP296 with G9a and GLP. These results show that ZFP296 plays essential roles in maintaining the global epigenetic state of ESCs through multiple mechanisms including activation of Dppa3, attenuation of chromatin accessibility, and repression of H3K9 methylation, but that Zfp296-KO ESCs retain a unique state of pluripotency while lacking the teratoma-forming ability.</p>',
'date' => '2023-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37488353',
'doi' => '10.1038/s42003-023-05148-8',
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'name' => 'YAP/BRD4-controlled ROR1 promotes tumor-initiating cells andhyperproliferation in pancreatic cancer.',
'authors' => 'Yamazaki M. et al.',
'description' => '<p><span>Tumor-initiating cells are major drivers of chemoresistance and attractive targets for cancer therapy, however, their identity in human pancreatic ductal adenocarcinoma (PDAC) and the key molecules underlying their traits remain poorly understood. Here, we show that a cellular subpopulation with partial epithelial-mesenchymal transition (EMT)-like signature marked by high expression of receptor tyrosine kinase-like orphan receptor 1 (ROR1) is the origin of heterogeneous tumor cells in PDAC. We demonstrate that ROR1 depletion suppresses tumor growth, recurrence after chemotherapy, and metastasis. Mechanistically, ROR1 induces the expression of Aurora kinase B (AURKB) by activating E2F through c-Myc to enhance PDAC proliferation. Furthermore, epigenomic analyses reveal that ROR1 is transcriptionally dependent on YAP/BRD4 binding at the enhancer region, and targeting this pathway reduces ROR1 expression and prevents PDAC growth. Collectively, our findings reveal a critical role for ROR1high cells as tumor-initiating cells and the functional importance of ROR1 in PDAC progression, thereby highlighting its therapeutic targetability.</span></p>',
'date' => '2023-04-01',
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'name' => 'Analyzing genomic and epigenetic profiles in single cells by hybridtransposase (scGET-seq).',
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'description' => '<p>scGET-seq simultaneously profiles euchromatin and heterochromatin. scGET-seq exploits the concurrent action of transposase Tn5 and its hybrid form TnH, which targets H3K9me3 domains. Here we present a step-by-step protocol to profile single cells by scGET-seq using a 10× Chromium Controller. We describe steps for transposomes preparation and validation. We detail nuclei preparation and transposition, followed by encapsulation, library preparation, sequencing, and data analysis. For complete details on the use and execution of this protocol, please refer to Tedesco et al. (2022) and de Pretis and Cittaro (2022)..</p>',
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'name' => 'A neurodevelopmental epigenetic programme mediated bySMARCD3-DAB1-Reelin signalling is hijacked to promote medulloblastomametastasis.',
'authors' => 'Zou Han et al.',
'description' => '<p>How abnormal neurodevelopment relates to the tumour aggressiveness of medulloblastoma (MB), the most common type of embryonal tumour, remains elusive. Here we uncover a neurodevelopmental epigenomic programme that is hijacked to induce MB metastatic dissemination. Unsupervised analyses of integrated publicly available datasets with our newly generated data reveal that SMARCD3 (also known as BAF60C) regulates Disabled 1 (DAB1)-mediated Reelin signalling in Purkinje cell migration and MB metastasis by orchestrating cis-regulatory elements at the DAB1 locus. We further identify that a core set of transcription factors, enhancer of zeste homologue 2 (EZH2) and nuclear factor I X (NFIX), coordinates with the cis-regulatory elements at the SMARCD3 locus to form a chromatin hub to control SMARCD3 expression in the developing cerebellum and in metastatic MB. Increased SMARCD3 expression activates Reelin-DAB1-mediated Src kinase signalling, which results in a MB response to Src inhibition. These data deepen our understanding of how neurodevelopmental programming influences disease progression and provide a potential therapeutic option for patients with MB.</p>',
'date' => '2023-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36849558',
'doi' => '10.1038/s41556-023-01093-0',
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'name' => 'Physiological reprogramming in vivo mediated by Sox4 pioneer factoractivity',
'authors' => 'Katsuda T. et al.',
'description' => '<p>Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate “reprogramming” by opening new chromatin sites for expression that can attract transcription factors from the starting cell’s enhancers. Here we report that Sox4 is sufficient to initiate hepatobiliary metaplasia in the adult liver. In lineage-traced cells, we assessed the timing of Sox4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, Sox4 directly binds to and closes hepatocyte regulatory sequences via a motif it overlaps with Hnf4a, a hepatocyte master regulator. Subsequently, Sox4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.</p>',
'date' => '2023-01-01',
'pmid' => 'https://doi.org/10.1101%2F2023.02.14.528556',
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'name' => 'EBF1 is continuously required for stabilizing local chromatinaccessibility in pro-B cells.',
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'description' => '<p>The establishment of de novo chromatin accessibility in lymphoid progenitors requires the "pioneering" function of transcription factor (TF) early B cell factor 1 (EBF1), which binds to naïve chromatin and induces accessibility by recruiting the BRG1 chromatin remodeler subunit. However, it remains unclear whether the function of EBF1 is continuously required for stabilizing local chromatin accessibility. To this end, we replaced EBF1 by EBF1-FKBP in pro-B cells, allowing the rapid degradation by adding the degradation TAG13 (dTAG13) dimerizer. EBF1 degradation results in a loss of genome-wide EBF1 occupancy and EBF1-targeted BRG1 binding. Chromatin accessibility was rapidly diminished at EBF1-binding sites with a preference for sites whose occupancy requires the pioneering activity of the C-terminal domain of EBF1. Diminished chromatin accessibility correlated with altered gene expression. Thus, continuous activity of EBF1 is required for the stable maintenance of the transcriptional and epigenetic state of pro-B cells.</p>',
