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<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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<p>Diagenode Tagmentase is a hyperactive Tn5 transposase with the potential to enhance epigenetic studies. Its ability to cut DNA and insert sequences of interest in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq, ChIPmentation, CHANGE-seq and other. The enzyme is not loaded with DNA oligos, providing flexibility of application. To ensure optimal results the concentration may be adjusted with Diagenode <a href="https://www.diagenode.com/en/p/tagmentase-dilution-buffer">Tagmentase Dilution Buffer</a> (Cat. No. C01070011), available separately.</p>
<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) you may also need:</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
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<p>Looking for loaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) - loaded</a>.</p>',
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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'description' => '<p>Diagenode Tagmentase is a hyperactive transposase with the ability to cut DNA and insert sequences of interest into any target DNA in one step. This enzyme is not loaded with DNA oligos.</p>',
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'name' => 'Combined Analysis of mRNA Expression and Open Chromatin in Microglia',
'authors' => 'Scholz R.et al.',
'description' => '<p><span>The advance of single-cell RNA-sequencing technologies in the past years has enabled unprecedented insights into the complexity and heterogeneity of microglial cell states in the homeostatic and diseased brain. This includes rather complex proteomic, metabolomic, morphological, transcriptomic, and epigenetic adaptations to external stimuli and challenges resulting in a novel concept of core microglia properties and functions. To uncover the regulatory programs facilitating the rapid transcriptomic adaptation in response to changes in the local microenvironment, the accessibility of gene bodies and gene regulatory elements can be assessed. Here, we describe the application of a previously published method for simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) on microglia nuclei isolated from frozen mouse brain tissue.</span></p>',
'date' => '2023-08-29',
'pmid' => 'https://link.springer.com/protocol/10.1007/978-1-0716-3437-0_35',
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'name' => 'Spatial epigenome-transcriptome co-profiling of mammalian tissues.',
'authors' => 'Zhang D. et al.',
'description' => '<p>Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context. However, current methods capture only one layer of omics information at a time, precluding the possibility of examining the mechanistic relationship across the central dogma of molecular biology. Here, we present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications (H3K27me3, H3K27ac or H3K4me3) and gene expression on the same tissue section at near-single-cell resolution. These were applied to embryonic and juvenile mouse brain, as well as adult human brain, to map how epigenetic mechanisms control transcriptional phenotype and cell dynamics in tissue. Although highly concordant tissue features were identified by either spatial epigenome or spatial transcriptome we also observed distinct patterns, suggesting their differential roles in defining cell states. Linking epigenome to transcriptome pixel by pixel allows the uncovering of new insights in spatial epigenetic priming, differentiation and gene regulation within the tissue architecture. These technologies are of great interest in life science and biomedical research.</p>',
'date' => '2023-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36922587',
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'description' => '<p>scGET-seq simultaneously profiles euchromatin and heterochromatin. scGET-seq exploits the concurrent action of transposase Tn5 and its hybrid form TnH, which targets H3K9me3 domains. Here we present a step-by-step protocol to profile single cells by scGET-seq using a 10× Chromium Controller. We describe steps for transposomes preparation and validation. We detail nuclei preparation and transposition, followed by encapsulation, library preparation, sequencing, and data analysis. For complete details on the use and execution of this protocol, please refer to Tedesco et al. (2022) and de Pretis and Cittaro (2022)..</p>',
'date' => '2023-03-01',
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'name' => 'Imaging Chromatin Accessibility by Assay ofTransposase-Accessible Chromatin with Visualization.',
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'description' => '<p>Chromatin accessibility is one of the fundamental structures regulating genome functions including transcription and DNA repair. Recent technological advantages to analyze chromatin accessibility begun to explore the dynamics of local chromatin structures. Here I describe protocols for Assay of Transposase-Accessible Chromatin with Visualization (ATAC-see), which allows us to analyze subnuclear localization of accessible chromatin and quantify accessible chromatin at single-cell level.</p>',
'date' => '2023-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36173568',
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'name' => 'Mouse kidney nuclear isolation and library preparation for single-cell combinatorial indexing RNA sequencing',
'authors' => 'Li Haikuo and Humphreys Benjamin D.',
'description' => '<p>Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq3) enables high-throughput single-nucleus transcriptomic profiling of multiple samples in one experiment. Here, we describe an optimized protocol of mouse kidney nuclei isolation and sci-RNA-seq3 library preparation. The use of a dounce tissue homogenizer enables nuclei extraction with high yield. Fixed nuclei are processed for sci-RNA-seq3, and self-loaded transposome Tn5 is used for tagmentation in library generation. The step-by-step protocol allows researchers to generate scalable single-cell transcriptomic data with common laboratory supplies at low cost.</p>',
