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'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
<ul>
<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
</ul>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
<div id="more" class="content">
<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
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<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
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<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
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<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
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<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
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<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
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'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
<ul>
<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
</ul>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
<div id="more" class="content">
<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
</div>
</li>
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<div class="container">
<div class="row" style="background: rgba(255,255,255,0.1); height: 241px;">
<div class="large-12 columns slick">
<div>
<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
</div>
</div>
</div>
</div>
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'description' => '<p><strong>An updated version of this kit using D-Plex technology is available for superior performance.</strong></p>
<h4><span>Discover our <strong>NEW<a href="https://www.diagenode.com/en/p/D-Plex-mRNA-seq-Library-Prep-x24"><span> </span>D-Plex mRNA-seq Kit for Illumina</a></strong>.</span></h4>',
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'description' => '<div class="small-12 medium-12 large-12 columns" style="border: 3px solid #B02736; padding: 10px; margin: 10px;">
<h2>Product Features</h2>
<ul style="list-style-type: disc;">
<li><span style="font-weight: 400;">An innovative technology with template switching and UMIs</span></li>
<li><span>Ultra-sensitive methodology with low input capability down to 10 ng</span></li>
<li><span>High efficiency for greater gene detection and biomarker identification</span></li>
<li><span>Consistent gene expression profiling, optimal for gene signature definition</span></li>
<li><span>Precise measurement of strand orientation for anti-sense transcription detection</span></li>
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<h4></h4>
<center><a class="chip diahome button" href="https://www.diagenode.com/files/products/kits/dplex-mRNA-manual.pdf" target="_blank" title="dplex total rnaseq user manual"><strong>Download the manual</strong></a></center>
<p></p>
<p>The D-Plex mRNA-seq Library Preparation Kit is a tool designed for gene expression analysis. <span>The kit utilizes the</span><a href="https://www.diagenode.com/en/pages/dplex" target="_blank"><span> </span>D-Plex technology</a><span><span> </span>to generate directional libraries for Illumina sequencing directly from total RNAs.</span></p>
<p><span>The D-Plex technology utilizes two innovative ligation-free mechanisms - poly(A) tailing and template switching - to produce sequencing libraries from low input samples, down to 10 ng of total RNAs. Combined with unique molecular identifiers (UMI), this complete solution delivers a high-sensitivity detection method for gene expression analysis and discovery applications in the coding transcriptome.</span></p>
<p><span></span><span>The D-Plex mRNA-seq Kit offers a time-saving protocol that can be completed within 6 hours and requires minimal hands-on time. <span>The library preparation takes place in a </span><span>single tube</span><span>, increasing the efficiency tremendously. This new solution has been developped to capture an increased number of genes for great discovery efficiency.</span></span></p>
<p><span><span>The D-Plex mRNA-seq Kit includes all buffers and enzymes necessary for mRNA capture and library preparation. Specific D-Plex Unique Dual Indexes were designed and validated to fit the D-Plex technology and are available separately:</span></span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
</ul>
<div class="extra-spaced" align="center"></div>
<div class="row">
<div class="carrousel" style="background-position: center;">
<div class="slick">
<div>
<h3>Greater gene discovery efficiency at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/UHR_mRNA.png" alt="total RNA kit" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit enables the detection of higher numbers of genes even for low RNA inputs. Increased number of genes detected at 10x coverage is an indicator of greater sensitivity.</p>
</div>
</div>
<div>
<h3>High mappability to the coding transcriptome</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_biotypes.png" alt="total RNA diversity" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq libraries capture efficiently coding exons and introns present in the sample of interest.</p>
</div>
</div>
<div>
<h3>Consistent, sensitive gene expression profiling</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_violin_tpm_10.png" alt="total RNA" height="200px" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>Gene expression profiling obtained with D-Plex mRNA-seq kit is conserved across a broad dynamic range of inputs, especially for the lowest RNA inputs.</p>
</div>
</div>
<div>
<h3>Exceptional data concordance at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/robustness_corr_HUR_mrna.png" alt="total RNA" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit produces quality data with high data concordance between low and high RNA inputs. This result demonstrates that D-Plex is an ideal solution for precious samples with limited starting material.</p>
</div>
</div>
</div>
</div>
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'info2' => '<p><span>Specific D-Plex indexes </span><span>were designed and validated to fit the D-Plex technology for Illumina sequencing and </span><span>are not included in the kit. They can be bought separately according to your needs. Please choose the format that suits you best among the compatible references to:</span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
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<p><span></span></p>
<p><span>The use of UDI is highly recommended to mitigate errors introduced by read misassignment, including index hopping frequently observed with patterned flow cells such as Illumina’s NovaSeq system.</span></p>
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<p><span style="font-weight: 400;">Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to </span><a href="../applications/dna-rna-shearing"><span style="font-weight: 400;">fragmented DNA or RNA</span></a><span style="font-weight: 400;"> prior to sequencing</span></p>
<p><span style="font-weight: 400;">After input DNA has been fragmented, it is end-repaired and blunt-ended</span><span style="font-weight: 400;">. The next step is a A-tailing in which dAMP is added to the 3´ end of the blunt phosphorylated DNA fragments to prevent concatemerization and to allow the ligation of adaptors with complementary dT overhangs. In addition, barcoded adapters can be incorporated to facilitate multiplexing prior to or during amplification.</span></p>
<center><img src="https://www.diagenode.com/img/categories/library-prep/flux.png" /></center>
<p><span style="font-weight: 400;">Diagenode offers a comprehensive product portfolio for library preparation:<br /></span></p>
<strong><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">D-Plex RNA-seq Library Preparation Kits</a></strong><br />
<p><span style="font-weight: 400;">Diagenode’s new RNA-sequencing solutions utilize the innovative c</span><span style="font-weight: 400;">apture and a</span><span style="font-weight: 400;">mplification by t</span><span style="font-weight: 400;">ailing and s</span><span style="font-weight: 400;">witching”</span><span style="font-weight: 400;">, a ligation-free method to produce DNA libraries for next generation sequencing from low input amounts of RNA. </span><span style="font-weight: 400;"></span><a href="../categories/Library-preparation-for-RNA-seq">Learn more</a></p>
<strong><a href="../categories/library-preparation-for-ChIP-seq">ChIP-seq and DNA sequencing library preparation solutions</a></strong><br />
<p><span style="font-weight: 400;">Our kits have been optimized for DNA library preparation used for next generation sequencing for a wide range of inputs. Using a simple three-step protocols, our</span><a href="http://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><span style="font-weight: 400;"> </span></a><span style="font-weight: 400;">kits are an optimal choice for library preparation from DNA inputs down to 50 pg. </span><a href="../categories/library-preparation-for-ChIP-seq">Learn more</a></p>
<a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span><strong>Bioruptor Pico - short fragments</strong></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">Our well-cited Bioruptor Pico is the shearing device of choice for chromatin and DNA fragmentation. Obtain uniform and tight fragment distributions between 150bp -2kb. </span><a href="../p/bioruptor-pico-sonication-device">Learn more</a></p>
<strong><a href="../p/megaruptor2-1-unit"><span href="../p/bioruptor-pico-sonication-device">Megaruptor</span>® - long fragments</a></strong><a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">The Megaruptor is designed to shear DNA from 3kb-75kb for long-read sequencing. <a href="../p/megaruptor2-1-unit">Learn more</a></span></p>
<span href="../p/bioruptor-pico-sonication-device"></span><span style="font-weight: 400;"></span></div>
