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<li>5-hmC, 5-mC and unmethylated DNA sequences and primer pairs</li>
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<li><strong>Fast & sensitive capture</strong> of methylated DNA</li>
<li><strong>High capture efficiency</strong></li>
<li><strong>Differential fractionation</strong> of methylated DNA by CpG density (3 eluted fractions)</li>
<li><strong>Automation compatibility</strong><strong></strong>
<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>F</strong><strong>igure 1.</strong><span> </span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
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<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
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<div class="large-12 columns">Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on a genome-wide scale. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</div>
<div class="large-12 columns"></div>
<h5 class="large-12 columns"><strong></strong></h5>
<h5 class="large-12 columns"><strong>The ChIP-seq workflow</strong></h5>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/chip-seq-diagram.png" /></div>
<div class="large-12 columns"><br />
<ol>
<li class="large-12 columns"><strong>Chromatin preparation: </strong>Crosslink chromatin-bound proteins (histones or transcription factors) to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing:</strong> Fragment chromatin by sonication to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: Capture protein-DNA complexes with <strong><a href="../categories/chip-seq-grade-antibodies">specific ChIP-seq grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: Reverse cross-links, elute, and purify </li>
<li class="large-12 columns"><strong>NGS Library Preparation</strong>: Ligate adapters and amplify IP'd material</li>
<li class="large-12 columns"><strong>Bioinformatic analysis</strong>: Perform r<span style="font-weight: 400;">ead filtering and trimming</span>, r<span style="font-weight: 400;">ead specific alignment, enrichment specific peak calling, QC metrics, multi-sample cross-comparison etc. </span></li>
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<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="../pages/which-kit-to-choose"><img alt="" src="https://www.diagenode.com/img/banners/banner-decide.png" /></a></div>
<div class="small-6 medium-6 large-6 columns"><a href="../pages/chip-kit-customizer-1"><img alt="" src="https://www.diagenode.com/img/banners/banner-customizer.png" /></a></div>
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<div class="layoutArea">
<div class="column">
<p><span>Diagenode’s Auto IPure kit v2 is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from ChIP and MeDIP (Chromatin IP and Methylated DNA IP) experiments. </span></p>
<p><span>It’s a simple and straightforward protocol that delivers pure DNA ready for any downstream application (e.g. next generation sequencing). This approach guarantees a minimal loss of DNA and reaches significantly higher yields than a column purification (see results page...). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. </span></p>
<p><span>Diagenode’s IP-Star system uses the principle of bead-based magnetic separation. Magnetic beads bound with chromatin or DNA are brought to the inner wall of the tip when a strong magnetic force is applied. This differs from other systems that collect the bound DNA on the bottom of a reaction well, resulting in cleaner assays and less carryover. </span></p>
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'name' => 'Comprehensive characterization of the epigenetic landscape in Multiple Myeloma',
'authors' => 'Elina Alaterre et al.',
'description' => '<p>Background: Human multiple myeloma (MM) cell lines (HMCLs) have been widely used to understand the<br />molecular processes that drive MM biology. Epigenetic modifications are involved in MM development,<br />progression, and drug resistance. A comprehensive characterization of the epigenetic landscape of MM would<br />advance our understanding of MM pathophysiology and may attempt to identify new therapeutic targets.<br />Methods: We performed chromatin immunoprecipitation sequencing to analyze histone mark changes<br />(H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3) on 16 HMCLs.<br />Results: Differential analysis of histone modification profiles highlighted links between histone modifications<br />and cytogenetic abnormalities or recurrent mutations. Using histone modifications associated to enhancer<br />regions, we identified super-enhancers (SE) associated with genes involved in MM biology. We also identified<br />promoters of genes enriched in H3K9me3 and H3K27me3 repressive marks associated to potential tumor<br />suppressor functions. The prognostic value of genes associated with repressive domains and SE was used to<br />build two distinct scores identifying high-risk MM patients in two independent cohorts (CoMMpass cohort; n =<br />674 and Montpellier cohort; n = 69). Finally, we explored H3K4me3 marks comparing drug-resistant and<br />-sensitive HMCLs to identify regions involved in drug resistance. From these data, we developed epigenetic<br />biomarkers based on the H3K4me3 modification predicting MM cell response to lenalidomide and histone<br />deacetylase inhibitors (HDACi).<br />Conclusions: The epigenetic landscape of MM cells represents a unique resource for future biological studies.<br />Furthermore, risk-scores based on SE and repressive regions together with epigenetic biomarkers of drug<br />response could represent new tools for precision medicine in MM.</p>',
'date' => '2022-01-16',
'pmid' => 'https://www.thno.org/v12p1715',
'doi' => '10.7150/thno.54453',
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'name' => 'EZH2 and KDM6B Expressions Are Associated with Specific EpigeneticSignatures during EMT in Non Small Cell Lung Carcinomas.',
'authors' => 'Lachat C. et al. ',
'description' => '<p>The role of Epigenetics in Epithelial Mesenchymal Transition (EMT) has recently emerged. Two epigenetic enzymes with paradoxical roles have previously been associated to EMT, EZH2 (Enhancer of Zeste 2 Polycomb Repressive Complex 2 (PRC2) Subunit), a lysine methyltranserase able to add the H3K27me3 mark, and the histone demethylase KDM6B (Lysine Demethylase 6B), which can remove the H3K27me3 mark. Nevertheless, it still remains unclear how these enzymes, with apparent opposite activities, could both promote EMT. In this study, we evaluated the function of these two enzymes using an EMT-inducible model, the lung cancer A549 cell line. ChIP-seq coupled with transcriptomic analysis showed that EZH2 and KDM6B were able to target and modulate the expression of different genes during EMT. Based on this analysis, we described INHBB, WTN5B, and ADAMTS6 as new EMT markers regulated by epigenetic modifications and directly implicated in EMT induction.</p>',
'date' => '2020-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33291363',
'doi' => '10.3390/cancers12123649',
'modified' => '2022-01-13 14:50:18',
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'name' => 'EZH2 is overexpressed in transitional preplasmablasts and is involved in human plasma cell differentiation.',
'authors' => 'Herviou L, Jourdan M, Martinez AM, Cavalli G, Moreaux J',
'description' => '<p>Plasma cells (PCs) play a major role in the defense of the host organism against pathogens. We have shown that PC generation can be modeled using multi-step culture systems that reproduce the sequential cell differentiation occurring in vivo. Using this unique model, we investigated the role of EZH2 during PC differentiation (PCD) using H3K27me3 and EZH2 ChIP-binding profiles. We then studied the effect of the inhibition of EZH2 enzymatic activity to understand how EZH2 regulates the key functions involved in PCD. EZH2 expression significantly increases in preplasmablasts with H3K27me3 mediated repression of genes involved in B cell and plasma cell identity. EZH2 was also found to be recruited to H3K27me3-free promoters of transcriptionally active genes known to regulate cell proliferation. Inhibition the catalytic activity of EZH2 resulted in B to PC transcriptional changes associated with PC maturation induction, as well as higher immunoglobulin secretion. Altogether, our data suggest that EZH2 is involved in the maintenance of preplasmablast transitory immature proliferative state that supports their amplification.</p>',
'date' => '2019-02-12',
'pmid' => 'http://www.pubmed.gov/30755708',
'doi' => '10.1038/s41375-019-0392-1',
'modified' => '2019-03-21 17:17:48',
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'id' => '3661',
'name' => 'Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues.',
'authors' => 'Amorim BR, Dos Santos PAC, de Lima CL, Andia DC, Mazzeu JF, Acevedo AC',
'description' => '<p>This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification methods are detailed. In addition, protocols for cell culture establishment and characterization from patients with inherited dental anomalies are described.</p>',
'date' => '2019-01-01',
'pmid' => 'http://www.pubmed.gov/30838595',
'doi' => '10.1007/978-1-4939-9012-2_37,',
'modified' => '2019-07-01 11:47:27',
'created' => '2019-06-21 14:55:31',
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'id' => '3552',
'name' => 'PRC2 targeting is a therapeutic strategy for EZ score defined high-risk multiple myeloma patients and overcome resistance to IMiDs.',
'authors' => 'Herviou L, Kassambara A, Boireau S, Robert N, Requirand G, Müller-Tidow C, Vincent L, Seckinger A, Goldschmidt H, Cartron G, Hose D, Cavalli G, Moreaux J',