'date' => '2022-12-01',
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'description' => '<p>Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that has historically exhibited variable performance on different tissues, as well as lower sensitivity than alternative methods. Here, we report a simplified, optimized version of the sci-RNA-seq protocol with three rounds of split-pool indexing that is faster, more robust and more sensitive and has a higher yield than the original protocol, with reagent costs on the order of 1 cent per cell or less. The total hands-on time from nuclei isolation to final library preparation takes 2-3 d, depending on the number of samples sharing the experiment. The improvements also allow RNA profiling from tissues rich in RNases like older mouse embryos or adult tissues that were problematic for the original method. We showcase the optimized protocol via whole-organism analysis of an E16.5 mouse embryo, profiling ~380,000 nuclei in a single experiment. Finally, we introduce a 'Tiny-Sci' protocol for experiments in which input material is very limited.</p>',
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'name' => 'Spatial profiling of chromatin accessibility in mouse and human tissues',
'authors' => 'Yanxiang Deng et al.',
'description' => '<p><span>Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Perkel, J. M. Starfish enterprise: finding RNA patterns in single cells. Nature 572, 549–551 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR1" id="ref-link-section-d163865808e834">1</a></sup><span>. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. Y. & Zhuang, X. W. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR2" id="ref-link-section-d163865808e838">2</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Eng, C. L. et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature 568, 235–239 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR3" id="ref-link-section-d163865808e838_1">3</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Rodriques, S. G. et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR4" id="ref-link-section-d163865808e838_2">4</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681 (2020)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR5" id="ref-link-section-d163865808e841">5</a></sup><span>, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 6" title="Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR6" id="ref-link-section-d163865808e845">6</a></sup><span><span> </span>and microfluidic deterministic barcoding</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681 (2020)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR5" id="ref-link-section-d163865808e849">5</a></sup><span>. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.</span></p>',
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'name' => 'Spatially resolved epigenome-transcriptome co-profiling of mammalian tissues at the cellular level',
'authors' => 'Fan Rong et al.',
'description' => '<p>Emerging spatial technologies including spatial transcriptomics and spatial epigenomics are becoming powerful tools for profiling cellular states in the tissue context. However, current methods capture only one layer of omics information at a time precluding the possibility to examine the mechanistic relationship across the cental dogma of molecular biology. Here, we present two spatial multi-omics technologies for spatially resolved genome-wide joint mapping of epigenome and transcriptome by coprofiling chromatin accessibility and gene expression (spatial-ATAC-RNA-seq) or histone modification and gene expression (spatial-CUT\&Tag-RNA-seq) on the same tissue section at a resolution near single cells. They were applied to embryonic and neonatal mouse brain as well as adult human brain to map how epigenetic states or modifications regulate cell type and dynamics in tissue. Although distinct tissue features were identified by either spatial epigenome or spatial transcriptome alone with high concordance, we observed their differential roles in defining cell states. In general, epigenetic state proceeds the development of transcriptional phenotype in relation to epigenetic lineage priming. We also observed high expression canonical markers such as PROX1 in the granular cell layer of the human hippocampus showed low chromatin accessibility that corresponded to a low level of RNA turnover rate, highlighting a divergent need for open chromatin or transcription to control cell identity and dynamics. Spatial epigenome-transcriptome co-profiling is a highly informative tool to study the mechanism of gene expression regulation in tissue and may enable a wide range of applications in life science and biomedical research.</p>',
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'description' => '<p>Prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and recurrence of PCR-positive tests have been widely reported in patients after recovery from COVID-19, but some of these patients do not appear to shed infectious virus. We investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the DNA of human cells in culture and that transcription of the integrated sequences might account for some of the positive PCR tests seen in patients. In support of this hypothesis, we found that DNA copies of SARS-CoV-2 sequences can be integrated into the genome of infected human cells. We found target site duplications flanking the viral sequences and consensus LINE1 endonuclease recognition sequences at the integration sites, consistent with a LINE1 retrotransposon-mediated, target-primed reverse transcription and retroposition mechanism. We also found, in some patient-derived tissues, evidence suggesting that a large fraction of the viral sequences is transcribed from integrated DNA copies of viral sequences, generating viral–host chimeric transcripts. The integration and transcription of viral sequences may thus contribute to the detection of viral RNA by PCR in patients after infection and clinical recovery. Because we have detected only subgenomic sequences derived mainly from the 3′ end of the viral genome integrated into the DNA of the host cell, infectious virus cannot be produced from the integrated subgenomic SARS-CoV-2 sequences.</p>',