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'description' => '<p>: There is no standard chemotherapy for refractory or relapsing malignant pleural mesothelioma (MPM). Our previous reports nevertheless indicated that a combination of an anthracycline (doxorubicin) and a lysine deacetylase inhibitor (valproic acid, VPA) synergize to induce the apoptosis of MPM cells and reduce tumor growth in mouse models. A Phase I/II clinical trial indicated that this regimen is a promising therapeutic option for a proportion of MPM patients. : The transcriptomes of mesothelioma cells were compared after Illumina HiSeq 4000 sequencing. The expression of differentially expressed genes was inhibited by RNA interference. Apoptosis was determined by cell cycle analysis and Annexin V/7-AAD labeling. Protein expression was assessed by immunoblotting. Preclinical efficacy was evaluated in BALB/c and NOD-SCID mice. : To understand the mechanisms involved in chemoresistance, the transcriptomes of two MPM cell lines displaying different responses to VPA-doxorubicin were compared. Among the differentially expressed genes, transforming growth factor alpha (TGFα) was associated with resistance to this regimen. The silencing of TGFα by RNA interference correlated with a significant increase in apoptosis, whereas the overexpression of TGFα desensitized MPM cells to the apoptosis induced by VPA and doxorubicin. The multi-targeted inhibition of histone deacetylase (HDAC), HER2 and TGFα receptor (epidermal growth factor receptor/EGFR) improved treatment efficacy in vitro and reduced tumor growth in two MPM mouse models. Finally, TGFα expression but not EGFR correlated with patient survival. : Our data show that TGFα but not its receptor EGFR is a key factor in resistance to MPM chemotherapy. This observation may contribute to casting light on the promising but still controversial role of EGFR signaling in MPM therapy.</p>',
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'description' => '<p>While interstitial fibrosis plays a significant role in heart failure, our understanding of disease progression in humans is limited. To address this limitation, we have engineered a cardiac-fibrosis-on-a-chip model consisting of a microfabricated device with live force measurement capabilities using co-cultured human cardiac fibroblasts and pluripotent stem cell-derived cardiomyocytes. Transforming growth factor-β was used as a trigger for fibrosis. Here, we have reproduced the classic hallmarks of fibrosis-induced heart failure including high collagen deposition, increased tissue stiffness, BNP secretion, and passive tension. Force of contraction was significantly decreased in fibrotic tissues that displayed a transcriptomic signature consistent with human cardiac fibrosis/heart failure. Treatment with an anti-fibrotic drug decreased tissue stiffness and BNP secretion, with corresponding changes in the transcriptomic signature. This model represents an accessible approach to study human heart failure in vitro, and allows for testing anti-fibrotic drugs while facilitating the real-time assessment of cardiomyocyte function.</p>',
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'description' => '<p>While interstitial fibrosis plays a significant role in heart failure, our understanding of disease progression in humans is limited. To address this limitation, we have engineered a cardiac-fibrosis-on-a-chip model consisting of a microfabricated device with live force measurement capabilities using co-cultured human cardiac fibroblasts and pluripotent stem cell-derived cardiomyocytes. Transforming growth factor-β was used as a trigger for fibrosis. Here, we have reproduced the classic hallmarks of fibrosis-induced heart failure including high collagen deposition, increased tissue stiffness, BNP secretion, and passive tension. Force of contraction was significantly decreased in fibrotic tissues that displayed a transcriptomic signature consistent with human cardiac fibrosis/heart failure. Treatment with an anti-fibrotic drug decreased tissue stiffness and BNP secretion, with corresponding changes in the transcriptomic signature. This model represents an accessible approach to study human heart failure in vitro, and allows for testing anti-fibrotic drugs while facilitating the real-time assessment of cardiomyocyte function.</p>',
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'description' => '<p>BACKGROUND: ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS: To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS: Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS: We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.</p>',
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'name' => 'CATS mRNA-seq Kit (with polyA selection) v2 x96',
'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
<ul>
<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
</ul>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
<div id="more" class="content">
<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
</div>
</li>
</ul>
<div class="carrousel" style="background-position: center;">
<div class="container">
<div class="row" style="background: rgba(255,255,255,0.1); height: 241px;">
<div class="large-12 columns slick">
<div>
<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
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<div>
<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
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<p><strong><input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/></strong>D-Plex mRNA-seq Kit for Illumina個カートに追加。</p>
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<h6 style="height:60px">D-Plex mRNA-seq Kit for Illumina</h6>
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<h2>Product Features</h2>
<ul style="list-style-type: disc;">
<li><span style="font-weight: 400;">An innovative technology with template switching and UMIs</span></li>
<li><span>Ultra-sensitive methodology with low input capability down to 10 ng</span></li>
<li><span>High efficiency for greater gene detection and biomarker identification</span></li>
<li><span>Consistent gene expression profiling, optimal for gene signature definition</span></li>
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<h4></h4>
<center><a class="chip diahome button" href="https://www.diagenode.com/files/products/kits/dplex-mRNA-manual.pdf" target="_blank" title="dplex total rnaseq user manual"><strong>Download the manual</strong></a></center>
<p></p>
<p>The D-Plex mRNA-seq Library Preparation Kit is a tool designed for gene expression analysis. <span>The kit utilizes the</span><a href="https://www.diagenode.com/en/pages/dplex" target="_blank"><span> </span>D-Plex technology</a><span><span> </span>to generate directional libraries for Illumina sequencing directly from total RNAs.</span></p>
<p><span>The D-Plex technology utilizes two innovative ligation-free mechanisms - poly(A) tailing and template switching - to produce sequencing libraries from low input samples, down to 10 ng of total RNAs. Combined with unique molecular identifiers (UMI), this complete solution delivers a high-sensitivity detection method for gene expression analysis and discovery applications in the coding transcriptome.</span></p>
<p><span></span><span>The D-Plex mRNA-seq Kit offers a time-saving protocol that can be completed within 6 hours and requires minimal hands-on time. <span>The library preparation takes place in a </span><span>single tube</span><span>, increasing the efficiency tremendously. This new solution has been developped to capture an increased number of genes for great discovery efficiency.</span></span></p>
<p><span><span>The D-Plex mRNA-seq Kit includes all buffers and enzymes necessary for mRNA capture and library preparation. Specific D-Plex Unique Dual Indexes were designed and validated to fit the D-Plex technology and are available separately:</span></span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
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<h3>Greater gene discovery efficiency at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/UHR_mRNA.png" alt="total RNA kit" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit enables the detection of higher numbers of genes even for low RNA inputs. Increased number of genes detected at 10x coverage is an indicator of greater sensitivity.</p>
</div>
</div>
<div>
<h3>High mappability to the coding transcriptome</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_biotypes.png" alt="total RNA diversity" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq libraries capture efficiently coding exons and introns present in the sample of interest.</p>
</div>
</div>
<div>
<h3>Consistent, sensitive gene expression profiling</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_violin_tpm_10.png" alt="total RNA" height="200px" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>Gene expression profiling obtained with D-Plex mRNA-seq kit is conserved across a broad dynamic range of inputs, especially for the lowest RNA inputs.</p>
</div>
</div>
<div>
<h3>Exceptional data concordance at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/robustness_corr_HUR_mrna.png" alt="total RNA" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit produces quality data with high data concordance between low and high RNA inputs. This result demonstrates that D-Plex is an ideal solution for precious samples with limited starting material.</p>
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<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
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<p><span>The use of UDI is highly recommended to mitigate errors introduced by read misassignment, including index hopping frequently observed with patterned flow cells such as Illumina’s NovaSeq system.</span></p>
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'name' => 'ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells.',
'authors' => 'Sen M, Wang X, Hamdan FH, Rapp J, Eggert J, Kosinsky RL, Wegwitz F, Kutschat AP, Younesi FS, Gaedcke J, Grade M, Hessmann E, Papantonis A, Strӧbel P, Johnsen SA',
'description' => '<p>BACKGROUND: ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS: To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS: Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS: We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.</p>',
'date' => '2019-06-19',
'pmid' => 'http://www.pubmed.gov/31217031',
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'meta_keywords' => 'CATS, mRNA-seq, coding RNA, transcriptome, polyA selection, RNA-seq library preparation, low input, easy, user-friendly',
