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What We Offer | Donnelly Centre for Cellular and Biomolecular Research
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<nav role="navigation" aria-labelledby="system-breadcrumb" class="m-breadcrumbs"> <h2 class="visually-hidden" id="system-breadcrumb">Breadcrumbs</h2> <ol class="m-breadcrumbs__list"> <li class="m-breadcrumbs__item"> <a class="m-breadcrumbs__link" href="/">Home</a> </li> <li class="m-breadcrumbs__item"> <a class="m-breadcrumbs__link" href="/platforms">Platforms</a> </li> <li class="m-breadcrumbs__item"> <a class="m-breadcrumbs__link" href="/donnelly-sequencing-centre">Donnelly Sequencing Centre</a> </li> <li class="m-breadcrumbs__item"> What We Offer </li> </ol> </nav> </div> </div> <div class="l-main-2col__utility"> <div data-drupal-messages-fallback class="hidden"></div> </div> <div class="l-main-2col__content"> <div class="o-content-header"> <h1 class="a-heading__t1 " > What We Offer </h1> </div> <div class="wp-layout-sidebar-section"> <div class="l-section-bg l-section-1"> <div class="l-section-1__zone-1 l-flex " > <div class="paragraph--published"> <div class="m-text"> <div class="m-text__content s-wysiwyg"> <div class="s-wysiwyg"><p>We offer sequencing, <a href="https://live-w2-donnelly-centre.pantheonsite.io/node/365/edit#Library%20Prep" target="_blank">library preparation</a>, and <a href="https://live-w2-donnelly-centre.pantheonsite.io/node/365/edit#Other" target="_blank">other services</a>. Take a look at what’s available at the DSC, and then proceed to <a data-entity-substitution="canonical" data-entity-type="node" data-entity-uuid="db36e054-0bc0-4853-9fda-191f9ba9a335" href="/getting-started" target="_blank" title="Getting Started">Getting Started</a> to take the first step in your project.</p> <h2>Sequencing</h2> <p>We accept libraries prepared by you and submitted directly to us for sequencing. Use the table below to explore which instrument best fits your project – grey cells indicate available run modes and Illumina’s expected data output in gigabases.</p></div> </div> </div> </div> <div class="paragraph--published"> <div class="m-image"> <div class="m-image-wrap width--100"> <picture> <source srcset="/sites/default/files/styles/landscape_3_2_400/public/assets/images/sequencers5.webp?itok=DmLSBjAR 400w, /sites/default/files/styles/landscape_3_2_600/public/assets/images/sequencers5.webp?itok=GznRa2b- 600w, /sites/default/files/styles/landscape_3_2_860/public/assets/images/sequencers5.webp?itok=BduoLWL4 900w, /sites/default/files/styles/landscape_3_2_1200/public/assets/images/sequencers5.webp?itok=UTyULvxH 1200w, /sites/default/files/styles/landscape_3_2_1500/public/assets/images/sequencers5.webp?itok=Nu766J3l 1500w, /sites/default/files/styles/landscape_3_2_1800/public/assets/images/sequencers5.webp?itok=fuMr0Hg8 1800w" type="image/webp" sizes="(min-width:1280px) 820px, (min-width:900px) 70vw, 100vw - 48px" width="900" height="600"/> <source srcset="/sites/default/files/styles/landscape_3_2_400/public/assets/images/sequencers5.png?itok=DmLSBjAR 400w, /sites/default/files/styles/landscape_3_2_600/public/assets/images/sequencers5.png?itok=GznRa2b- 600w, /sites/default/files/styles/landscape_3_2_860/public/assets/images/sequencers5.png?itok=BduoLWL4 900w, /sites/default/files/styles/landscape_3_2_1200/public/assets/images/sequencers5.png?itok=UTyULvxH 1200w, /sites/default/files/styles/landscape_3_2_1500/public/assets/images/sequencers5.png?itok=Nu766J3l 1500w, /sites/default/files/styles/landscape_3_2_1800/public/assets/images/sequencers5.png?itok=fuMr0Hg8 1800w" type="image/png" sizes="(min-width:1280px) 820px, (min-width:900px) 70vw, 100vw - 48px" width="900" height="600"/> <img width="900" height="600" srcset="/sites/default/files/styles/landscape_3_2_400/public/assets/images/sequencers5.png?itok=DmLSBjAR 400w, /sites/default/files/styles/landscape_3_2_600/public/assets/images/sequencers5.png?itok=GznRa2b- 600w, /sites/default/files/styles/landscape_3_2_860/public/assets/images/sequencers5.png?itok=BduoLWL4 900w, /sites/default/files/styles/landscape_3_2_1200/public/assets/images/sequencers5.png?itok=UTyULvxH 1200w, /sites/default/files/styles/landscape_3_2_1500/public/assets/images/sequencers5.png?itok=Nu766J3l 