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'description' => '<p>Background: RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming – to allow analysis of a broader range of transcripts – remains challenging. Results: We here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for generating stranded RNAseq libraries from very low numbers of FACS sorted cells without RNA purification steps. Conclusion: T-RHEX-RNAseq provides an easy-to-use, time efficient and automation compatible method for generating stranded RNAseq libraries from rare cells.</p>',
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<div class="small-12 medium-8 large-8 columns"><br />
<p>Diagenode Tagmentase is a hyperactive Tn5 transposase with the potential to enhance epigenetic studies. Its ability to cut DNA and insert sequences of interest in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq, ChIPmentation, CHANGE-seq and other. The enzyme is not loaded with DNA oligos, providing flexibility of application. To ensure optimal results the concentration may be adjusted with Diagenode <a href="https://www.diagenode.com/en/p/tagmentase-dilution-buffer">Tagmentase Dilution Buffer</a> (Cat. No. C01070011), available separately.</p>
<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) you may also need:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for loaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) - loaded</a>.</p>',
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<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
<p>Using Diagenode’s Tagmentase (Tn5 transposase) you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for loaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) - loaded</a>.</p>',
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<div class="row">
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<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
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Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
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<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
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'description' => '<p><span>The advance of single-cell RNA-sequencing technologies in the past years has enabled unprecedented insights into the complexity and heterogeneity of microglial cell states in the homeostatic and diseased brain. This includes rather complex proteomic, metabolomic, morphological, transcriptomic, and epigenetic adaptations to external stimuli and challenges resulting in a novel concept of core microglia properties and functions. To uncover the regulatory programs facilitating the rapid transcriptomic adaptation in response to changes in the local microenvironment, the accessibility of gene bodies and gene regulatory elements can be assessed. Here, we describe the application of a previously published method for simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) on microglia nuclei isolated from frozen mouse brain tissue.</span></p>',
'date' => '2023-08-29',
'pmid' => 'https://link.springer.com/protocol/10.1007/978-1-0716-3437-0_35',
'doi' => '10.1007/978-1-0716-3437-0_35',
'modified' => '2023-08-31 11:25:45',
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'id' => '4781',
'name' => 'Spatial epigenome-transcriptome co-profiling of mammalian tissues.',
'authors' => 'Zhang D. et al.',
'description' => '<p>Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context. However, current methods capture only one layer of omics information at a time, precluding the possibility of examining the mechanistic relationship across the central dogma of molecular biology. Here, we present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications (H3K27me3, H3K27ac or H3K4me3) and gene expression on the same tissue section at near-single-cell resolution. These were applied to embryonic and juvenile mouse brain, as well as adult human brain, to map how epigenetic mechanisms control transcriptional phenotype and cell dynamics in tissue. Although highly concordant tissue features were identified by either spatial epigenome or spatial transcriptome we also observed distinct patterns, suggesting their differential roles in defining cell states. Linking epigenome to transcriptome pixel by pixel allows the uncovering of new insights in spatial epigenetic priming, differentiation and gene regulation within the tissue architecture. These technologies are of great interest in life science and biomedical research.</p>',
'date' => '2023-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36922587',
'doi' => '10.1038/s41586-023-05795-1',
'modified' => '2023-06-13 09:17:26',
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'id' => '4757',
'name' => 'Analyzing genomic and epigenetic profiles in single cells by hybridtransposase (scGET-seq).',
'authors' => 'Cittaro D. et al.',
'description' => '<p>scGET-seq simultaneously profiles euchromatin and heterochromatin. scGET-seq exploits the concurrent action of transposase Tn5 and its hybrid form TnH, which targets H3K9me3 domains. Here we present a step-by-step protocol to profile single cells by scGET-seq using a 10× Chromium Controller. We describe steps for transposomes preparation and validation. We detail nuclei preparation and transposition, followed by encapsulation, library preparation, sequencing, and data analysis. For complete details on the use and execution of this protocol, please refer to Tedesco et al. (2022) and de Pretis and Cittaro (2022)..</p>',