'meta_description' => 'Capture and Amplification by Tailing and Switching(CATS) mRNA-seq Kit is a ligation-free assay providng increased efficiency and minimum bias, with low inputs down to 100 picograms. User-friendly with reduced hands-on time and fewer steps than competing solutions ',
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'name' => 'CATS mRNA-seq Kit (with polyA selection) v2 x24',
'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
<ul>
<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
</ul>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
<div id="more" class="content">
<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
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<div>
<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
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'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
<ul>
<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
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<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
<div id="more" class="content">
<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
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<div>
<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
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<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
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<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
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<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
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<div>
<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
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'description' => '<p><strong>An updated version of this kit using D-Plex technology is available for superior performance.</strong></p>
<h4><span>Discover our <strong>NEW<a href="https://www.diagenode.com/en/p/D-Plex-mRNA-seq-Library-Prep-x24"><span> </span>D-Plex mRNA-seq Kit for Illumina</a></strong>.</span></h4>',
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'description' => '<div class="small-12 medium-12 large-12 columns" style="border: 3px solid #B02736; padding: 10px; margin: 10px;">
<h2>Product Features</h2>
<ul style="list-style-type: disc;">
<li><span style="font-weight: 400;">An innovative technology with template switching and UMIs</span></li>
<li><span>Ultra-sensitive methodology with low input capability down to 10 ng</span></li>
<li><span>High efficiency for greater gene detection and biomarker identification</span></li>
<li><span>Consistent gene expression profiling, optimal for gene signature definition</span></li>
<li><span>Precise measurement of strand orientation for anti-sense transcription detection</span></li>
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<h4></h4>
<center><a class="chip diahome button" href="https://www.diagenode.com/files/products/kits/dplex-mRNA-manual.pdf" target="_blank" title="dplex total rnaseq user manual"><strong>Download the manual</strong></a></center>
<p></p>
<p>The D-Plex mRNA-seq Library Preparation Kit is a tool designed for gene expression analysis. <span>The kit utilizes the</span><a href="https://www.diagenode.com/en/pages/dplex" target="_blank"><span> </span>D-Plex technology</a><span><span> </span>to generate directional libraries for Illumina sequencing directly from total RNAs.</span></p>
<p><span>The D-Plex technology utilizes two innovative ligation-free mechanisms - poly(A) tailing and template switching - to produce sequencing libraries from low input samples, down to 10 ng of total RNAs. Combined with unique molecular identifiers (UMI), this complete solution delivers a high-sensitivity detection method for gene expression analysis and discovery applications in the coding transcriptome.</span></p>
<p><span></span><span>The D-Plex mRNA-seq Kit offers a time-saving protocol that can be completed within 6 hours and requires minimal hands-on time. <span>The library preparation takes place in a </span><span>single tube</span><span>, increasing the efficiency tremendously. This new solution has been developped to capture an increased number of genes for great discovery efficiency.</span></span></p>
<p><span><span>The D-Plex mRNA-seq Kit includes all buffers and enzymes necessary for mRNA capture and library preparation. Specific D-Plex Unique Dual Indexes were designed and validated to fit the D-Plex technology and are available separately:</span></span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
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<div class="extra-spaced" align="center"></div>
<div class="row">
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<h3>Greater gene discovery efficiency at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/UHR_mRNA.png" alt="total RNA kit" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit enables the detection of higher numbers of genes even for low RNA inputs. Increased number of genes detected at 10x coverage is an indicator of greater sensitivity.</p>
</div>
</div>
<div>
<h3>High mappability to the coding transcriptome</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_biotypes.png" alt="total RNA diversity" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq libraries capture efficiently coding exons and introns present in the sample of interest.</p>
</div>
</div>
<div>
<h3>Consistent, sensitive gene expression profiling</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_violin_tpm_10.png" alt="total RNA" height="200px" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>Gene expression profiling obtained with D-Plex mRNA-seq kit is conserved across a broad dynamic range of inputs, especially for the lowest RNA inputs.</p>
</div>
</div>
<div>
<h3>Exceptional data concordance at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/robustness_corr_HUR_mrna.png" alt="total RNA" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit produces quality data with high data concordance between low and high RNA inputs. This result demonstrates that D-Plex is an ideal solution for precious samples with limited starting material.</p>
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<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
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<p><span>The use of UDI is highly recommended to mitigate errors introduced by read misassignment, including index hopping frequently observed with patterned flow cells such as Illumina’s NovaSeq system.</span></p>
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<p><span style="font-weight: 400;">Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to </span><a href="../applications/dna-rna-shearing"><span style="font-weight: 400;">fragmented DNA or RNA</span></a><span style="font-weight: 400;"> prior to sequencing</span></p>
<p><span style="font-weight: 400;">After input DNA has been fragmented, it is end-repaired and blunt-ended</span><span style="font-weight: 400;">. The next step is a A-tailing in which dAMP is added to the 3´ end of the blunt phosphorylated DNA fragments to prevent concatemerization and to allow the ligation of adaptors with complementary dT overhangs. In addition, barcoded adapters can be incorporated to facilitate multiplexing prior to or during amplification.</span></p>
<center><img src="https://www.diagenode.com/img/categories/library-prep/flux.png" /></center>
<p><span style="font-weight: 400;">Diagenode offers a comprehensive product portfolio for library preparation:<br /></span></p>
<strong><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">D-Plex RNA-seq Library Preparation Kits</a></strong><br />
<p><span style="font-weight: 400;">Diagenode’s new RNA-sequencing solutions utilize the innovative c</span><span style="font-weight: 400;">apture and a</span><span style="font-weight: 400;">mplification by t</span><span style="font-weight: 400;">ailing and s</span><span style="font-weight: 400;">witching”</span><span style="font-weight: 400;">, a ligation-free method to produce DNA libraries for next generation sequencing from low input amounts of RNA. </span><span style="font-weight: 400;"></span><a href="../categories/Library-preparation-for-RNA-seq">Learn more</a></p>
<strong><a href="../categories/library-preparation-for-ChIP-seq">ChIP-seq and DNA sequencing library preparation solutions</a></strong><br />
<p><span style="font-weight: 400;">Our kits have been optimized for DNA library preparation used for next generation sequencing for a wide range of inputs. Using a simple three-step protocols, our</span><a href="http://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><span style="font-weight: 400;"> </span></a><span style="font-weight: 400;">kits are an optimal choice for library preparation from DNA inputs down to 50 pg. </span><a href="../categories/library-preparation-for-ChIP-seq">Learn more</a></p>
<a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span><strong>Bioruptor Pico - short fragments</strong></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">Our well-cited Bioruptor Pico is the shearing device of choice for chromatin and DNA fragmentation. Obtain uniform and tight fragment distributions between 150bp -2kb. </span><a href="../p/bioruptor-pico-sonication-device">Learn more</a></p>
<strong><a href="../p/megaruptor2-1-unit"><span href="../p/bioruptor-pico-sonication-device">Megaruptor</span>® - long fragments</a></strong><a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">The Megaruptor is designed to shear DNA from 3kb-75kb for long-read sequencing. <a href="../p/megaruptor2-1-unit">Learn more</a></span></p>
<span href="../p/bioruptor-pico-sonication-device"></span><span style="font-weight: 400;"></span></div>
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'description' => '<p>While interstitial fibrosis plays a significant role in heart failure, our understanding of disease progression in humans is limited. To address this limitation, we have engineered a cardiac-fibrosis-on-a-chip model consisting of a microfabricated device with live force measurement capabilities using co-cultured human cardiac fibroblasts and pluripotent stem cell-derived cardiomyocytes. Transforming growth factor-β was used as a trigger for fibrosis. Here, we have reproduced the classic hallmarks of fibrosis-induced heart failure including high collagen deposition, increased tissue stiffness, BNP secretion, and passive tension. Force of contraction was significantly decreased in fibrotic tissues that displayed a transcriptomic signature consistent with human cardiac fibrosis/heart failure. Treatment with an anti-fibrotic drug decreased tissue stiffness and BNP secretion, with corresponding changes in the transcriptomic signature. This model represents an accessible approach to study human heart failure in vitro, and allows for testing anti-fibrotic drugs while facilitating the real-time assessment of cardiomyocyte function.</p>',