'description' => '<p>BACKGROUND: Multiple myeloma (MM) is a malignant plasma cell disease with a poor survival, characterized by the accumulation of myeloma cells (MMCs) within the bone marrow. Epigenetic modifications in MM are associated not only with cancer development and progression, but also with drug resistance. METHODS: We identified a significant upregulation of the polycomb repressive complex 2 (PRC2) core genes in MM cells in association with proliferation. We used EPZ-6438, a specific small molecule inhibitor of EZH2 methyltransferase activity, to evaluate its effects on MM cells phenotype and gene expression prolile. RESULTS: PRC2 targeting results in growth inhibition due to cell cycle arrest and apoptosis together with polycomb, DNA methylation, TP53, and RB1 target genes induction. Resistance to EZH2 inhibitor is mediated by DNA methylation of PRC2 target genes. We also demonstrate a synergistic effect of EPZ-6438 and lenalidomide, a conventional drug used for MM treatment, activating B cell transcription factors and tumor suppressor gene expression in concert with MYC repression. We establish a gene expression-based EZ score allowing to identify poor prognosis patients that could benefit from EZH2 inhibitor treatment. CONCLUSIONS: These data suggest that PRC2 targeting in association with IMiDs could have a therapeutic interest in MM patients characterized by high EZ score values, reactivating B cell transcription factors, and tumor suppressor genes.</p>',
'date' => '2018-10-03',
'pmid' => 'http://www.pubmed.org/30285865',
'doi' => '10.1186/s13148-018-0554-4',
'modified' => '2019-03-21 16:45:55',
'created' => '2019-03-21 14:12:08',
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[maximum depth reached]
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(int) 5 => array(
'id' => '3471',
'name' => 'An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.',
'authors' => 'Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverino W, Puigdomènech P, Casacuberta JM, Garcia-Mas J',
'description' => '<p>We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net . The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species.</p>',
'date' => '2018-05-24',
'pmid' => 'http://www.pubmed.gov/29795526',
'doi' => '10.1038/s41598-018-26416-2',
'modified' => '2019-02-15 21:07:00',
'created' => '2019-02-14 15:01:22',
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'id' => '3595',
'name' => 'Reciprocal signalling by Notch-Collagen V-CALCR retains muscle stem cells in their niche.',
'authors' => 'Baghdadi MB, Castel D, Machado L, Fukada SI, Birk DE, Relaix F, Tajbakhsh S, Mourikis P',
'description' => '<p>The cell microenvironment, which is critical for stem cell maintenance, contains both cellular and non-cellular components, including secreted growth factors and the extracellular matrix. Although Notch and other signalling pathways have previously been reported to regulate quiescence of stem cells, the composition and source of molecules that maintain the stem cell niche remain largely unknown. Here we show that adult muscle satellite (stem) cells in mice produce extracellular matrix collagens to maintain quiescence in a cell-autonomous manner. Using chromatin immunoprecipitation followed by sequencing, we identified NOTCH1/RBPJ-bound regulatory elements adjacent to specific collagen genes, the expression of which is deregulated in Notch-mutant mice. Moreover, we show that Collagen V (COLV) produced by satellite cells is a critical component of the quiescent niche, as depletion of COLV by conditional deletion of the Col5a1 gene leads to anomalous cell cycle entry and gradual diminution of the stem cell pool. Notably, the interaction of COLV with satellite cells is mediated by the Calcitonin receptor, for which COLV acts as a surrogate local ligand. Systemic administration of a calcitonin derivative is sufficient to rescue the quiescence and self-renewal defects found in COLV-null satellite cells. This study reveals a Notch-COLV-Calcitonin receptor signalling cascade that maintains satellite cells in a quiescent state in a cell-autonomous fashion, and raises the possibility that similar reciprocal mechanisms act in diverse stem cell populations.</p>',
'date' => '2018-05-23',
'pmid' => 'http://www.pubmed.gov/29795344',
'doi' => '10.1038/s41586-018-0144-9',
'modified' => '2019-04-17 15:12:55',
'created' => '2019-04-16 12:25:30',
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(int) 7 => array(
'id' => '3306',
'name' => 'Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing',
'authors' => 'Staunstrup N.H. et al.',
'description' => '<p><b></b>Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest in peripheral surrogate tissues. Whereas most work has been conducted on blood, saliva is now becoming recognized as an interesting alternative due to the simple and non-invasive manner of collection allowing for self-sampling. Results: In this study we have evaluated if saliva samples are suitable for DNA methylation studies using methylated DNA immunoprecipitation coupled to next-generation sequencing (MeDIP-seq). This was done by comparing the DNA methylation profile in saliva against the benchmark profile of peripheral blood from three individuals. We show that the output, quality, and depth of paired-end 50 bp sequencing reads are comparable between saliva and peripheral blood and, moreover, that the distribution of reads along genomic regions are similar and follow canonical methylation patterns. Conclusion: In summary, we show that high-quality MeDIP-seq data can be generated using saliva, thus supporting the future use of saliva in the generation of DNA methylation information at annotated genes, non-RefSeq genes, and repetitive elements relevant to human disease.</p>',
'date' => '2017-10-19',
'pmid' => 'http://www.mdpi.com/2075-4655/1/3/14',
'doi' => '',
'modified' => '2018-01-04 09:57:38',
'created' => '2018-01-04 09:57:38',
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[maximum depth reached]
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(int) 8 => array(
'id' => '3340',
'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
'date' => '2017-06-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/',
'doi' => '',
'modified' => '2018-02-15 10:35:55',
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(int) 9 => array(
'id' => '2991',
'name' => 'Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots',
'authors' => 'Nicklas H. Staunstrup et al.',
'description' => '<p><strong>Background</strong> In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.</p>
<p><strong>Results</strong> Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.</p>
<p><strong>Conclusions</strong> In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.</p>',
'date' => '2016-07-26',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27462375',
'doi' => '10.1186/s13148-016-0242-1',
'modified' => '2016-08-03 10:40:55',
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'name' => 'H4K5 histone acetylation of BRG1 is associated with heroin administration rather than addiction',
'authors' => 'Xu L et al.',
'description' => '<p>Diacetylmorphine hydrochloride (heroin) addiction is a chronic relapsing brain disorder that is a heavy public health burden worldwide. Brm/SWI2-related gene-1 (BRG1) is a tumor suppressor gene that can influence embryogenesis and the development of the cerebellum. The current study aimed to investigate the effect of histone H4 lysine 5 (H4K5) modifications on the BRG1 gene in brain tissue of the ventral tegmental area (VTA) of heroin‑addicted rats. A total of 21 male Sprague Dawley rats were raised in a standard manner and underwent heroin self‑administration training. Rats were randomly divided into three equal groups: Group A, self-administered delivery of heroin; group B, yoked delivery of heroin; and group C, yoked delivery of saline. The VTA was harvested and subjected to chromatin immunoprecipitation (ChIP) analysis. Gene expression was evaluated by quantitative polymerase chain reaction. We calculated the recovery rate, which indicated the percentage of the total input BRG1 recovered by ChIP. Our results showed that BRG1 was less associated with H4K5 histone modification in the group of rats that underwent heroin self‑administration than in the other two groups (A vs. B, P=0.031; A vs. C, P=0.067). The recovery fold changes of the self‑administration group and the passive-administration group were significantly different from those of the group with yoked saline (A vs. C, P=0.013; B vs. C, P=0.009; A vs. B, P=0.731). The results of the current study demonstrated that H4K5 histone acetylation of BRG1 in the VTA may be associated with heroin administration, but not addiction.</p>',
'date' => '2016-07-13',
'pmid' => 'https://www.spandidos-publications.com/etm/12/3/1929',
'doi' => '',
'modified' => '2016-08-31 11:47:20',
'created' => '2016-08-31 10:33:27',
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<p><span>It’s a simple and straightforward protocol that delivers pure DNA ready for any downstream application (e.g. next generation sequencing). This approach guarantees a minimal loss of DNA and reaches significantly higher yields than a column purification (see results page...). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. </span></p>
<p><span>Diagenode’s IP-Star system uses the principle of bead-based magnetic separation. Magnetic beads bound with chromatin or DNA are brought to the inner wall of the tip when a strong magnetic force is applied. This differs from other systems that collect the bound DNA on the bottom of a reaction well, resulting in cleaner assays and less carryover. </span></p>