'date' => '2023-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37000619',
'doi' => '10.1016/j.xpro.2023.102176',
'modified' => '2023-04-17 09:04:55',
'created' => '2023-04-14 13:41:22',
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'id' => '4548',
'name' => 'Imaging Chromatin Accessibility by Assay ofTransposase-Accessible Chromatin with Visualization.',
'authors' => 'Miyanari Yusuke',
'description' => '<p>Chromatin accessibility is one of the fundamental structures regulating genome functions including transcription and DNA repair. Recent technological advantages to analyze chromatin accessibility begun to explore the dynamics of local chromatin structures. Here I describe protocols for Assay of Transposase-Accessible Chromatin with Visualization (ATAC-see), which allows us to analyze subnuclear localization of accessible chromatin and quantify accessible chromatin at single-cell level.</p>',
'date' => '2023-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36173568',
'doi' => '10.1007/978-1-0716-2724-2_7',
'modified' => '2022-11-24 10:28:08',
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'id' => '4654',
'name' => 'Mouse kidney nuclear isolation and library preparation for single-cell combinatorial indexing RNA sequencing',
'authors' => 'Li Haikuo and Humphreys Benjamin D.',
'description' => '<p>Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq3) enables high-throughput single-nucleus transcriptomic profiling of multiple samples in one experiment. Here, we describe an optimized protocol of mouse kidney nuclei isolation and sci-RNA-seq3 library preparation. The use of a dounce tissue homogenizer enables nuclei extraction with high yield. Fixed nuclei are processed for sci-RNA-seq3, and self-loaded transposome Tn5 is used for tagmentation in library generation. The step-by-step protocol allows researchers to generate scalable single-cell transcriptomic data with common laboratory supplies at low cost.</p>',
'date' => '2022-12-01',
'pmid' => 'https://doi.org/10.1016%2Fj.xpro.2022.101904',
'doi' => '10.1016/j.xpro.2022.101904',
'modified' => '2023-08-01 14:23:49',
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'id' => '4546',
'name' => 'Optimized single-nucleus transcriptional profiling by combinatorialindexing.',
'authors' => 'Martin Beth K et al.',
'description' => '<p>Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that has historically exhibited variable performance on different tissues, as well as lower sensitivity than alternative methods. Here, we report a simplified, optimized version of the sci-RNA-seq protocol with three rounds of split-pool indexing that is faster, more robust and more sensitive and has a higher yield than the original protocol, with reagent costs on the order of 1 cent per cell or less. The total hands-on time from nuclei isolation to final library preparation takes 2-3 d, depending on the number of samples sharing the experiment. The improvements also allow RNA profiling from tissues rich in RNases like older mouse embryos or adult tissues that were problematic for the original method. We showcase the optimized protocol via whole-organism analysis of an E16.5 mouse embryo, profiling ~380,000 nuclei in a single experiment. Finally, we introduce a 'Tiny-Sci' protocol for experiments in which input material is very limited.</p>',
'date' => '2022-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36261634',
'doi' => '10.1038/s41596-022-00752-0',
'modified' => '2022-11-24 10:26:25',
'created' => '2022-11-24 08:49:52',
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(int) 6 => array(
'id' => '4412',
'name' => 'Spatial profiling of chromatin accessibility in mouse and human tissues',
'authors' => 'Yanxiang Deng et al.',
'description' => '<p><span>Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Perkel, J. M. Starfish enterprise: finding RNA patterns in single cells. Nature 572, 549–551 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR1" id="ref-link-section-d163865808e834">1</a></sup><span>. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. Y. & Zhuang, X. W. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR2" id="ref-link-section-d163865808e838">2</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Eng, C. L. et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature 568, 235–239 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR3" id="ref-link-section-d163865808e838_1">3</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Rodriques, S. G. et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR4" id="ref-link-section-d163865808e838_2">4</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681 (2020)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR5" id="ref-link-section-d163865808e841">5</a></sup><span>, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 6" title="Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR6" id="ref-link-section-d163865808e845">6</a></sup><span><span> </span>and microfluidic deterministic barcoding</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681 (2020)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR5" id="ref-link-section-d163865808e849">5</a></sup><span>. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.</span></p>',
'date' => '2022-08-05',
'pmid' => 'https://www.nature.com/articles/s41586-022-05094-1',
'doi' => 'https://doi.org/10.1038/s41586-022-05094-1',
'modified' => '2022-08-23 11:54:39',
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'id' => '4389',
'name' => 'Spatially resolved epigenome-transcriptome co-profiling of mammalian tissues at the cellular level',
'authors' => 'Fan Rong et al.',