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'description' => '<p>While interstitial fibrosis plays a significant role in heart failure, our understanding of disease progression in humans is limited. To address this limitation, we have engineered a cardiac-fibrosis-on-a-chip model consisting of a microfabricated device with live force measurement capabilities using co-cultured human cardiac fibroblasts and pluripotent stem cell-derived cardiomyocytes. Transforming growth factor-β was used as a trigger for fibrosis. Here, we have reproduced the classic hallmarks of fibrosis-induced heart failure including high collagen deposition, increased tissue stiffness, BNP secretion, and passive tension. Force of contraction was significantly decreased in fibrotic tissues that displayed a transcriptomic signature consistent with human cardiac fibrosis/heart failure. Treatment with an anti-fibrotic drug decreased tissue stiffness and BNP secretion, with corresponding changes in the transcriptomic signature. This model represents an accessible approach to study human heart failure in vitro, and allows for testing anti-fibrotic drugs while facilitating the real-time assessment of cardiomyocyte function.</p>',
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'description' => '<p>BACKGROUND: ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS: To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS: Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS: We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.</p>',
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'name' => 'CATS mRNA-seq Kit (with polyA selection) v2 x96',
'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
<ul>
<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
</ul>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
<div id="more" class="content">
<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
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<div>
<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
</div>
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<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
</div>
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<h6 style="height:60px">D-Plex mRNA-seq Kit for Illumina</h6>
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'description' => '<div class="small-12 medium-12 large-12 columns" style="border: 3px solid #B02736; padding: 10px; margin: 10px;">
<h2>Product Features</h2>
<ul style="list-style-type: disc;">
<li><span style="font-weight: 400;">An innovative technology with template switching and UMIs</span></li>
<li><span>Ultra-sensitive methodology with low input capability down to 10 ng</span></li>
<li><span>High efficiency for greater gene detection and biomarker identification</span></li>
<li><span>Consistent gene expression profiling, optimal for gene signature definition</span></li>
<li><span>Precise measurement of strand orientation for anti-sense transcription detection</span></li>
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<h4></h4>
<center><a class="chip diahome button" href="https://www.diagenode.com/files/products/kits/dplex-mRNA-manual.pdf" target="_blank" title="dplex total rnaseq user manual"><strong>Download the manual</strong></a></center>
<p></p>
<p>The D-Plex mRNA-seq Library Preparation Kit is a tool designed for gene expression analysis. <span>The kit utilizes the</span><a href="https://www.diagenode.com/en/pages/dplex" target="_blank"><span> </span>D-Plex technology</a><span><span> </span>to generate directional libraries for Illumina sequencing directly from total RNAs.</span></p>
<p><span>The D-Plex technology utilizes two innovative ligation-free mechanisms - poly(A) tailing and template switching - to produce sequencing libraries from low input samples, down to 10 ng of total RNAs. Combined with unique molecular identifiers (UMI), this complete solution delivers a high-sensitivity detection method for gene expression analysis and discovery applications in the coding transcriptome.</span></p>
<p><span></span><span>The D-Plex mRNA-seq Kit offers a time-saving protocol that can be completed within 6 hours and requires minimal hands-on time. <span>The library preparation takes place in a </span><span>single tube</span><span>, increasing the efficiency tremendously. This new solution has been developped to capture an increased number of genes for great discovery efficiency.</span></span></p>
<p><span><span>The D-Plex mRNA-seq Kit includes all buffers and enzymes necessary for mRNA capture and library preparation. Specific D-Plex Unique Dual Indexes were designed and validated to fit the D-Plex technology and are available separately:</span></span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
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<h3>Greater gene discovery efficiency at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/UHR_mRNA.png" alt="total RNA kit" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit enables the detection of higher numbers of genes even for low RNA inputs. Increased number of genes detected at 10x coverage is an indicator of greater sensitivity.</p>
</div>
</div>
<div>
<h3>High mappability to the coding transcriptome</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_biotypes.png" alt="total RNA diversity" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq libraries capture efficiently coding exons and introns present in the sample of interest.</p>
</div>
</div>
<div>
<h3>Consistent, sensitive gene expression profiling</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_violin_tpm_10.png" alt="total RNA" height="200px" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>Gene expression profiling obtained with D-Plex mRNA-seq kit is conserved across a broad dynamic range of inputs, especially for the lowest RNA inputs.</p>
</div>
</div>
<div>
<h3>Exceptional data concordance at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/robustness_corr_HUR_mrna.png" alt="total RNA" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit produces quality data with high data concordance between low and high RNA inputs. This result demonstrates that D-Plex is an ideal solution for precious samples with limited starting material.</p>
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<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
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<p><span>The use of UDI is highly recommended to mitigate errors introduced by read misassignment, including index hopping frequently observed with patterned flow cells such as Illumina’s NovaSeq system.</span></p>
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'name' => 'ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells.',
'authors' => 'Sen M, Wang X, Hamdan FH, Rapp J, Eggert J, Kosinsky RL, Wegwitz F, Kutschat AP, Younesi FS, Gaedcke J, Grade M, Hessmann E, Papantonis A, Strӧbel P, Johnsen SA',
'description' => '<p>BACKGROUND: ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS: To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS: Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS: We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.</p>',
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'meta_keywords' => 'CATS, mRNA-seq, coding RNA, transcriptome, polyA selection, RNA-seq library preparation, low input, easy, user-friendly',
'meta_description' => 'Capture and Amplification by Tailing and Switching(CATS) mRNA-seq Kit is a ligation-free assay providng increased efficiency and minimum bias, with low inputs down to 100 picograms. User-friendly with reduced hands-on time and fewer steps than competing solutions ',
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'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
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<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
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<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
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<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
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<div>
<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
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<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
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<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
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<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
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<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
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'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
<ul>
<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
</ul>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
<div id="more" class="content">
<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
</div>
</li>
</ul>
<div class="carrousel" style="background-position: center;">
<div class="container">
<div class="row" style="background: rgba(255,255,255,0.1); height: 241px;">
<div class="large-12 columns slick">
<div>
<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
</div>
</div>
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'name' => 'CATS mRNA-seq Kit (with polyA selection) v2 x24',
'description' => '<p><strong>An updated version of this kit using D-Plex technology is available for superior performance.</strong></p>
<h4><span>Discover our <strong>NEW<a href="https://www.diagenode.com/en/p/D-Plex-mRNA-seq-Library-Prep-x24"><span> </span>D-Plex mRNA-seq Kit for Illumina</a></strong>.</span></h4>',
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'description' => '<div class="small-12 medium-12 large-12 columns" style="border: 3px solid #B02736; padding: 10px; margin: 10px;">