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'description' => '<p>Diacetylmorphine hydrochloride (heroin) addiction is a chronic relapsing brain disorder that is a heavy public health burden worldwide. Brm/SWI2-related gene-1 (BRG1) is a tumor suppressor gene that can influence embryogenesis and the development of the cerebellum. The current study aimed to investigate the effect of histone H4 lysine 5 (H4K5) modifications on the BRG1 gene in brain tissue of the ventral tegmental area (VTA) of heroin‑addicted rats. A total of 21 male Sprague Dawley rats were raised in a standard manner and underwent heroin self‑administration training. Rats were randomly divided into three equal groups: Group A, self-administered delivery of heroin; group B, yoked delivery of heroin; and group C, yoked delivery of saline. The VTA was harvested and subjected to chromatin immunoprecipitation (ChIP) analysis. Gene expression was evaluated by quantitative polymerase chain reaction. We calculated the recovery rate, which indicated the percentage of the total input BRG1 recovered by ChIP. Our results showed that BRG1 was less associated with H4K5 histone modification in the group of rats that underwent heroin self‑administration than in the other two groups (A vs. B, P=0.031; A vs. C, P=0.067). The recovery fold changes of the self‑administration group and the passive-administration group were significantly different from those of the group with yoked saline (A vs. C, P=0.013; B vs. C, P=0.009; A vs. B, P=0.731). The results of the current study demonstrated that H4K5 histone acetylation of BRG1 in the VTA may be associated with heroin administration, but not addiction.</p>',
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<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
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<div class="large-12 columns">Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on a genome-wide scale. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</div>
<div class="large-12 columns"></div>
<h5 class="large-12 columns"><strong></strong></h5>
<h5 class="large-12 columns"><strong>The ChIP-seq workflow</strong></h5>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/chip-seq-diagram.png" /></div>
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<li class="large-12 columns"><strong>Chromatin preparation: </strong>Crosslink chromatin-bound proteins (histones or transcription factors) to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing:</strong> Fragment chromatin by sonication to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: Capture protein-DNA complexes with <strong><a href="../categories/chip-seq-grade-antibodies">specific ChIP-seq grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: Reverse cross-links, elute, and purify </li>
<li class="large-12 columns"><strong>NGS Library Preparation</strong>: Ligate adapters and amplify IP'd material</li>
<li class="large-12 columns"><strong>Bioinformatic analysis</strong>: Perform r<span style="font-weight: 400;">ead filtering and trimming</span>, r<span style="font-weight: 400;">ead specific alignment, enrichment specific peak calling, QC metrics, multi-sample cross-comparison etc. </span></li>
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<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="../pages/which-kit-to-choose"><img alt="" src="https://www.diagenode.com/img/banners/banner-decide.png" /></a></div>
<div class="small-6 medium-6 large-6 columns"><a href="../pages/chip-kit-customizer-1"><img alt="" src="https://www.diagenode.com/img/banners/banner-customizer.png" /></a></div>
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<p><span>Diagenode’s Auto IPure kit v2 is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from ChIP and MeDIP (Chromatin IP and Methylated DNA IP) experiments. </span></p>
<p><span>It’s a simple and straightforward protocol that delivers pure DNA ready for any downstream application (e.g. next generation sequencing). This approach guarantees a minimal loss of DNA and reaches significantly higher yields than a column purification (see results page...). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. </span></p>
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'name' => 'Comprehensive characterization of the epigenetic landscape in Multiple Myeloma',
'authors' => 'Elina Alaterre et al.',
'description' => '<p>Background: Human multiple myeloma (MM) cell lines (HMCLs) have been widely used to understand the<br />molecular processes that drive MM biology. Epigenetic modifications are involved in MM development,<br />progression, and drug resistance. A comprehensive characterization of the epigenetic landscape of MM would<br />advance our understanding of MM pathophysiology and may attempt to identify new therapeutic targets.<br />Methods: We performed chromatin immunoprecipitation sequencing to analyze histone mark changes<br />(H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3) on 16 HMCLs.<br />Results: Differential analysis of histone modification profiles highlighted links between histone modifications<br />and cytogenetic abnormalities or recurrent mutations. Using histone modifications associated to enhancer<br />regions, we identified super-enhancers (SE) associated with genes involved in MM biology. We also identified<br />promoters of genes enriched in H3K9me3 and H3K27me3 repressive marks associated to potential tumor<br />suppressor functions. The prognostic value of genes associated with repressive domains and SE was used to<br />build two distinct scores identifying high-risk MM patients in two independent cohorts (CoMMpass cohort; n =<br />674 and Montpellier cohort; n = 69). Finally, we explored H3K4me3 marks comparing drug-resistant and<br />-sensitive HMCLs to identify regions involved in drug resistance. From these data, we developed epigenetic<br />biomarkers based on the H3K4me3 modification predicting MM cell response to lenalidomide and histone<br />deacetylase inhibitors (HDACi).<br />Conclusions: The epigenetic landscape of MM cells represents a unique resource for future biological studies.<br />Furthermore, risk-scores based on SE and repressive regions together with epigenetic biomarkers of drug<br />response could represent new tools for precision medicine in MM.</p>',
'date' => '2022-01-16',
'pmid' => 'https://www.thno.org/v12p1715',
'doi' => '10.7150/thno.54453',
'modified' => '2022-01-27 13:17:28',
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'id' => '4207',
'name' => 'EZH2 and KDM6B Expressions Are Associated with Specific EpigeneticSignatures during EMT in Non Small Cell Lung Carcinomas.',
'authors' => 'Lachat C. et al. ',
'description' => '<p>The role of Epigenetics in Epithelial Mesenchymal Transition (EMT) has recently emerged. Two epigenetic enzymes with paradoxical roles have previously been associated to EMT, EZH2 (Enhancer of Zeste 2 Polycomb Repressive Complex 2 (PRC2) Subunit), a lysine methyltranserase able to add the H3K27me3 mark, and the histone demethylase KDM6B (Lysine Demethylase 6B), which can remove the H3K27me3 mark. Nevertheless, it still remains unclear how these enzymes, with apparent opposite activities, could both promote EMT. In this study, we evaluated the function of these two enzymes using an EMT-inducible model, the lung cancer A549 cell line. ChIP-seq coupled with transcriptomic analysis showed that EZH2 and KDM6B were able to target and modulate the expression of different genes during EMT. Based on this analysis, we described INHBB, WTN5B, and ADAMTS6 as new EMT markers regulated by epigenetic modifications and directly implicated in EMT induction.</p>',
'date' => '2020-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33291363',
'doi' => '10.3390/cancers12123649',
'modified' => '2022-01-13 14:50:18',
'created' => '2021-12-06 15:53:19',
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'id' => '3563',
'name' => 'EZH2 is overexpressed in transitional preplasmablasts and is involved in human plasma cell differentiation.',
'authors' => 'Herviou L, Jourdan M, Martinez AM, Cavalli G, Moreaux J',
'description' => '<p>Plasma cells (PCs) play a major role in the defense of the host organism against pathogens. We have shown that PC generation can be modeled using multi-step culture systems that reproduce the sequential cell differentiation occurring in vivo. Using this unique model, we investigated the role of EZH2 during PC differentiation (PCD) using H3K27me3 and EZH2 ChIP-binding profiles. We then studied the effect of the inhibition of EZH2 enzymatic activity to understand how EZH2 regulates the key functions involved in PCD. EZH2 expression significantly increases in preplasmablasts with H3K27me3 mediated repression of genes involved in B cell and plasma cell identity. EZH2 was also found to be recruited to H3K27me3-free promoters of transcriptionally active genes known to regulate cell proliferation. Inhibition the catalytic activity of EZH2 resulted in B to PC transcriptional changes associated with PC maturation induction, as well as higher immunoglobulin secretion. Altogether, our data suggest that EZH2 is involved in the maintenance of preplasmablast transitory immature proliferative state that supports their amplification.</p>',
'date' => '2019-02-12',
'pmid' => 'http://www.pubmed.gov/30755708',
'doi' => '10.1038/s41375-019-0392-1',
'modified' => '2019-03-21 17:17:48',
'created' => '2019-03-21 14:12:08',
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'id' => '3661',
'name' => 'Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues.',
'authors' => 'Amorim BR, Dos Santos PAC, de Lima CL, Andia DC, Mazzeu JF, Acevedo AC',
'description' => '<p>This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification methods are detailed. In addition, protocols for cell culture establishment and characterization from patients with inherited dental anomalies are described.</p>',