'description' => '<p>Emerging spatial technologies including spatial transcriptomics and spatial epigenomics are becoming powerful tools for profiling cellular states in the tissue context. However, current methods capture only one layer of omics information at a time precluding the possibility to examine the mechanistic relationship across the cental dogma of molecular biology. Here, we present two spatial multi-omics technologies for spatially resolved genome-wide joint mapping of epigenome and transcriptome by coprofiling chromatin accessibility and gene expression (spatial-ATAC-RNA-seq) or histone modification and gene expression (spatial-CUT\&Tag-RNA-seq) on the same tissue section at a resolution near single cells. They were applied to embryonic and neonatal mouse brain as well as adult human brain to map how epigenetic states or modifications regulate cell type and dynamics in tissue. Although distinct tissue features were identified by either spatial epigenome or spatial transcriptome alone with high concordance, we observed their differential roles in defining cell states. In general, epigenetic state proceeds the development of transcriptional phenotype in relation to epigenetic lineage priming. We also observed high expression canonical markers such as PROX1 in the granular cell layer of the human hippocampus showed low chromatin accessibility that corresponded to a low level of RNA turnover rate, highlighting a divergent need for open chromatin or transcription to control cell identity and dynamics. Spatial epigenome-transcriptome co-profiling is a highly informative tool to study the mechanism of gene expression regulation in tissue and may enable a wide range of applications in life science and biomedical research.</p>',
'date' => '2022-06-13',
'pmid' => 'https://www.researchsquare.com/article/rs-1728747/v1',
'doi' => '10.21203/rs.3.rs-1728747/v1',
'modified' => '2022-08-11 15:20:45',
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'name' => 'Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues',
'authors' => 'Liguo Zhang et al.',
'description' => '<p>Prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and recurrence of PCR-positive tests have been widely reported in patients after recovery from COVID-19, but some of these patients do not appear to shed infectious virus. We investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the DNA of human cells in culture and that transcription of the integrated sequences might account for some of the positive PCR tests seen in patients. In support of this hypothesis, we found that DNA copies of SARS-CoV-2 sequences can be integrated into the genome of infected human cells. We found target site duplications flanking the viral sequences and consensus LINE1 endonuclease recognition sequences at the integration sites, consistent with a LINE1 retrotransposon-mediated, target-primed reverse transcription and retroposition mechanism. We also found, in some patient-derived tissues, evidence suggesting that a large fraction of the viral sequences is transcribed from integrated DNA copies of viral sequences, generating viral–host chimeric transcripts. The integration and transcription of viral sequences may thus contribute to the detection of viral RNA by PCR in patients after infection and clinical recovery. Because we have detected only subgenomic sequences derived mainly from the 3′ end of the viral genome integrated into the DNA of the host cell, infectious virus cannot be produced from the integrated subgenomic SARS-CoV-2 sequences.</p>',
'date' => '2021-05-25',
'pmid' => 'https://www.pnas.org/content/118/21/e2105968118',
'doi' => 'https://doi.org/10.1073/pnas.2105968118',
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'authors' => 'Gustafsson Charlotte et al.',
'description' => '<p>Background: RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming – to allow analysis of a broader range of transcripts – remains challenging. Results: We here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for generating stranded RNAseq libraries from very low numbers of FACS sorted cells without RNA purification steps. Conclusion: T-RHEX-RNAseq provides an easy-to-use, time efficient and automation compatible method for generating stranded RNAseq libraries from rare cells.</p>',
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'name' => 'Tagmentase (Tn5 transposase) - unloaded',
'description' => '<div class="extra-spaced"><center><img alt="Tagmentase (Tn5 transposase)" src="https://www.diagenode.com/img/banners/banner-tagmentase.jpg" caption="false" width="787" height="236" /></center></div>
<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p>Diagenode Tagmentase is a hyperactive Tn5 transposase with the potential to enhance epigenetic studies. Its ability to cut DNA and insert sequences of interest in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq, ChIPmentation, CHANGE-seq and other. The enzyme is not loaded with DNA oligos, providing flexibility of application. To ensure optimal results the concentration may be adjusted with Diagenode <a href="https://www.diagenode.com/en/p/tagmentase-dilution-buffer">Tagmentase Dilution Buffer</a> (Cat. No. C01070011), available separately.</p>
<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) you may also need:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for loaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) - loaded</a>.</p>',
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<p><img alt="Tn5 transposase" src="https://www.diagenode.com/img/product/reagents/tagmentase-figure-1a.jpg" style="display: block; margin-left: auto; margin-right: auto;" width="653" height="282" /></p>
<p><img alt="Tagmentase Tn5 transposase" src="https://www.diagenode.com/img/product/reagents/tagmentase-figure-1b.jpg" style="display: block; margin-left: auto; margin-right: auto;" width="645" height="278" /></p>
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</div>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<div class="row">