<h2>Product Features</h2>
<ul style="list-style-type: disc;">
<li><span style="font-weight: 400;">An innovative technology with template switching and UMIs</span></li>
<li><span>Ultra-sensitive methodology with low input capability down to 10 ng</span></li>
<li><span>High efficiency for greater gene detection and biomarker identification</span></li>
<li><span>Consistent gene expression profiling, optimal for gene signature definition</span></li>
<li><span>Precise measurement of strand orientation for anti-sense transcription detection</span></li>
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</div>
<h4></h4>
<center><a class="chip diahome button" href="https://www.diagenode.com/files/products/kits/dplex-mRNA-manual.pdf" target="_blank" title="dplex total rnaseq user manual"><strong>Download the manual</strong></a></center>
<p></p>
<p>The D-Plex mRNA-seq Library Preparation Kit is a tool designed for gene expression analysis. <span>The kit utilizes the</span><a href="https://www.diagenode.com/en/pages/dplex" target="_blank"><span> </span>D-Plex technology</a><span><span> </span>to generate directional libraries for Illumina sequencing directly from total RNAs.</span></p>
<p><span>The D-Plex technology utilizes two innovative ligation-free mechanisms - poly(A) tailing and template switching - to produce sequencing libraries from low input samples, down to 10 ng of total RNAs. Combined with unique molecular identifiers (UMI), this complete solution delivers a high-sensitivity detection method for gene expression analysis and discovery applications in the coding transcriptome.</span></p>
<p><span></span><span>The D-Plex mRNA-seq Kit offers a time-saving protocol that can be completed within 6 hours and requires minimal hands-on time. <span>The library preparation takes place in a </span><span>single tube</span><span>, increasing the efficiency tremendously. This new solution has been developped to capture an increased number of genes for great discovery efficiency.</span></span></p>
<p><span><span>The D-Plex mRNA-seq Kit includes all buffers and enzymes necessary for mRNA capture and library preparation. Specific D-Plex Unique Dual Indexes were designed and validated to fit the D-Plex technology and are available separately:</span></span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
</ul>
<div class="extra-spaced" align="center"></div>
<div class="row">
<div class="carrousel" style="background-position: center;">
<div class="slick">
<div>
<h3>Greater gene discovery efficiency at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/UHR_mRNA.png" alt="total RNA kit" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit enables the detection of higher numbers of genes even for low RNA inputs. Increased number of genes detected at 10x coverage is an indicator of greater sensitivity.</p>
</div>
</div>
<div>
<h3>High mappability to the coding transcriptome</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_biotypes.png" alt="total RNA diversity" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq libraries capture efficiently coding exons and introns present in the sample of interest.</p>
</div>
</div>
<div>
<h3>Consistent, sensitive gene expression profiling</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_violin_tpm_10.png" alt="total RNA" height="200px" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>Gene expression profiling obtained with D-Plex mRNA-seq kit is conserved across a broad dynamic range of inputs, especially for the lowest RNA inputs.</p>
</div>
</div>
<div>
<h3>Exceptional data concordance at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/robustness_corr_HUR_mrna.png" alt="total RNA" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit produces quality data with high data concordance between low and high RNA inputs. This result demonstrates that D-Plex is an ideal solution for precious samples with limited starting material.</p>
</div>
</div>
</div>
</div>
</div>
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'info2' => '<p><span>Specific D-Plex indexes </span><span>were designed and validated to fit the D-Plex technology for Illumina sequencing and </span><span>are not included in the kit. They can be bought separately according to your needs. Please choose the format that suits you best among the compatible references to:</span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
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<p><span></span></p>
<p><span>The use of UDI is highly recommended to mitigate errors introduced by read misassignment, including index hopping frequently observed with patterned flow cells such as Illumina’s NovaSeq system.</span></p>
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<p><img src="https://www.diagenode.com/img/product/kits/dplex/bioinfoPipe.png" alt="small RNA sequencing bioinformatics pipeline" caption="false" width="925" height="196" /></p>
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<div class="small-12 medium-12 large-12 columns">
<p><span style="font-weight: 400;">Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to </span><a href="../applications/dna-rna-shearing"><span style="font-weight: 400;">fragmented DNA or RNA</span></a><span style="font-weight: 400;"> prior to sequencing</span></p>
<p><span style="font-weight: 400;">After input DNA has been fragmented, it is end-repaired and blunt-ended</span><span style="font-weight: 400;">. The next step is a A-tailing in which dAMP is added to the 3´ end of the blunt phosphorylated DNA fragments to prevent concatemerization and to allow the ligation of adaptors with complementary dT overhangs. In addition, barcoded adapters can be incorporated to facilitate multiplexing prior to or during amplification.</span></p>
<center><img src="https://www.diagenode.com/img/categories/library-prep/flux.png" /></center>
<p><span style="font-weight: 400;">Diagenode offers a comprehensive product portfolio for library preparation:<br /></span></p>
<strong><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">D-Plex RNA-seq Library Preparation Kits</a></strong><br />
<p><span style="font-weight: 400;">Diagenode’s new RNA-sequencing solutions utilize the innovative c</span><span style="font-weight: 400;">apture and a</span><span style="font-weight: 400;">mplification by t</span><span style="font-weight: 400;">ailing and s</span><span style="font-weight: 400;">witching”</span><span style="font-weight: 400;">, a ligation-free method to produce DNA libraries for next generation sequencing from low input amounts of RNA. </span><span style="font-weight: 400;"></span><a href="../categories/Library-preparation-for-RNA-seq">Learn more</a></p>
<strong><a href="../categories/library-preparation-for-ChIP-seq">ChIP-seq and DNA sequencing library preparation solutions</a></strong><br />
<p><span style="font-weight: 400;">Our kits have been optimized for DNA library preparation used for next generation sequencing for a wide range of inputs. Using a simple three-step protocols, our</span><a href="http://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><span style="font-weight: 400;"> </span></a><span style="font-weight: 400;">kits are an optimal choice for library preparation from DNA inputs down to 50 pg. </span><a href="../categories/library-preparation-for-ChIP-seq">Learn more</a></p>
<a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span><strong>Bioruptor Pico - short fragments</strong></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">Our well-cited Bioruptor Pico is the shearing device of choice for chromatin and DNA fragmentation. Obtain uniform and tight fragment distributions between 150bp -2kb. </span><a href="../p/bioruptor-pico-sonication-device">Learn more</a></p>
<strong><a href="../p/megaruptor2-1-unit"><span href="../p/bioruptor-pico-sonication-device">Megaruptor</span>® - long fragments</a></strong><a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">The Megaruptor is designed to shear DNA from 3kb-75kb for long-read sequencing. <a href="../p/megaruptor2-1-unit">Learn more</a></span></p>
<span href="../p/bioruptor-pico-sonication-device"></span><span style="font-weight: 400;"></span></div>
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'description' => '<p>: There is no standard chemotherapy for refractory or relapsing malignant pleural mesothelioma (MPM). Our previous reports nevertheless indicated that a combination of an anthracycline (doxorubicin) and a lysine deacetylase inhibitor (valproic acid, VPA) synergize to induce the apoptosis of MPM cells and reduce tumor growth in mouse models. A Phase I/II clinical trial indicated that this regimen is a promising therapeutic option for a proportion of MPM patients. : The transcriptomes of mesothelioma cells were compared after Illumina HiSeq 4000 sequencing. The expression of differentially expressed genes was inhibited by RNA interference. Apoptosis was determined by cell cycle analysis and Annexin V/7-AAD labeling. Protein expression was assessed by immunoblotting. Preclinical efficacy was evaluated in BALB/c and NOD-SCID mice. : To understand the mechanisms involved in chemoresistance, the transcriptomes of two MPM cell lines displaying different responses to VPA-doxorubicin were compared. Among the differentially expressed genes, transforming growth factor alpha (TGFα) was associated with resistance to this regimen. The silencing of TGFα by RNA interference correlated with a significant increase in apoptosis, whereas the overexpression of TGFα desensitized MPM cells to the apoptosis induced by VPA and doxorubicin. The multi-targeted inhibition of histone deacetylase (HDAC), HER2 and TGFα receptor (epidermal growth factor receptor/EGFR) improved treatment efficacy in vitro and reduced tumor growth in two MPM mouse models. Finally, TGFα expression but not EGFR correlated with patient survival. : Our data show that TGFα but not its receptor EGFR is a key factor in resistance to MPM chemotherapy. This observation may contribute to casting light on the promising but still controversial role of EGFR signaling in MPM therapy.</p>',