'date' => '2019-01-01',
'pmid' => 'http://www.pubmed.gov/30838595',
'doi' => '10.1007/978-1-4939-9012-2_37,',
'modified' => '2019-07-01 11:47:27',
'created' => '2019-06-21 14:55:31',
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'id' => '3552',
'name' => 'PRC2 targeting is a therapeutic strategy for EZ score defined high-risk multiple myeloma patients and overcome resistance to IMiDs.',
'authors' => 'Herviou L, Kassambara A, Boireau S, Robert N, Requirand G, Müller-Tidow C, Vincent L, Seckinger A, Goldschmidt H, Cartron G, Hose D, Cavalli G, Moreaux J',
'description' => '<p>BACKGROUND: Multiple myeloma (MM) is a malignant plasma cell disease with a poor survival, characterized by the accumulation of myeloma cells (MMCs) within the bone marrow. Epigenetic modifications in MM are associated not only with cancer development and progression, but also with drug resistance. METHODS: We identified a significant upregulation of the polycomb repressive complex 2 (PRC2) core genes in MM cells in association with proliferation. We used EPZ-6438, a specific small molecule inhibitor of EZH2 methyltransferase activity, to evaluate its effects on MM cells phenotype and gene expression prolile. RESULTS: PRC2 targeting results in growth inhibition due to cell cycle arrest and apoptosis together with polycomb, DNA methylation, TP53, and RB1 target genes induction. Resistance to EZH2 inhibitor is mediated by DNA methylation of PRC2 target genes. We also demonstrate a synergistic effect of EPZ-6438 and lenalidomide, a conventional drug used for MM treatment, activating B cell transcription factors and tumor suppressor gene expression in concert with MYC repression. We establish a gene expression-based EZ score allowing to identify poor prognosis patients that could benefit from EZH2 inhibitor treatment. CONCLUSIONS: These data suggest that PRC2 targeting in association with IMiDs could have a therapeutic interest in MM patients characterized by high EZ score values, reactivating B cell transcription factors, and tumor suppressor genes.</p>',
'date' => '2018-10-03',
'pmid' => 'http://www.pubmed.org/30285865',
'doi' => '10.1186/s13148-018-0554-4',
'modified' => '2019-03-21 16:45:55',
'created' => '2019-03-21 14:12:08',
'ProductsPublication' => array(
[maximum depth reached]
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(int) 5 => array(
'id' => '3471',
'name' => 'An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.',
'authors' => 'Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverino W, Puigdomènech P, Casacuberta JM, Garcia-Mas J',
'description' => '<p>We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net . The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species.</p>',
'date' => '2018-05-24',
'pmid' => 'http://www.pubmed.gov/29795526',
'doi' => '10.1038/s41598-018-26416-2',
'modified' => '2019-02-15 21:07:00',
'created' => '2019-02-14 15:01:22',
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'id' => '3595',
'name' => 'Reciprocal signalling by Notch-Collagen V-CALCR retains muscle stem cells in their niche.',
'authors' => 'Baghdadi MB, Castel D, Machado L, Fukada SI, Birk DE, Relaix F, Tajbakhsh S, Mourikis P',
'description' => '<p>The cell microenvironment, which is critical for stem cell maintenance, contains both cellular and non-cellular components, including secreted growth factors and the extracellular matrix. Although Notch and other signalling pathways have previously been reported to regulate quiescence of stem cells, the composition and source of molecules that maintain the stem cell niche remain largely unknown. Here we show that adult muscle satellite (stem) cells in mice produce extracellular matrix collagens to maintain quiescence in a cell-autonomous manner. Using chromatin immunoprecipitation followed by sequencing, we identified NOTCH1/RBPJ-bound regulatory elements adjacent to specific collagen genes, the expression of which is deregulated in Notch-mutant mice. Moreover, we show that Collagen V (COLV) produced by satellite cells is a critical component of the quiescent niche, as depletion of COLV by conditional deletion of the Col5a1 gene leads to anomalous cell cycle entry and gradual diminution of the stem cell pool. Notably, the interaction of COLV with satellite cells is mediated by the Calcitonin receptor, for which COLV acts as a surrogate local ligand. Systemic administration of a calcitonin derivative is sufficient to rescue the quiescence and self-renewal defects found in COLV-null satellite cells. This study reveals a Notch-COLV-Calcitonin receptor signalling cascade that maintains satellite cells in a quiescent state in a cell-autonomous fashion, and raises the possibility that similar reciprocal mechanisms act in diverse stem cell populations.</p>',
'date' => '2018-05-23',
'pmid' => 'http://www.pubmed.gov/29795344',
'doi' => '10.1038/s41586-018-0144-9',
'modified' => '2019-04-17 15:12:55',
'created' => '2019-04-16 12:25:30',
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[maximum depth reached]
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(int) 7 => array(
'id' => '3306',
'name' => 'Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing',
'authors' => 'Staunstrup N.H. et al.',
'description' => '<p><b></b>Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest in peripheral surrogate tissues. Whereas most work has been conducted on blood, saliva is now becoming recognized as an interesting alternative due to the simple and non-invasive manner of collection allowing for self-sampling. Results: In this study we have evaluated if saliva samples are suitable for DNA methylation studies using methylated DNA immunoprecipitation coupled to next-generation sequencing (MeDIP-seq). This was done by comparing the DNA methylation profile in saliva against the benchmark profile of peripheral blood from three individuals. We show that the output, quality, and depth of paired-end 50 bp sequencing reads are comparable between saliva and peripheral blood and, moreover, that the distribution of reads along genomic regions are similar and follow canonical methylation patterns. Conclusion: In summary, we show that high-quality MeDIP-seq data can be generated using saliva, thus supporting the future use of saliva in the generation of DNA methylation information at annotated genes, non-RefSeq genes, and repetitive elements relevant to human disease.</p>',
'date' => '2017-10-19',
'pmid' => 'http://www.mdpi.com/2075-4655/1/3/14',
'doi' => '',
'modified' => '2018-01-04 09:57:38',
'created' => '2018-01-04 09:57:38',
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[maximum depth reached]
)
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(int) 8 => array(
'id' => '3340',
'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
'date' => '2017-06-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/',
'doi' => '',
'modified' => '2018-02-15 10:35:55',
'created' => '2018-02-15 10:35:55',
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[maximum depth reached]
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(int) 9 => array(
'id' => '2991',
'name' => 'Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots',
'authors' => 'Nicklas H. Staunstrup et al.',
'description' => '<p><strong>Background</strong> In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.</p>
<p><strong>Results</strong> Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.</p>
<p><strong>Conclusions</strong> In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.</p>',
'date' => '2016-07-26',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27462375',
'doi' => '10.1186/s13148-016-0242-1',
'modified' => '2016-08-03 10:40:55',
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'name' => 'H4K5 histone acetylation of BRG1 is associated with heroin administration rather than addiction',
'authors' => 'Xu L et al.',
'description' => '<p>Diacetylmorphine hydrochloride (heroin) addiction is a chronic relapsing brain disorder that is a heavy public health burden worldwide. Brm/SWI2-related gene-1 (BRG1) is a tumor suppressor gene that can influence embryogenesis and the development of the cerebellum. The current study aimed to investigate the effect of histone H4 lysine 5 (H4K5) modifications on the BRG1 gene in brain tissue of the ventral tegmental area (VTA) of heroin‑addicted rats. A total of 21 male Sprague Dawley rats were raised in a standard manner and underwent heroin self‑administration training. Rats were randomly divided into three equal groups: Group A, self-administered delivery of heroin; group B, yoked delivery of heroin; and group C, yoked delivery of saline. The VTA was harvested and subjected to chromatin immunoprecipitation (ChIP) analysis. Gene expression was evaluated by quantitative polymerase chain reaction. We calculated the recovery rate, which indicated the percentage of the total input BRG1 recovered by ChIP. Our results showed that BRG1 was less associated with H4K5 histone modification in the group of rats that underwent heroin self‑administration than in the other two groups (A vs. B, P=0.031; A vs. C, P=0.067). The recovery fold changes of the self‑administration group and the passive-administration group were significantly different from those of the group with yoked saline (A vs. C, P=0.013; B vs. C, P=0.009; A vs. B, P=0.731). The results of the current study demonstrated that H4K5 histone acetylation of BRG1 in the VTA may be associated with heroin administration, but not addiction.</p>',
'date' => '2016-07-13',
'pmid' => 'https://www.spandidos-publications.com/etm/12/3/1929',
'doi' => '',
'modified' => '2016-08-31 11:47:20',