<div class="small-12 medium-12 large-12 columns"><center><img alt="Tn5 transposase perfect for NGS" src="https://www.diagenode.com/img/product/reagents/tagmentase-figure2.jpg" width="754" height="492" /></center></div>
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<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
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<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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include - APP/View/Products/view.ctp, line 755
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View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
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<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
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<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
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'description' => '<p>Chromatin accessibility is one of the fundamental structures regulating genome functions including transcription and DNA repair. Recent technological advantages to analyze chromatin accessibility begun to explore the dynamics of local chromatin structures. Here I describe protocols for Assay of Transposase-Accessible Chromatin with Visualization (ATAC-see), which allows us to analyze subnuclear localization of accessible chromatin and quantify accessible chromatin at single-cell level.</p>',
'date' => '2023-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36173568',
'doi' => '10.1007/978-1-0716-2724-2_7',
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'name' => 'Mouse kidney nuclear isolation and library preparation for single-cell combinatorial indexing RNA sequencing',
'authors' => 'Li Haikuo and Humphreys Benjamin D.',
'description' => '<p>Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq3) enables high-throughput single-nucleus transcriptomic profiling of multiple samples in one experiment. Here, we describe an optimized protocol of mouse kidney nuclei isolation and sci-RNA-seq3 library preparation. The use of a dounce tissue homogenizer enables nuclei extraction with high yield. Fixed nuclei are processed for sci-RNA-seq3, and self-loaded transposome Tn5 is used for tagmentation in library generation. The step-by-step protocol allows researchers to generate scalable single-cell transcriptomic data with common laboratory supplies at low cost.</p>',
'date' => '2022-12-01',
'pmid' => 'https://doi.org/10.1016%2Fj.xpro.2022.101904',
'doi' => '10.1016/j.xpro.2022.101904',
'modified' => '2023-08-01 14:23:49',
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'id' => '4546',
'name' => 'Optimized single-nucleus transcriptional profiling by combinatorialindexing.',
'authors' => 'Martin Beth K et al.',
'description' => '<p>Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that has historically exhibited variable performance on different tissues, as well as lower sensitivity than alternative methods. Here, we report a simplified, optimized version of the sci-RNA-seq protocol with three rounds of split-pool indexing that is faster, more robust and more sensitive and has a higher yield than the original protocol, with reagent costs on the order of 1 cent per cell or less. The total hands-on time from nuclei isolation to final library preparation takes 2-3 d, depending on the number of samples sharing the experiment. The improvements also allow RNA profiling from tissues rich in RNases like older mouse embryos or adult tissues that were problematic for the original method. We showcase the optimized protocol via whole-organism analysis of an E16.5 mouse embryo, profiling ~380,000 nuclei in a single experiment. Finally, we introduce a 'Tiny-Sci' protocol for experiments in which input material is very limited.</p>',
'date' => '2022-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36261634',
'doi' => '10.1038/s41596-022-00752-0',
'modified' => '2022-11-24 10:26:25',
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'id' => '4412',
'name' => 'Spatial profiling of chromatin accessibility in mouse and human tissues',
'authors' => 'Yanxiang Deng et al.',
'description' => '<p><span>Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Perkel, J. M. Starfish enterprise: finding RNA patterns in single cells. Nature 572, 549–551 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR1" id="ref-link-section-d163865808e834">1</a></sup><span>. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. Y. & Zhuang, X. W. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR2" id="ref-link-section-d163865808e838">2</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Eng, C. L. et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature 568, 235–239 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR3" id="ref-link-section-d163865808e838_1">3</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Rodriques, S. G. et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR4" id="ref-link-section-d163865808e838_2">4</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681 (2020)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR5" id="ref-link-section-d163865808e841">5</a></sup><span>, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 6" title="Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR6" id="ref-link-section-d163865808e845">6</a></sup><span><span> </span>and microfluidic deterministic barcoding</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681 (2020)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR5" id="ref-link-section-d163865808e849">5</a></sup><span>. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.</span></p>',
'date' => '2022-08-05',
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'name' => 'Spatially resolved epigenome-transcriptome co-profiling of mammalian tissues at the cellular level',
'authors' => 'Fan Rong et al.',