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'description' => '<p>While interstitial fibrosis plays a significant role in heart failure, our understanding of disease progression in humans is limited. To address this limitation, we have engineered a cardiac-fibrosis-on-a-chip model consisting of a microfabricated device with live force measurement capabilities using co-cultured human cardiac fibroblasts and pluripotent stem cell-derived cardiomyocytes. Transforming growth factor-β was used as a trigger for fibrosis. Here, we have reproduced the classic hallmarks of fibrosis-induced heart failure including high collagen deposition, increased tissue stiffness, BNP secretion, and passive tension. Force of contraction was significantly decreased in fibrotic tissues that displayed a transcriptomic signature consistent with human cardiac fibrosis/heart failure. Treatment with an anti-fibrotic drug decreased tissue stiffness and BNP secretion, with corresponding changes in the transcriptomic signature. This model represents an accessible approach to study human heart failure in vitro, and allows for testing anti-fibrotic drugs while facilitating the real-time assessment of cardiomyocyte function.</p>',
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'description' => '<p>While interstitial fibrosis plays a significant role in heart failure, our understanding of disease progression in humans is limited. To address this limitation, we have engineered a cardiac-fibrosis-on-a-chip model consisting of a microfabricated device with live force measurement capabilities using co-cultured human cardiac fibroblasts and pluripotent stem cell-derived cardiomyocytes. Transforming growth factor-β was used as a trigger for fibrosis. Here, we have reproduced the classic hallmarks of fibrosis-induced heart failure including high collagen deposition, increased tissue stiffness, BNP secretion, and passive tension. Force of contraction was significantly decreased in fibrotic tissues that displayed a transcriptomic signature consistent with human cardiac fibrosis/heart failure. Treatment with an anti-fibrotic drug decreased tissue stiffness and BNP secretion, with corresponding changes in the transcriptomic signature. This model represents an accessible approach to study human heart failure in vitro, and allows for testing anti-fibrotic drugs while facilitating the real-time assessment of cardiomyocyte function.</p>',
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'description' => '<p>BACKGROUND: ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS: To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS: Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS: We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.</p>',
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'pmid' => 'http://www.pubmed.gov/31217031',
'doi' => '10.1186/s13148-019-0690-5',
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'name' => 'CATS mRNA-seq Kit (with polyA selection) v2 x96',
'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
<ul>
<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
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<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
<div id="more" class="content">
<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
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<div class="container">
<div class="row" style="background: rgba(255,255,255,0.1); height: 241px;">
<div class="large-12 columns slick">
<div>
<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
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<div>
<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
</div>
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<h6 style="height:60px">D-Plex mRNA-seq Kit for Illumina</h6>
</div>
</div>
</li>
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'description' => '<div class="small-12 medium-12 large-12 columns" style="border: 3px solid #B02736; padding: 10px; margin: 10px;">
<h2>Product Features</h2>
<ul style="list-style-type: disc;">
<li><span style="font-weight: 400;">An innovative technology with template switching and UMIs</span></li>
<li><span>Ultra-sensitive methodology with low input capability down to 10 ng</span></li>
<li><span>High efficiency for greater gene detection and biomarker identification</span></li>
<li><span>Consistent gene expression profiling, optimal for gene signature definition</span></li>
<li><span>Precise measurement of strand orientation for anti-sense transcription detection</span></li>
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<h4></h4>
<center><a class="chip diahome button" href="https://www.diagenode.com/files/products/kits/dplex-mRNA-manual.pdf" target="_blank" title="dplex total rnaseq user manual"><strong>Download the manual</strong></a></center>
<p></p>
<p>The D-Plex mRNA-seq Library Preparation Kit is a tool designed for gene expression analysis. <span>The kit utilizes the</span><a href="https://www.diagenode.com/en/pages/dplex" target="_blank"><span> </span>D-Plex technology</a><span><span> </span>to generate directional libraries for Illumina sequencing directly from total RNAs.</span></p>
<p><span>The D-Plex technology utilizes two innovative ligation-free mechanisms - poly(A) tailing and template switching - to produce sequencing libraries from low input samples, down to 10 ng of total RNAs. Combined with unique molecular identifiers (UMI), this complete solution delivers a high-sensitivity detection method for gene expression analysis and discovery applications in the coding transcriptome.</span></p>
<p><span></span><span>The D-Plex mRNA-seq Kit offers a time-saving protocol that can be completed within 6 hours and requires minimal hands-on time. <span>The library preparation takes place in a </span><span>single tube</span><span>, increasing the efficiency tremendously. This new solution has been developped to capture an increased number of genes for great discovery efficiency.</span></span></p>
<p><span><span>The D-Plex mRNA-seq Kit includes all buffers and enzymes necessary for mRNA capture and library preparation. Specific D-Plex Unique Dual Indexes were designed and validated to fit the D-Plex technology and are available separately:</span></span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
</ul>
<div class="extra-spaced" align="center"></div>
<div class="row">
<div class="carrousel" style="background-position: center;">
<div class="slick">
<div>
<h3>Greater gene discovery efficiency at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/UHR_mRNA.png" alt="total RNA kit" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit enables the detection of higher numbers of genes even for low RNA inputs. Increased number of genes detected at 10x coverage is an indicator of greater sensitivity.</p>
</div>
</div>
<div>
<h3>High mappability to the coding transcriptome</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_biotypes.png" alt="total RNA diversity" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq libraries capture efficiently coding exons and introns present in the sample of interest.</p>
</div>
</div>
<div>
<h3>Consistent, sensitive gene expression profiling</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_violin_tpm_10.png" alt="total RNA" height="200px" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>Gene expression profiling obtained with D-Plex mRNA-seq kit is conserved across a broad dynamic range of inputs, especially for the lowest RNA inputs.</p>
</div>
</div>
<div>
<h3>Exceptional data concordance at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/robustness_corr_HUR_mrna.png" alt="total RNA" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit produces quality data with high data concordance between low and high RNA inputs. This result demonstrates that D-Plex is an ideal solution for precious samples with limited starting material.</p>
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<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
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<p><span>The use of UDI is highly recommended to mitigate errors introduced by read misassignment, including index hopping frequently observed with patterned flow cells such as Illumina’s NovaSeq system.</span></p>
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<p><img src="https://www.diagenode.com/img/product/kits/dplex/bioinfoPipe.png" alt="small RNA sequencing bioinformatics pipeline" caption="false" width="925" height="196" /></p>
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'name' => 'ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells.',
'authors' => 'Sen M, Wang X, Hamdan FH, Rapp J, Eggert J, Kosinsky RL, Wegwitz F, Kutschat AP, Younesi FS, Gaedcke J, Grade M, Hessmann E, Papantonis A, Strӧbel P, Johnsen SA',
'description' => '<p>BACKGROUND: ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS: To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS: Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS: We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.</p>',
'date' => '2019-06-19',
'pmid' => 'http://www.pubmed.gov/31217031',
'doi' => '10.1186/s13148-019-0690-5',
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'meta_description' => 'Capture and Amplification by Tailing and Switching(CATS) mRNA-seq Kit is a ligation-free assay providng increased efficiency and minimum bias, with low inputs down to 100 picograms. User-friendly with reduced hands-on time and fewer steps than competing solutions ',
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'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
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<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
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<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
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<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
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<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
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<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
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<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
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<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
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<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
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<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