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<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>
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<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
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<center><img src="https://www.diagenode.com/img/product/kits/tagmentase-loaded-fig1.png" width="700" alt="Tn5 transposase Enxzymes" caption="false" /></center>
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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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<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>
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'description' => '<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>
<p>Using Diagenode’s Tagmentase (Tn5 transposase) - loaded you may need also:</p>
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<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>
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<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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<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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<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>
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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>
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<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>
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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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<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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<li style="text-align: justify;"><strong>DNA methylation kits and antibodies</strong> - Validated NGS-compatible kits for MeDIP, MBD pull-down, whole genome bisulfite sequencing, and reduced representation bisulfite sequencing. Official provider for the original clone for 5-mC 33D3.</li>
<li style="text-align: justify;"><strong>ChIP and ChIP-seq kits for industry-leading specificity and sensitivity</strong> - MicroChIP/MicroPlex Kit for ChIP-seq with only 10,000 cells and the iDeal ChIP-seq Kits optimized for both transcription factors and histones. Our kits feature full reagents for ChIP-seq including control primers, control antibodies, magnetics beads, and purification reagents.</li>
<li style="text-align: justify;"><strong>Library preparation kits</strong> tailored for your specific requirements. The MicroPlex Library Preparation Kit simplifies library preparation requiring only 3 simple steps and allowing inputs of only 50 pg. </li>
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'date' => '2023-04-01',
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'description' => '<p>How abnormal neurodevelopment relates to the tumour aggressiveness of medulloblastoma (MB), the most common type of embryonal tumour, remains elusive. Here we uncover a neurodevelopmental epigenomic programme that is hijacked to induce MB metastatic dissemination. Unsupervised analyses of integrated publicly available datasets with our newly generated data reveal that SMARCD3 (also known as BAF60C) regulates Disabled 1 (DAB1)-mediated Reelin signalling in Purkinje cell migration and MB metastasis by orchestrating cis-regulatory elements at the DAB1 locus. We further identify that a core set of transcription factors, enhancer of zeste homologue 2 (EZH2) and nuclear factor I X (NFIX), coordinates with the cis-regulatory elements at the SMARCD3 locus to form a chromatin hub to control SMARCD3 expression in the developing cerebellum and in metastatic MB. Increased SMARCD3 expression activates Reelin-DAB1-mediated Src kinase signalling, which results in a MB response to Src inhibition. These data deepen our understanding of how neurodevelopmental programming influences disease progression and provide a potential therapeutic option for patients with MB.</p>',
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'description' => '<p>Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate “reprogramming” by opening new chromatin sites for expression that can attract transcription factors from the starting cell’s enhancers. Here we report that Sox4 is sufficient to initiate hepatobiliary metaplasia in the adult liver. In lineage-traced cells, we assessed the timing of Sox4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, Sox4 directly binds to and closes hepatocyte regulatory sequences via a motif it overlaps with Hnf4a, a hepatocyte master regulator. Subsequently, Sox4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.</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>
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<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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<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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<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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<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>
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<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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<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">
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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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<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>
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<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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'description' => '<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>
<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>
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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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