'description' => '<p>Emerging spatial technologies including spatial transcriptomics and spatial epigenomics are becoming powerful tools for profiling cellular states in the tissue context. However, current methods capture only one layer of omics information at a time precluding the possibility to examine the mechanistic relationship across the cental dogma of molecular biology. Here, we present two spatial multi-omics technologies for spatially resolved genome-wide joint mapping of epigenome and transcriptome by coprofiling chromatin accessibility and gene expression (spatial-ATAC-RNA-seq) or histone modification and gene expression (spatial-CUT\&Tag-RNA-seq) on the same tissue section at a resolution near single cells. They were applied to embryonic and neonatal mouse brain as well as adult human brain to map how epigenetic states or modifications regulate cell type and dynamics in tissue. Although distinct tissue features were identified by either spatial epigenome or spatial transcriptome alone with high concordance, we observed their differential roles in defining cell states. In general, epigenetic state proceeds the development of transcriptional phenotype in relation to epigenetic lineage priming. We also observed high expression canonical markers such as PROX1 in the granular cell layer of the human hippocampus showed low chromatin accessibility that corresponded to a low level of RNA turnover rate, highlighting a divergent need for open chromatin or transcription to control cell identity and dynamics. Spatial epigenome-transcriptome co-profiling is a highly informative tool to study the mechanism of gene expression regulation in tissue and may enable a wide range of applications in life science and biomedical research.</p>',
'date' => '2022-06-13',
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'name' => 'Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues',
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'description' => '<p>Prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and recurrence of PCR-positive tests have been widely reported in patients after recovery from COVID-19, but some of these patients do not appear to shed infectious virus. We investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the DNA of human cells in culture and that transcription of the integrated sequences might account for some of the positive PCR tests seen in patients. In support of this hypothesis, we found that DNA copies of SARS-CoV-2 sequences can be integrated into the genome of infected human cells. We found target site duplications flanking the viral sequences and consensus LINE1 endonuclease recognition sequences at the integration sites, consistent with a LINE1 retrotransposon-mediated, target-primed reverse transcription and retroposition mechanism. We also found, in some patient-derived tissues, evidence suggesting that a large fraction of the viral sequences is transcribed from integrated DNA copies of viral sequences, generating viral–host chimeric transcripts. The integration and transcription of viral sequences may thus contribute to the detection of viral RNA by PCR in patients after infection and clinical recovery. Because we have detected only subgenomic sequences derived mainly from the 3′ end of the viral genome integrated into the DNA of the host cell, infectious virus cannot be produced from the integrated subgenomic SARS-CoV-2 sequences.</p>',
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'description' => '<p>Background: RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming – to allow analysis of a broader range of transcripts – remains challenging. Results: We here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for generating stranded RNAseq libraries from very low numbers of FACS sorted cells without RNA purification steps. Conclusion: T-RHEX-RNAseq provides an easy-to-use, time efficient and automation compatible method for generating stranded RNAseq libraries from rare cells.</p>',
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'description' => '<div class="extra-spaced"><center><img alt="Tagmentase (Tn5 transposase)" src="https://www.diagenode.com/img/banners/banner-tagmentase.jpg" caption="false" width="787" height="236" /></center></div>
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<p>Diagenode Tagmentase is a hyperactive Tn5 transposase with the potential to enhance epigenetic studies. Its ability to cut DNA and insert sequences of interest in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq, ChIPmentation, CHANGE-seq and other. The enzyme is not loaded with DNA oligos, providing flexibility of application. To ensure optimal results the concentration may be adjusted with Diagenode <a href="https://www.diagenode.com/en/p/tagmentase-dilution-buffer">Tagmentase Dilution Buffer</a> (Cat. No. C01070011), available separately.</p>
<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) you may also need:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for loaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) - loaded</a>.</p>',
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<p><img alt="Tagmentase Tn5 transposase" src="https://www.diagenode.com/img/product/reagents/tagmentase-figure-1b.jpg" style="display: block; margin-left: auto; margin-right: auto;" width="645" height="278" /></p>
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<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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<p>Diagenode Tagmentase is a hyperactive Tn5 transposase with the potential to enhance epigenetic studies. Its ability to cut DNA and insert sequences of interest in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq, ChIPmentation, CHANGE-seq and other. The enzyme is not loaded with DNA oligos, providing flexibility of application. To ensure optimal results the concentration may be adjusted with Diagenode <a href="https://www.diagenode.com/en/p/tagmentase-dilution-buffer">Tagmentase Dilution Buffer</a> (Cat. No. C01070011), available separately.</p>