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<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
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<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<h3>Very reproducible library preparation method</h3>
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<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
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<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
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<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
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<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
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<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
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<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
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<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
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<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
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<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
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<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
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'description' => '<p><strong>An updated version of this kit using D-Plex technology is available for superior performance.</strong></p>
<h4><span>Discover our <strong>NEW<a href="https://www.diagenode.com/en/p/D-Plex-mRNA-seq-Library-Prep-x24"><span> </span>D-Plex mRNA-seq Kit for Illumina</a></strong>.</span></h4>',
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<h2>Product Features</h2>
<ul style="list-style-type: disc;">
<li><span style="font-weight: 400;">An innovative technology with template switching and UMIs</span></li>
<li><span>Ultra-sensitive methodology with low input capability down to 10 ng</span></li>
<li><span>High efficiency for greater gene detection and biomarker identification</span></li>
<li><span>Consistent gene expression profiling, optimal for gene signature definition</span></li>
<li><span>Precise measurement of strand orientation for anti-sense transcription detection</span></li>
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<h4></h4>
<center><a class="chip diahome button" href="https://www.diagenode.com/files/products/kits/dplex-mRNA-manual.pdf" target="_blank" title="dplex total rnaseq user manual"><strong>Download the manual</strong></a></center>
<p></p>
<p>The D-Plex mRNA-seq Library Preparation Kit is a tool designed for gene expression analysis. <span>The kit utilizes the</span><a href="https://www.diagenode.com/en/pages/dplex" target="_blank"><span> </span>D-Plex technology</a><span><span> </span>to generate directional libraries for Illumina sequencing directly from total RNAs.</span></p>
<p><span>The D-Plex technology utilizes two innovative ligation-free mechanisms - poly(A) tailing and template switching - to produce sequencing libraries from low input samples, down to 10 ng of total RNAs. Combined with unique molecular identifiers (UMI), this complete solution delivers a high-sensitivity detection method for gene expression analysis and discovery applications in the coding transcriptome.</span></p>
<p><span></span><span>The D-Plex mRNA-seq Kit offers a time-saving protocol that can be completed within 6 hours and requires minimal hands-on time. <span>The library preparation takes place in a </span><span>single tube</span><span>, increasing the efficiency tremendously. This new solution has been developped to capture an increased number of genes for great discovery efficiency.</span></span></p>
<p><span><span>The D-Plex mRNA-seq Kit includes all buffers and enzymes necessary for mRNA capture and library preparation. Specific D-Plex Unique Dual Indexes were designed and validated to fit the D-Plex technology and are available separately:</span></span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
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<div class="extra-spaced" align="center"></div>
<div class="row">
<div class="carrousel" style="background-position: center;">
<div class="slick">
<div>
<h3>Greater gene discovery efficiency at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/UHR_mRNA.png" alt="total RNA kit" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit enables the detection of higher numbers of genes even for low RNA inputs. Increased number of genes detected at 10x coverage is an indicator of greater sensitivity.</p>
</div>
</div>
<div>
<h3>High mappability to the coding transcriptome</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_biotypes.png" alt="total RNA diversity" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq libraries capture efficiently coding exons and introns present in the sample of interest.</p>
</div>
</div>
<div>
<h3>Consistent, sensitive gene expression profiling</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_violin_tpm_10.png" alt="total RNA" height="200px" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>Gene expression profiling obtained with D-Plex mRNA-seq kit is conserved across a broad dynamic range of inputs, especially for the lowest RNA inputs.</p>
</div>
</div>
<div>
<h3>Exceptional data concordance at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/robustness_corr_HUR_mrna.png" alt="total RNA" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit produces quality data with high data concordance between low and high RNA inputs. This result demonstrates that D-Plex is an ideal solution for precious samples with limited starting material.</p>
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<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
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<p><span>The use of UDI is highly recommended to mitigate errors introduced by read misassignment, including index hopping frequently observed with patterned flow cells such as Illumina’s NovaSeq system.</span></p>
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<p><span style="font-weight: 400;">Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to </span><a href="../applications/dna-rna-shearing"><span style="font-weight: 400;">fragmented DNA or RNA</span></a><span style="font-weight: 400;"> prior to sequencing</span></p>
<p><span style="font-weight: 400;">After input DNA has been fragmented, it is end-repaired and blunt-ended</span><span style="font-weight: 400;">. The next step is a A-tailing in which dAMP is added to the 3´ end of the blunt phosphorylated DNA fragments to prevent concatemerization and to allow the ligation of adaptors with complementary dT overhangs. In addition, barcoded adapters can be incorporated to facilitate multiplexing prior to or during amplification.</span></p>
<center><img src="https://www.diagenode.com/img/categories/library-prep/flux.png" /></center>
<p><span style="font-weight: 400;">Diagenode offers a comprehensive product portfolio for library preparation:<br /></span></p>
<strong><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">D-Plex RNA-seq Library Preparation Kits</a></strong><br />
<p><span style="font-weight: 400;">Diagenode’s new RNA-sequencing solutions utilize the innovative c</span><span style="font-weight: 400;">apture and a</span><span style="font-weight: 400;">mplification by t</span><span style="font-weight: 400;">ailing and s</span><span style="font-weight: 400;">witching”</span><span style="font-weight: 400;">, a ligation-free method to produce DNA libraries for next generation sequencing from low input amounts of RNA. </span><span style="font-weight: 400;"></span><a href="../categories/Library-preparation-for-RNA-seq">Learn more</a></p>
<strong><a href="../categories/library-preparation-for-ChIP-seq">ChIP-seq and DNA sequencing library preparation solutions</a></strong><br />
<p><span style="font-weight: 400;">Our kits have been optimized for DNA library preparation used for next generation sequencing for a wide range of inputs. Using a simple three-step protocols, our</span><a href="http://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><span style="font-weight: 400;"> </span></a><span style="font-weight: 400;">kits are an optimal choice for library preparation from DNA inputs down to 50 pg. </span><a href="../categories/library-preparation-for-ChIP-seq">Learn more</a></p>
<a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span><strong>Bioruptor Pico - short fragments</strong></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">Our well-cited Bioruptor Pico is the shearing device of choice for chromatin and DNA fragmentation. Obtain uniform and tight fragment distributions between 150bp -2kb. </span><a href="../p/bioruptor-pico-sonication-device">Learn more</a></p>
<strong><a href="../p/megaruptor2-1-unit"><span href="../p/bioruptor-pico-sonication-device">Megaruptor</span>® - long fragments</a></strong><a href="../p/bioruptor-pico-sonication-device"><span style="font-weight: 400;"></span></a><a href="../categories/library-preparation-for-ChIP-seq-and-DNA-sequencing"><span style="font-weight: 400;"></span></a><br />
<p><span style="font-weight: 400;"></span><span style="font-weight: 400;">The Megaruptor is designed to shear DNA from 3kb-75kb for long-read sequencing. <a href="../p/megaruptor2-1-unit">Learn more</a></span></p>
<span href="../p/bioruptor-pico-sonication-device"></span><span style="font-weight: 400;"></span></div>
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'name' => 'ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells.',
'authors' => 'Sen M, Wang X, Hamdan FH, Rapp J, Eggert J, Kosinsky RL, Wegwitz F, Kutschat AP, Younesi FS, Gaedcke J, Grade M, Hessmann E, Papantonis A, Strӧbel P, Johnsen SA',
'description' => '<p>BACKGROUND: ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS: To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS: Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS: We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.</p>',
'date' => '2019-06-19',
'pmid' => 'http://www.pubmed.gov/31217031',
'doi' => '10.1186/s13148-019-0690-5',