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<p><span>It’s a simple and straightforward protocol that delivers pure DNA ready for any downstream application (e.g. next generation sequencing). This approach guarantees a minimal loss of DNA and reaches significantly higher yields than a column purification (see results page...). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. </span></p>
<p><span>Diagenode’s IP-Star system uses the principle of bead-based magnetic separation. Magnetic beads bound with chromatin or DNA are brought to the inner wall of the tip when a strong magnetic force is applied. This differs from other systems that collect the bound DNA on the bottom of a reaction well, resulting in cleaner assays and less carryover. </span></p>
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<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
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<div class="large-12 columns">Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on a genome-wide scale. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</div>
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<h5 class="large-12 columns"><strong></strong></h5>
<h5 class="large-12 columns"><strong>The ChIP-seq workflow</strong></h5>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/chip-seq-diagram.png" /></div>
<div class="large-12 columns"><br />
<ol>
<li class="large-12 columns"><strong>Chromatin preparation: </strong>Crosslink chromatin-bound proteins (histones or transcription factors) to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing:</strong> Fragment chromatin by sonication to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: Capture protein-DNA complexes with <strong><a href="../categories/chip-seq-grade-antibodies">specific ChIP-seq grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: Reverse cross-links, elute, and purify </li>
<li class="large-12 columns"><strong>NGS Library Preparation</strong>: Ligate adapters and amplify IP'd material</li>
<li class="large-12 columns"><strong>Bioinformatic analysis</strong>: Perform r<span style="font-weight: 400;">ead filtering and trimming</span>, r<span style="font-weight: 400;">ead specific alignment, enrichment specific peak calling, QC metrics, multi-sample cross-comparison etc. </span></li>
</ol>
</div>
</div>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
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<div class="layoutArea">
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<p><span>Diagenode’s Auto IPure kit v2 is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from ChIP and MeDIP (Chromatin IP and Methylated DNA IP) experiments. </span></p>
<p><span>It’s a simple and straightforward protocol that delivers pure DNA ready for any downstream application (e.g. next generation sequencing). This approach guarantees a minimal loss of DNA and reaches significantly higher yields than a column purification (see results page...). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. </span></p>
<p><span>Diagenode’s IP-Star system uses the principle of bead-based magnetic separation. Magnetic beads bound with chromatin or DNA are brought to the inner wall of the tip when a strong magnetic force is applied. This differs from other systems that collect the bound DNA on the bottom of a reaction well, resulting in cleaner assays and less carryover. </span></p>
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'name' => 'Comprehensive characterization of the epigenetic landscape in Multiple Myeloma',
'authors' => 'Elina Alaterre et al.',
'description' => '<p>Background: Human multiple myeloma (MM) cell lines (HMCLs) have been widely used to understand the<br />molecular processes that drive MM biology. Epigenetic modifications are involved in MM development,<br />progression, and drug resistance. A comprehensive characterization of the epigenetic landscape of MM would<br />advance our understanding of MM pathophysiology and may attempt to identify new therapeutic targets.<br />Methods: We performed chromatin immunoprecipitation sequencing to analyze histone mark changes<br />(H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3) on 16 HMCLs.<br />Results: Differential analysis of histone modification profiles highlighted links between histone modifications<br />and cytogenetic abnormalities or recurrent mutations. Using histone modifications associated to enhancer<br />regions, we identified super-enhancers (SE) associated with genes involved in MM biology. We also identified<br />promoters of genes enriched in H3K9me3 and H3K27me3 repressive marks associated to potential tumor<br />suppressor functions. The prognostic value of genes associated with repressive domains and SE was used to<br />build two distinct scores identifying high-risk MM patients in two independent cohorts (CoMMpass cohort; n =<br />674 and Montpellier cohort; n = 69). Finally, we explored H3K4me3 marks comparing drug-resistant and<br />-sensitive HMCLs to identify regions involved in drug resistance. From these data, we developed epigenetic<br />biomarkers based on the H3K4me3 modification predicting MM cell response to lenalidomide and histone<br />deacetylase inhibitors (HDACi).<br />Conclusions: The epigenetic landscape of MM cells represents a unique resource for future biological studies.<br />Furthermore, risk-scores based on SE and repressive regions together with epigenetic biomarkers of drug<br />response could represent new tools for precision medicine in MM.</p>',
'date' => '2022-01-16',
'pmid' => 'https://www.thno.org/v12p1715',
'doi' => '10.7150/thno.54453',
'modified' => '2022-01-27 13:17:28',
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'name' => 'EZH2 and KDM6B Expressions Are Associated with Specific EpigeneticSignatures during EMT in Non Small Cell Lung Carcinomas.',
'authors' => 'Lachat C. et al. ',
'description' => '<p>The role of Epigenetics in Epithelial Mesenchymal Transition (EMT) has recently emerged. Two epigenetic enzymes with paradoxical roles have previously been associated to EMT, EZH2 (Enhancer of Zeste 2 Polycomb Repressive Complex 2 (PRC2) Subunit), a lysine methyltranserase able to add the H3K27me3 mark, and the histone demethylase KDM6B (Lysine Demethylase 6B), which can remove the H3K27me3 mark. Nevertheless, it still remains unclear how these enzymes, with apparent opposite activities, could both promote EMT. In this study, we evaluated the function of these two enzymes using an EMT-inducible model, the lung cancer A549 cell line. ChIP-seq coupled with transcriptomic analysis showed that EZH2 and KDM6B were able to target and modulate the expression of different genes during EMT. Based on this analysis, we described INHBB, WTN5B, and ADAMTS6 as new EMT markers regulated by epigenetic modifications and directly implicated in EMT induction.</p>',
'date' => '2020-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33291363',
'doi' => '10.3390/cancers12123649',
'modified' => '2022-01-13 14:50:18',
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'name' => 'EZH2 is overexpressed in transitional preplasmablasts and is involved in human plasma cell differentiation.',
'authors' => 'Herviou L, Jourdan M, Martinez AM, Cavalli G, Moreaux J',
'description' => '<p>Plasma cells (PCs) play a major role in the defense of the host organism against pathogens. We have shown that PC generation can be modeled using multi-step culture systems that reproduce the sequential cell differentiation occurring in vivo. Using this unique model, we investigated the role of EZH2 during PC differentiation (PCD) using H3K27me3 and EZH2 ChIP-binding profiles. We then studied the effect of the inhibition of EZH2 enzymatic activity to understand how EZH2 regulates the key functions involved in PCD. EZH2 expression significantly increases in preplasmablasts with H3K27me3 mediated repression of genes involved in B cell and plasma cell identity. EZH2 was also found to be recruited to H3K27me3-free promoters of transcriptionally active genes known to regulate cell proliferation. Inhibition the catalytic activity of EZH2 resulted in B to PC transcriptional changes associated with PC maturation induction, as well as higher immunoglobulin secretion. Altogether, our data suggest that EZH2 is involved in the maintenance of preplasmablast transitory immature proliferative state that supports their amplification.</p>',
'date' => '2019-02-12',
'pmid' => 'http://www.pubmed.gov/30755708',
'doi' => '10.1038/s41375-019-0392-1',
'modified' => '2019-03-21 17:17:48',
'created' => '2019-03-21 14:12:08',
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(int) 3 => array(
'id' => '3661',
'name' => 'Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues.',
'authors' => 'Amorim BR, Dos Santos PAC, de Lima CL, Andia DC, Mazzeu JF, Acevedo AC',
'description' => '<p>This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification methods are detailed. In addition, protocols for cell culture establishment and characterization from patients with inherited dental anomalies are described.</p>',
'date' => '2019-01-01',
'pmid' => 'http://www.pubmed.gov/30838595',
'doi' => '10.1007/978-1-4939-9012-2_37,',
'modified' => '2019-07-01 11:47:27',
'created' => '2019-06-21 14:55:31',
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(int) 4 => array(
'id' => '3552',
'name' => 'PRC2 targeting is a therapeutic strategy for EZ score defined high-risk multiple myeloma patients and overcome resistance to IMiDs.',
'authors' => 'Herviou L, Kassambara A, Boireau S, Robert N, Requirand G, Müller-Tidow C, Vincent L, Seckinger A, Goldschmidt H, Cartron G, Hose D, Cavalli G, Moreaux J',