<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) you may also need:</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
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<p>Looking for loaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) - loaded</a>.</p>',
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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'description' => '<p><span>Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 1" title="Perkel, J. M. Starfish enterprise: finding RNA patterns in single cells. Nature 572, 549–551 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR1" id="ref-link-section-d163865808e834">1</a></sup><span>. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. Y. & Zhuang, X. W. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR2" id="ref-link-section-d163865808e838">2</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Eng, C. L. et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature 568, 235–239 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR3" id="ref-link-section-d163865808e838_1">3</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" title="Rodriques, S. G. et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467 (2019)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR4" id="ref-link-section-d163865808e838_2">4</a>,<a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681 (2020)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR5" id="ref-link-section-d163865808e841">5</a></sup><span>, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 6" title="Corces, M. R. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR6" id="ref-link-section-d163865808e845">6</a></sup><span><span> </span>and microfluidic deterministic barcoding</span><sup><a data-track="click" data-track-action="reference anchor" data-track-label="link" data-test="citation-ref" aria-label="Reference 5" title="Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681 (2020)." href="https://www.nature.com/articles/s41586-022-05094-1#ref-CR5" id="ref-link-section-d163865808e849">5</a></sup><span>. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.</span></p>',
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<p>Diagenode Tagmentase is a hyperactive Tn5 transposase with the potential to enhance epigenetic studies. Its ability to cut DNA and insert sequences of interest in one step makes it the perfect companion for Next-Generation Sequencing experiments using powerful technologies such as ATAC-seq, ChIPmentation, CHANGE-seq and other. The enzyme is not loaded with DNA oligos, providing flexibility of application. To ensure optimal results the concentration may be adjusted with Diagenode <a href="https://www.diagenode.com/en/p/tagmentase-dilution-buffer">Tagmentase Dilution Buffer</a> (Cat. No. C01070011), available separately.</p>
<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
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<p>Using Diagenode’s Tagmentase (Tn5 transposase) you may also need:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for loaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) - loaded</a>.</p>',
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<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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<p><a href="https://www.diagenode.com/files/protocols/PRO-Transposome-Assembly-V2.pdf" target="_blank">Protocol for transposome assembly</a></p>
<p>Using Diagenode’s Tagmentase (Tn5 transposase) you may need also:</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-1x">Tagmentation Buffer (1x)</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation Buffer (2x)</a></li>
<li><a href="https://www.diagenode.com/en/p/24-unique-dual-indexes-for-tagmented-libraries-set1">24 UDI for tagmented libraries</a></li>
</ul>
<p>Looking for loaded Tagmentase? Please go to <a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase (Tn5 transposase) - loaded</a>.</p>',
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<p><img alt="Tn5 transposase" src="https://www.diagenode.com/img/product/reagents/tagmentase-figure-1a.jpg" style="display: block; margin-left: auto; margin-right: auto;" width="653" height="282" /></p>
<p><img alt="Tagmentase Tn5 transposase" src="https://www.diagenode.com/img/product/reagents/tagmentase-figure-1b.jpg" style="display: block; margin-left: auto; margin-right: auto;" width="645" height="278" /></p>
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<p><strong>Figure 1: Efficient fragmentation of the lambda DNA after incubation with the Tagmentase</strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with diluted Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). Profiles show the size of lambda DNA before (A) and after treatment with Tagmentase (B).</p>
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<div class="small-12 medium-12 large-12 columns"><center><img alt="Tn5 transposase perfect for NGS" src="https://www.diagenode.com/img/product/reagents/tagmentase-figure2.jpg" width="754" height="492" /></center></div>
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<p><strong>Figure 2: Fragmentation efficiency depending on the amount of Tagmentase </strong><br />For fragmentation, 100 ng of DNA from bacteriophage lambda were incubated with Diagenode Tagmentase (Cat. No. C01070010) and Tagmentation buffer (1x) (Cat. No. C01019042) for 7 min at 55°C. The Tagmentase was previously diluted with the Tagmentase Dilution Buffer (Cat. No.) at ¼ and 1/16 dilutions. The reaction was stopped by addition of SDS (0.2% final concentration). After clean-up using AMPure XP beads (Beckman Coulter) on Diagenode IP-Star robot, the size of the DNA was assessed on Fragment Analyzer (Agilent), using the HS Large Fragment 50kb Kit (Agilent). The migration of the samples shows variations of the size distribution according to the amount of Tagmentase used for the reaction.</p>
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