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'description' => '<p style="text-align: justify;">Diagenode’s CATS mRNA-seq Kit (with polyA selection) utilizes the innovative “<strong>C</strong>apture and <strong>A</strong>mplification by <strong>T</strong>ailing and <strong>S</strong>witching” (CATS), a <strong>ligation-free method</strong> to produce DNA libraries for next generation sequencing from low input amounts of RNA.</p>
<ul>
<li>Diverse transcripts detection</li>
<li>Excellent reproducibility with ultra low inputs down to 100 pg</li>
<li>Great performance on challenging samples</li>
</ul>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#more" style="color: #13b29c; background-color: transparent; display: inline; padding: 0;">Read more</a>
<div id="more" class="content">
<p style="text-align: justify;">CATS relies on polynucleotide tailing for capturing the 3’-ends of nucleic acids and the template switching ability of MMLV-RT to capture the 5’ ends for cDNA synthesis. This kit allows for generating Illumina compatible ready-to-sequence libraries from <strong>RNA inputs as low as 100 picograms</strong> of polyA selected material in just few hours.</p>
<p style="text-align: justify;">Libraries retain <strong>strand specificity</strong> of origin. Unlike competing solutions, our CATS RNA-seq kit exhibits <strong>higher library efficiency</strong> versus ligation-based methods providing <strong>higher complexity</strong> from better template capture and minimal bias due to <strong>lower amplification</strong> requirements.</p>
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<div>
<h3>Broad overview of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/polyA-mRNA-seq-1ng-10ng
.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. TPM ≥2. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Retained complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/Retained-complexity-at-low-inputs-figure.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Biotypes* represented in the libraries <strong>CATS v2 mRNA-seq Kit.</strong> TPM ≥2. <br /> Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). * < 0.04% of total detected transcripts at this threshold is rRNA</p>
</div>
</div>
<div>
<h3>Uniquely detected transcripts</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_1_M1_all_CATS_NEB_nolimit_NEW.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>All detected transcripts in <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional library preparation Kit. No threshold has been set for the analysis. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 36,245 transcripts found in both libraries.</p>
</div>
</div>
<div>
<h3>Consistency and wide representation of the transcriptome</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_2_M1_coding_CATS_SM.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Comparison on the number of coding transcripts detected with <strong>CATS v2 mRNA-seq Kit</strong> vs SMARTer stranded RNA-seq library preparation kit. TPM ≥2. <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000). 21,333 transcripts found in both libraries.</p>
</div>
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<div>
<h3>High-complexity at low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/high-complexity-low-inputs.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Mapped reads distribution for <strong>CATS v2 mRNA-seq Kit</strong> vs NEBNext Ultra I directional RNA-seq Kit. <br />Input: <strong>1 ng, 10 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
</div>
<div>
<h3>High correlation in transcripts detection across ultra low inputs</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_6_v1_M_scatter_inputs_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in 1 ng vs 0.1 ng samples of <strong>CATS v2 mRNA-seq libraries. </strong>TPM≥2. <br />Input: <strong>1 ng, 0.1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
</div>
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<div>
<h3>Very reproducible library preparation method</h3>
<div class="large-7 small-12 medium-7 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW-FIG_3_M1_scatter_replicates_CATS.png" /></div>
<div class="large-5 small-12 medium-5 columns">
<p>Transcripts detected in two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong> TPM≥2 <br />Input: <strong>1 ng</strong> poly(A) RNA from human universal total RNA (Agilent, 740000).</p>
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<div>
<h3>Few PCR cycles, less amplification bias</h3>
<div class="large-12 small-12 medium-12 columns"><img src="https://www.diagenode.com/img/product/kits/cats/NEW_1ng-polyA-RNA-CATSV2.png" /></div>
<div class="large-12 small-12 medium-12 columns">
<p>BioAnalyzer® electropherogram of two technical replicates of <strong>CATS v2 mRNA-seq libraries.</strong><br /> Input: <strong>1 ng</strong> rRNA(-) RNA from human universal total RNA (Agilent, 740000).</p>
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<h3>CATS saves time</h3>
<img src="https://www.diagenode.com/img/categories/library-prep/cats-save-time.png" /></div>
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<h6 style="height:60px">D-Plex mRNA-seq Kit for Illumina</h6>
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<h2>Product Features</h2>
<ul style="list-style-type: disc;">
<li><span style="font-weight: 400;">An innovative technology with template switching and UMIs</span></li>
<li><span>Ultra-sensitive methodology with low input capability down to 10 ng</span></li>
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<h4></h4>
<center><a class="chip diahome button" href="https://www.diagenode.com/files/products/kits/dplex-mRNA-manual.pdf" target="_blank" title="dplex total rnaseq user manual"><strong>Download the manual</strong></a></center>
<p></p>
<p>The D-Plex mRNA-seq Library Preparation Kit is a tool designed for gene expression analysis. <span>The kit utilizes the</span><a href="https://www.diagenode.com/en/pages/dplex" target="_blank"><span> </span>D-Plex technology</a><span><span> </span>to generate directional libraries for Illumina sequencing directly from total RNAs.</span></p>
<p><span>The D-Plex technology utilizes two innovative ligation-free mechanisms - poly(A) tailing and template switching - to produce sequencing libraries from low input samples, down to 10 ng of total RNAs. Combined with unique molecular identifiers (UMI), this complete solution delivers a high-sensitivity detection method for gene expression analysis and discovery applications in the coding transcriptome.</span></p>
<p><span></span><span>The D-Plex mRNA-seq Kit offers a time-saving protocol that can be completed within 6 hours and requires minimal hands-on time. <span>The library preparation takes place in a </span><span>single tube</span><span>, increasing the efficiency tremendously. This new solution has been developped to capture an increased number of genes for great discovery efficiency.</span></span></p>
<p><span><span>The D-Plex mRNA-seq Kit includes all buffers and enzymes necessary for mRNA capture and library preparation. Specific D-Plex Unique Dual Indexes were designed and validated to fit the D-Plex technology and are available separately:</span></span></p>
<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-B" title="D-Plex UDI Module - Set B" target="_blank"><span>C05030022</span> - D-Plex Unique Dual Indexes for Illumina - Set B</a></li>
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<div class="carrousel" style="background-position: center;">
<div class="slick">
<div>
<h3>Greater gene discovery efficiency at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/UHR_mRNA.png" alt="total RNA kit" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit enables the detection of higher numbers of genes even for low RNA inputs. Increased number of genes detected at 10x coverage is an indicator of greater sensitivity.</p>
</div>
</div>
<div>
<h3>High mappability to the coding transcriptome</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_biotypes.png" alt="total RNA diversity" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq libraries capture efficiently coding exons and introns present in the sample of interest.</p>
</div>
</div>
<div>
<h3>Consistent, sensitive gene expression profiling</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/HUR_mRNA_violin_tpm_10.png" alt="total RNA" height="200px" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>Gene expression profiling obtained with D-Plex mRNA-seq kit is conserved across a broad dynamic range of inputs, especially for the lowest RNA inputs.</p>
</div>
</div>
<div>
<h3>Exceptional data concordance at low inputs</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center><img src="https://www.diagenode.com/img/product/kits/dplex/robustness_corr_HUR_mrna.png" alt="total RNA" /></center></div>
<div class="large-6 small-12 medium-6 large-centered medium-centered small-centered columns">
<p></p>
<p>D-Plex mRNA-seq kit produces quality data with high data concordance between low and high RNA inputs. This result demonstrates that D-Plex is an ideal solution for precious samples with limited starting material.</p>
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<ul>
<li><a href="https://www.diagenode.com/en/p/D-Plex-24-Unique-Dual-Indexes-Set-A" title="D-Plex UDI Module - Set A" target="_blank"><span>C05030021</span> - D-Plex Unique Dual Indexes for Illumina - Set A</a></li>
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'name' => 'ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells.',
'authors' => 'Sen M, Wang X, Hamdan FH, Rapp J, Eggert J, Kosinsky RL, Wegwitz F, Kutschat AP, Younesi FS, Gaedcke J, Grade M, Hessmann E, Papantonis A, Strӧbel P, Johnsen SA',
'description' => '<p>BACKGROUND: ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS: To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS: Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS: We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.</p>',
'date' => '2019-06-19',
'pmid' => 'http://www.pubmed.gov/31217031',
'doi' => '10.1186/s13148-019-0690-5',
'modified' => '2019-08-06 16:37:28',
'created' => '2019-07-31 13:35:50',
'ProductsPublication' => array(
'id' => '3938',
'product_id' => '2847',
'publication_id' => '3743'
)
)
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View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118
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