'description' => '<p>BACKGROUND: Multiple myeloma (MM) is a malignant plasma cell disease with a poor survival, characterized by the accumulation of myeloma cells (MMCs) within the bone marrow. Epigenetic modifications in MM are associated not only with cancer development and progression, but also with drug resistance. METHODS: We identified a significant upregulation of the polycomb repressive complex 2 (PRC2) core genes in MM cells in association with proliferation. We used EPZ-6438, a specific small molecule inhibitor of EZH2 methyltransferase activity, to evaluate its effects on MM cells phenotype and gene expression prolile. RESULTS: PRC2 targeting results in growth inhibition due to cell cycle arrest and apoptosis together with polycomb, DNA methylation, TP53, and RB1 target genes induction. Resistance to EZH2 inhibitor is mediated by DNA methylation of PRC2 target genes. We also demonstrate a synergistic effect of EPZ-6438 and lenalidomide, a conventional drug used for MM treatment, activating B cell transcription factors and tumor suppressor gene expression in concert with MYC repression. We establish a gene expression-based EZ score allowing to identify poor prognosis patients that could benefit from EZH2 inhibitor treatment. CONCLUSIONS: These data suggest that PRC2 targeting in association with IMiDs could have a therapeutic interest in MM patients characterized by high EZ score values, reactivating B cell transcription factors, and tumor suppressor genes.</p>',
'date' => '2018-10-03',
'pmid' => 'http://www.pubmed.org/30285865',
'doi' => '10.1186/s13148-018-0554-4',
'modified' => '2019-03-21 16:45:55',
'created' => '2019-03-21 14:12:08',
'ProductsPublication' => array(
[maximum depth reached]
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(int) 5 => array(
'id' => '3471',
'name' => 'An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.',
'authors' => 'Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverino W, Puigdomènech P, Casacuberta JM, Garcia-Mas J',
'description' => '<p>We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net . The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species.</p>',
'date' => '2018-05-24',
'pmid' => 'http://www.pubmed.gov/29795526',
'doi' => '10.1038/s41598-018-26416-2',
'modified' => '2019-02-15 21:07:00',
'created' => '2019-02-14 15:01:22',
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'id' => '3595',
'name' => 'Reciprocal signalling by Notch-Collagen V-CALCR retains muscle stem cells in their niche.',
'authors' => 'Baghdadi MB, Castel D, Machado L, Fukada SI, Birk DE, Relaix F, Tajbakhsh S, Mourikis P',
'description' => '<p>The cell microenvironment, which is critical for stem cell maintenance, contains both cellular and non-cellular components, including secreted growth factors and the extracellular matrix. Although Notch and other signalling pathways have previously been reported to regulate quiescence of stem cells, the composition and source of molecules that maintain the stem cell niche remain largely unknown. Here we show that adult muscle satellite (stem) cells in mice produce extracellular matrix collagens to maintain quiescence in a cell-autonomous manner. Using chromatin immunoprecipitation followed by sequencing, we identified NOTCH1/RBPJ-bound regulatory elements adjacent to specific collagen genes, the expression of which is deregulated in Notch-mutant mice. Moreover, we show that Collagen V (COLV) produced by satellite cells is a critical component of the quiescent niche, as depletion of COLV by conditional deletion of the Col5a1 gene leads to anomalous cell cycle entry and gradual diminution of the stem cell pool. Notably, the interaction of COLV with satellite cells is mediated by the Calcitonin receptor, for which COLV acts as a surrogate local ligand. Systemic administration of a calcitonin derivative is sufficient to rescue the quiescence and self-renewal defects found in COLV-null satellite cells. This study reveals a Notch-COLV-Calcitonin receptor signalling cascade that maintains satellite cells in a quiescent state in a cell-autonomous fashion, and raises the possibility that similar reciprocal mechanisms act in diverse stem cell populations.</p>',
'date' => '2018-05-23',
'pmid' => 'http://www.pubmed.gov/29795344',
'doi' => '10.1038/s41586-018-0144-9',
'modified' => '2019-04-17 15:12:55',
'created' => '2019-04-16 12:25:30',
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(int) 7 => array(
'id' => '3306',
'name' => 'Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing',
'authors' => 'Staunstrup N.H. et al.',
'description' => '<p><b></b>Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest in peripheral surrogate tissues. Whereas most work has been conducted on blood, saliva is now becoming recognized as an interesting alternative due to the simple and non-invasive manner of collection allowing for self-sampling. Results: In this study we have evaluated if saliva samples are suitable for DNA methylation studies using methylated DNA immunoprecipitation coupled to next-generation sequencing (MeDIP-seq). This was done by comparing the DNA methylation profile in saliva against the benchmark profile of peripheral blood from three individuals. We show that the output, quality, and depth of paired-end 50 bp sequencing reads are comparable between saliva and peripheral blood and, moreover, that the distribution of reads along genomic regions are similar and follow canonical methylation patterns. Conclusion: In summary, we show that high-quality MeDIP-seq data can be generated using saliva, thus supporting the future use of saliva in the generation of DNA methylation information at annotated genes, non-RefSeq genes, and repetitive elements relevant to human disease.</p>',
'date' => '2017-10-19',
'pmid' => 'http://www.mdpi.com/2075-4655/1/3/14',
'doi' => '',
'modified' => '2018-01-04 09:57:38',
'created' => '2018-01-04 09:57:38',
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(int) 8 => array(
'id' => '3340',
'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
'date' => '2017-06-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/',
'doi' => '',
'modified' => '2018-02-15 10:35:55',
'created' => '2018-02-15 10:35:55',
'ProductsPublication' => array(
[maximum depth reached]
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(int) 9 => array(
'id' => '2991',
'name' => 'Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots',
'authors' => 'Nicklas H. Staunstrup et al.',
'description' => '<p><strong>Background</strong> In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.</p>
<p><strong>Results</strong> Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.</p>
<p><strong>Conclusions</strong> In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.</p>',
'date' => '2016-07-26',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27462375',
'doi' => '10.1186/s13148-016-0242-1',
'modified' => '2016-08-03 10:40:55',
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'name' => 'H4K5 histone acetylation of BRG1 is associated with heroin administration rather than addiction',
'authors' => 'Xu L et al.',
'description' => '<p>Diacetylmorphine hydrochloride (heroin) addiction is a chronic relapsing brain disorder that is a heavy public health burden worldwide. Brm/SWI2-related gene-1 (BRG1) is a tumor suppressor gene that can influence embryogenesis and the development of the cerebellum. The current study aimed to investigate the effect of histone H4 lysine 5 (H4K5) modifications on the BRG1 gene in brain tissue of the ventral tegmental area (VTA) of heroin‑addicted rats. A total of 21 male Sprague Dawley rats were raised in a standard manner and underwent heroin self‑administration training. Rats were randomly divided into three equal groups: Group A, self-administered delivery of heroin; group B, yoked delivery of heroin; and group C, yoked delivery of saline. The VTA was harvested and subjected to chromatin immunoprecipitation (ChIP) analysis. Gene expression was evaluated by quantitative polymerase chain reaction. We calculated the recovery rate, which indicated the percentage of the total input BRG1 recovered by ChIP. Our results showed that BRG1 was less associated with H4K5 histone modification in the group of rats that underwent heroin self‑administration than in the other two groups (A vs. B, P=0.031; A vs. C, P=0.067). The recovery fold changes of the self‑administration group and the passive-administration group were significantly different from those of the group with yoked saline (A vs. C, P=0.013; B vs. C, P=0.009; A vs. B, P=0.731). The results of the current study demonstrated that H4K5 histone acetylation of BRG1 in the VTA may be associated with heroin administration, but not addiction.</p>',
'date' => '2016-07-13',
'pmid' => 'https://www.spandidos-publications.com/etm/12/3/1929',
'doi' => '',
'modified' => '2016-08-31 11:47:20',
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<p>将 <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> Auto MethylCap kit</strong> 添加至我的购物车。</p>
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<p><span>It’s a simple and straightforward protocol that delivers pure DNA ready for any downstream application (e.g. next generation sequencing). This approach guarantees a minimal loss of DNA and reaches significantly higher yields than a column purification (see results page...). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. </span></p>
<p><span>Diagenode’s IP-Star system uses the principle of bead-based magnetic separation. Magnetic beads bound with chromatin or DNA are brought to the inner wall of the tip when a strong magnetic force is applied. This differs from other systems that collect the bound DNA on the bottom of a reaction well, resulting in cleaner assays and less carryover. </span></p>
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<h3>MBD-seq allows for detection of genomic regions with different CpG density</h3>
<p><img src="https://www.diagenode.com/img/product/kits/mbd_results1.png" alt="MBD-sequencing results have been validated by bisulfite sequencing" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>F</strong><strong>igure 1.</strong><span> </span>Using the MBD approach, two methylated regions were detected in different elution fractions according to their methylated CpG density (A). Low, Medium and High refer to the sequenced DNA from different elution fractions with increasing salt concentration. Methylated patterns of these two different methylated regions were validated by bisulfite conversion assay (B).<br /><strong></strong></p>
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<p>The figure shows the conversion efficiency in TERTBS1 and CTS56 genomic regions when using 1 μg, 500ng and 100 ng of genomic DNA. Between 1 and 5 clones were analyzed for the different amounts of genomic DNA</p>
<p><img src="https://www.diagenode.com/img/product/kits/auto-premium-bisulfite-clone.png" alt="Clone" /></p>',
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'description' => '<div class="row">
<div class="large-12 columns">Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on a genome-wide scale. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</div>
<div class="large-12 columns"></div>
<h5 class="large-12 columns"><strong></strong></h5>
<h5 class="large-12 columns"><strong>The ChIP-seq workflow</strong></h5>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/chip-seq-diagram.png" /></div>
<div class="large-12 columns"><br />
<ol>
<li class="large-12 columns"><strong>Chromatin preparation: </strong>Crosslink chromatin-bound proteins (histones or transcription factors) to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing:</strong> Fragment chromatin by sonication to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: Capture protein-DNA complexes with <strong><a href="../categories/chip-seq-grade-antibodies">specific ChIP-seq grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: Reverse cross-links, elute, and purify </li>
<li class="large-12 columns"><strong>NGS Library Preparation</strong>: Ligate adapters and amplify IP'd material</li>
<li class="large-12 columns"><strong>Bioinformatic analysis</strong>: Perform r<span style="font-weight: 400;">ead filtering and trimming</span>, r<span style="font-weight: 400;">ead specific alignment, enrichment specific peak calling, QC metrics, multi-sample cross-comparison etc. </span></li>
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<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="../pages/which-kit-to-choose"><img alt="" src="https://www.diagenode.com/img/banners/banner-decide.png" /></a></div>
<div class="small-6 medium-6 large-6 columns"><a href="../pages/chip-kit-customizer-1"><img alt="" src="https://www.diagenode.com/img/banners/banner-customizer.png" /></a></div>
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'meta_title' => 'Chromatin Immunoprecipitation - ChIP-seq Kits - Dna methylation | Diagenode',
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<div class="layoutArea">
<div class="column">
<p><span>Diagenode’s Auto IPure kit v2 is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from ChIP and MeDIP (Chromatin IP and Methylated DNA IP) experiments. </span></p>
<p><span>It’s a simple and straightforward protocol that delivers pure DNA ready for any downstream application (e.g. next generation sequencing). This approach guarantees a minimal loss of DNA and reaches significantly higher yields than a column purification (see results page...). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. </span></p>
<p><span>Diagenode’s IP-Star system uses the principle of bead-based magnetic separation. Magnetic beads bound with chromatin or DNA are brought to the inner wall of the tip when a strong magnetic force is applied. This differs from other systems that collect the bound DNA on the bottom of a reaction well, resulting in cleaner assays and less carryover. </span></p>
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'name' => 'Comprehensive characterization of the epigenetic landscape in Multiple Myeloma',
'authors' => 'Elina Alaterre et al.',
'description' => '<p>Background: Human multiple myeloma (MM) cell lines (HMCLs) have been widely used to understand the<br />molecular processes that drive MM biology. Epigenetic modifications are involved in MM development,<br />progression, and drug resistance. A comprehensive characterization of the epigenetic landscape of MM would<br />advance our understanding of MM pathophysiology and may attempt to identify new therapeutic targets.<br />Methods: We performed chromatin immunoprecipitation sequencing to analyze histone mark changes<br />(H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H3K36me3) on 16 HMCLs.<br />Results: Differential analysis of histone modification profiles highlighted links between histone modifications<br />and cytogenetic abnormalities or recurrent mutations. Using histone modifications associated to enhancer<br />regions, we identified super-enhancers (SE) associated with genes involved in MM biology. We also identified<br />promoters of genes enriched in H3K9me3 and H3K27me3 repressive marks associated to potential tumor<br />suppressor functions. The prognostic value of genes associated with repressive domains and SE was used to<br />build two distinct scores identifying high-risk MM patients in two independent cohorts (CoMMpass cohort; n =<br />674 and Montpellier cohort; n = 69). Finally, we explored H3K4me3 marks comparing drug-resistant and<br />-sensitive HMCLs to identify regions involved in drug resistance. From these data, we developed epigenetic<br />biomarkers based on the H3K4me3 modification predicting MM cell response to lenalidomide and histone<br />deacetylase inhibitors (HDACi).<br />Conclusions: The epigenetic landscape of MM cells represents a unique resource for future biological studies.<br />Furthermore, risk-scores based on SE and repressive regions together with epigenetic biomarkers of drug<br />response could represent new tools for precision medicine in MM.</p>',
'date' => '2022-01-16',
'pmid' => 'https://www.thno.org/v12p1715',
'doi' => '10.7150/thno.54453',
'modified' => '2022-01-27 13:17:28',
'created' => '2022-01-27 13:14:17',
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'name' => 'EZH2 and KDM6B Expressions Are Associated with Specific EpigeneticSignatures during EMT in Non Small Cell Lung Carcinomas.',
'authors' => 'Lachat C. et al. ',
'description' => '<p>The role of Epigenetics in Epithelial Mesenchymal Transition (EMT) has recently emerged. Two epigenetic enzymes with paradoxical roles have previously been associated to EMT, EZH2 (Enhancer of Zeste 2 Polycomb Repressive Complex 2 (PRC2) Subunit), a lysine methyltranserase able to add the H3K27me3 mark, and the histone demethylase KDM6B (Lysine Demethylase 6B), which can remove the H3K27me3 mark. Nevertheless, it still remains unclear how these enzymes, with apparent opposite activities, could both promote EMT. In this study, we evaluated the function of these two enzymes using an EMT-inducible model, the lung cancer A549 cell line. ChIP-seq coupled with transcriptomic analysis showed that EZH2 and KDM6B were able to target and modulate the expression of different genes during EMT. Based on this analysis, we described INHBB, WTN5B, and ADAMTS6 as new EMT markers regulated by epigenetic modifications and directly implicated in EMT induction.</p>',
'date' => '2020-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33291363',
'doi' => '10.3390/cancers12123649',
'modified' => '2022-01-13 14:50:18',
'created' => '2021-12-06 15:53:19',
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(int) 2 => array(
'id' => '3563',
'name' => 'EZH2 is overexpressed in transitional preplasmablasts and is involved in human plasma cell differentiation.',
'authors' => 'Herviou L, Jourdan M, Martinez AM, Cavalli G, Moreaux J',
'description' => '<p>Plasma cells (PCs) play a major role in the defense of the host organism against pathogens. We have shown that PC generation can be modeled using multi-step culture systems that reproduce the sequential cell differentiation occurring in vivo. Using this unique model, we investigated the role of EZH2 during PC differentiation (PCD) using H3K27me3 and EZH2 ChIP-binding profiles. We then studied the effect of the inhibition of EZH2 enzymatic activity to understand how EZH2 regulates the key functions involved in PCD. EZH2 expression significantly increases in preplasmablasts with H3K27me3 mediated repression of genes involved in B cell and plasma cell identity. EZH2 was also found to be recruited to H3K27me3-free promoters of transcriptionally active genes known to regulate cell proliferation. Inhibition the catalytic activity of EZH2 resulted in B to PC transcriptional changes associated with PC maturation induction, as well as higher immunoglobulin secretion. Altogether, our data suggest that EZH2 is involved in the maintenance of preplasmablast transitory immature proliferative state that supports their amplification.</p>',
'date' => '2019-02-12',
'pmid' => 'http://www.pubmed.gov/30755708',
'doi' => '10.1038/s41375-019-0392-1',
'modified' => '2019-03-21 17:17:48',
'created' => '2019-03-21 14:12:08',
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(int) 3 => array(
'id' => '3661',
'name' => 'Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues.',
'authors' => 'Amorim BR, Dos Santos PAC, de Lima CL, Andia DC, Mazzeu JF, Acevedo AC',
'description' => '<p>This chapter describes methods related to the diagnosis of genetic dental diseases. Based on the present knowledge, clinical phenotyping and next-generation sequencing techniques are discussed. Methods necessary for Sanger sequencing, multiplex ligation-dependent probe amplification, and epigenetic modification methods are detailed. In addition, protocols for cell culture establishment and characterization from patients with inherited dental anomalies are described.</p>',
'date' => '2019-01-01',
'pmid' => 'http://www.pubmed.gov/30838595',
'doi' => '10.1007/978-1-4939-9012-2_37,',
'modified' => '2019-07-01 11:47:27',
'created' => '2019-06-21 14:55:31',
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(int) 4 => array(
'id' => '3552',
'name' => 'PRC2 targeting is a therapeutic strategy for EZ score defined high-risk multiple myeloma patients and overcome resistance to IMiDs.',
'authors' => 'Herviou L, Kassambara A, Boireau S, Robert N, Requirand G, Müller-Tidow C, Vincent L, Seckinger A, Goldschmidt H, Cartron G, Hose D, Cavalli G, Moreaux J',
'description' => '<p>BACKGROUND: Multiple myeloma (MM) is a malignant plasma cell disease with a poor survival, characterized by the accumulation of myeloma cells (MMCs) within the bone marrow. Epigenetic modifications in MM are associated not only with cancer development and progression, but also with drug resistance. METHODS: We identified a significant upregulation of the polycomb repressive complex 2 (PRC2) core genes in MM cells in association with proliferation. We used EPZ-6438, a specific small molecule inhibitor of EZH2 methyltransferase activity, to evaluate its effects on MM cells phenotype and gene expression prolile. RESULTS: PRC2 targeting results in growth inhibition due to cell cycle arrest and apoptosis together with polycomb, DNA methylation, TP53, and RB1 target genes induction. Resistance to EZH2 inhibitor is mediated by DNA methylation of PRC2 target genes. We also demonstrate a synergistic effect of EPZ-6438 and lenalidomide, a conventional drug used for MM treatment, activating B cell transcription factors and tumor suppressor gene expression in concert with MYC repression. We establish a gene expression-based EZ score allowing to identify poor prognosis patients that could benefit from EZH2 inhibitor treatment. CONCLUSIONS: These data suggest that PRC2 targeting in association with IMiDs could have a therapeutic interest in MM patients characterized by high EZ score values, reactivating B cell transcription factors, and tumor suppressor genes.</p>',
'date' => '2018-10-03',
'pmid' => 'http://www.pubmed.org/30285865',
'doi' => '10.1186/s13148-018-0554-4',
'modified' => '2019-03-21 16:45:55',
'created' => '2019-03-21 14:12:08',
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'id' => '3471',
'name' => 'An improved assembly and annotation of the melon (Cucumis melo L.) reference genome.',
'authors' => 'Ruggieri V, Alexiou KG, Morata J, Argyris J, Pujol M, Yano R, Nonaka S, Ezura H, Latrasse D, Boualem A, Benhamed M, Bendahmane A, Cigliano RA, Sanseverino W, Puigdomènech P, Casacuberta JM, Garcia-Mas J',
'description' => '<p>We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net . The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species.</p>',
'date' => '2018-05-24',
'pmid' => 'http://www.pubmed.gov/29795526',
'doi' => '10.1038/s41598-018-26416-2',
'modified' => '2019-02-15 21:07:00',
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'id' => '3595',
'name' => 'Reciprocal signalling by Notch-Collagen V-CALCR retains muscle stem cells in their niche.',
'authors' => 'Baghdadi MB, Castel D, Machado L, Fukada SI, Birk DE, Relaix F, Tajbakhsh S, Mourikis P',
'description' => '<p>The cell microenvironment, which is critical for stem cell maintenance, contains both cellular and non-cellular components, including secreted growth factors and the extracellular matrix. Although Notch and other signalling pathways have previously been reported to regulate quiescence of stem cells, the composition and source of molecules that maintain the stem cell niche remain largely unknown. Here we show that adult muscle satellite (stem) cells in mice produce extracellular matrix collagens to maintain quiescence in a cell-autonomous manner. Using chromatin immunoprecipitation followed by sequencing, we identified NOTCH1/RBPJ-bound regulatory elements adjacent to specific collagen genes, the expression of which is deregulated in Notch-mutant mice. Moreover, we show that Collagen V (COLV) produced by satellite cells is a critical component of the quiescent niche, as depletion of COLV by conditional deletion of the Col5a1 gene leads to anomalous cell cycle entry and gradual diminution of the stem cell pool. Notably, the interaction of COLV with satellite cells is mediated by the Calcitonin receptor, for which COLV acts as a surrogate local ligand. Systemic administration of a calcitonin derivative is sufficient to rescue the quiescence and self-renewal defects found in COLV-null satellite cells. This study reveals a Notch-COLV-Calcitonin receptor signalling cascade that maintains satellite cells in a quiescent state in a cell-autonomous fashion, and raises the possibility that similar reciprocal mechanisms act in diverse stem cell populations.</p>',
'date' => '2018-05-23',
'pmid' => 'http://www.pubmed.gov/29795344',
'doi' => '10.1038/s41586-018-0144-9',
'modified' => '2019-04-17 15:12:55',
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'name' => 'Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing',
'authors' => 'Staunstrup N.H. et al.',
'description' => '<p><b></b>Background: Interrogation of DNA methylation profiles hold promise for improved diagnostics, as well as the delineation of the aetiology for common human diseases. However, as the primary tissue of the disease is often inaccessible without complicated and inconvenient interventions, there is an increasing interest in peripheral surrogate tissues. Whereas most work has been conducted on blood, saliva is now becoming recognized as an interesting alternative due to the simple and non-invasive manner of collection allowing for self-sampling. Results: In this study we have evaluated if saliva samples are suitable for DNA methylation studies using methylated DNA immunoprecipitation coupled to next-generation sequencing (MeDIP-seq). This was done by comparing the DNA methylation profile in saliva against the benchmark profile of peripheral blood from three individuals. We show that the output, quality, and depth of paired-end 50 bp sequencing reads are comparable between saliva and peripheral blood and, moreover, that the distribution of reads along genomic regions are similar and follow canonical methylation patterns. Conclusion: In summary, we show that high-quality MeDIP-seq data can be generated using saliva, thus supporting the future use of saliva in the generation of DNA methylation information at annotated genes, non-RefSeq genes, and repetitive elements relevant to human disease.</p>',
'date' => '2017-10-19',
'pmid' => 'http://www.mdpi.com/2075-4655/1/3/14',
'doi' => '',
'modified' => '2018-01-04 09:57:38',
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'name' => 'Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato',
'authors' => 'Roldan M.V.G. et al.',
'description' => '<p>Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, <em>jointless</em> (<em>j</em>) and <em>jointless-2</em> (<em>j-2</em>), controlling pedicel abscission zone formation have been documented but only <em>j-2</em> has been extensively used in breeding. <em>J</em> was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, <em>Solyc12g038510</em>, associated with <em>j-2</em> phenotype. Targeted knockout of <em>Solyc12g038510</em>, using CRISPR/Cas9 system, validated our hypothesis. <em>Solyc12g038510</em> encodes the MADS-box protein SlMBP21. Molecular analysis of <em>j-2</em> natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a <em>Rider</em> retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of <em>J</em> and <em>J-2</em> in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that <em>J</em> is epistatic to <em>J-2</em> and that the branched inflorescences and the leafy sepals observed in accessions harboring <em>j-2</em> alleles are likely the consequences of linkage drags.</p>',
'date' => '2017-06-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493662/',
'doi' => '',
'modified' => '2018-02-15 10:35:55',
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(int) 9 => array(
'id' => '2991',
'name' => 'Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots',
'authors' => 'Nicklas H. Staunstrup et al.',
'description' => '<p><strong>Background</strong> In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.</p>
<p><strong>Results</strong> Here we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.</p>
<p><strong>Conclusions</strong> In summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.</p>',
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'date' => '2016-07-13',
'pmid' => 'https://www.spandidos-publications.com/etm/12/3/1929',
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<p><span>It’s a simple and straightforward protocol that delivers pure DNA ready for any downstream application (e.g. next generation sequencing). This approach guarantees a minimal loss of DNA and reaches significantly higher yields than a column purification (see results page...). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. </span></p>
<p><span>Diagenode’s IP-Star system uses the principle of bead-based magnetic separation. Magnetic beads bound with chromatin or DNA are brought to the inner wall of the tip when a strong magnetic force is applied. This differs from other systems that collect the bound DNA on the bottom of a reaction well, resulting in cleaner assays and less carryover. </span></p>
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