1500w, /sites/default/files/styles/landscape_3_2_1800/public/assets/images/sequencers5.png?itok=fuMr0Hg8 1800w" sizes="(min-width:1280px) 820px, (min-width:900px) 70vw, 100vw - 48px" src="/sites/default/files/styles/landscape_3_2_1800/public/assets/images/sequencers5.png?itok=fuMr0Hg8" alt="Sequencers" loading="lazy" typeof="foaf:Image" /> </picture> </div> </div> </div> <div class="paragraph--published"> <div class="m-text"> <div class="m-text__content s-wysiwyg"> <div class="s-wysiwyg"><p>To help our users take advantage of the low cost/gigabase on the NovaSeq, we offer <strong>NovaSeq flex service</strong>, where we let you use part of a flowcell, and run your project alongside other compatible projects. Please note, however, that this can increase turnaround time as we wait for other projects – filling up a flowcell with your own samples is your best bet for getting data back quickly.</p> <p><a id="Library Prep" name="Library Prep"></a></p> <h2>Library preparation</h2> <p>We also offer complete library preparation services for a wide variety of sample types and analysis needs.</p> <table class="a-table--content-columns"> <thead> <tr> <th> <h2>DNA</h2> </th> <th> <h2>RNA</h2> </th> </tr> </thead> <tbody> <tr> <td> <p><strong>DNA-Seq (e.g. shotgun)</strong><br> NEB NEBNext Ultra II DNA<br> NEB NEBNext Ultra II FS DNA<br> Illumina Nextera DNA Flex<br> Illumina Nextera DNA XT</p> <p><strong>ChIP-Seq</strong><br> NEBNext Ultra II DNA for ChIP<br> Illumina TruSeq ChIP-Seq</p> <p><strong>Methylation</strong><br> Tecan Ovation RRBS Methyl-Seq*</p> <p><strong>Amplicon sequencing</strong><br> Illumina 16S rRNA metagenomics<br> Illumina ITS rRNA metagenomics<br> Illumina custom amplicon PCR<br> Custom CRISPR screen (single and dual guides)</p> <p><strong>Whole-exome sequencing</strong><br> Illumina Nextera Exome*</p> </td> <td> <p><strong>Ribo-depletion RNA-Seq – stranded</strong><br> NEB NEBNext Ultra II Directional RNA<br> Illumina TruSeq Stranded Total Ribo-Zero</p> <p><strong>mRNA-Seq – stranded </strong><br> <span><span><span>NEBNext® Poly(A) mRNA Magnetic Isolation Module</span></span></span><br> <span><span><span>NEB NEBNext Ultra II Directional RNA </span></span></span><br> <span><span><span>Illumina TruSeq Stranded mRNA</span></span></span><br> <span><span><span>SMARTer® Stranded RNA-Seq Kit</span></span></span></p> <p><strong>Small RNA-Seq</strong><br> Perkin Elmer NEXTFLEX® Small RNA-Seq Kit v4<br> Takara SMARTer smRNA-Seq<br> NEB NEBNext Small RNA</p> <p><strong>mi RNA-Seq</strong><br> QIAseq miRNA</p> <p><strong>3' end-Seq</strong><br> Lexogen Quantseq 3'mRNA-seq library REV</p> </td> </tr> </tbody> </table> <table> <tbody> </tbody> </table> <p>*Most kits listed here are kept in stock and available on-demand. For methylation sequencing, exome sequencing, and other methods not listed here, including Takara SMART chemistry, please <a href="mailto:dseqcentre@utoronto.ca">contact us</a> for a custom order. We're also happy to collaborate on method development for novel protocols.</p> <h2>Data distribution and storage</h2> <p>Sequence data are distributed on our servers as de-multiplexed compressed FASTQ files. Our default multiplex settings are trimming enabled, with 1 index mismatch allowed.</p> <p>For users who are newer to NGS and bioinformatics, we recommend trying Illumina’s <a href="https://basespace.illumina.com/">BaseSpace</a> application. If you’ve signed up for an account, include your BaseSpace information on your Sample Information Sheet and we’ll upload your data directly there (timing dependent on network availability). This will allow you to make use of their many cloud-based sequencing analysis applications, including BWA, Cufflinks, TopHat, Velvet, Issac, RNAexpress, DNAstar, and FASTQC. Sign up and explore their toolset at <a href="https://support.illumina.com/sequencing/sequencing_software/basespace.html">Illumina</a>.</p> <p><strong>Raw data (and samples) will be stored at the DSC for 3 months after project completion; demultiplexed fastq files are stored for two weeks.</strong></p> <p><a id="Other" name="Other"></a></p> <h2>Other services</h2> <p>Preparing libraries yourself but missing some key equipment? The DSC offers the following services:</p> <ul> <li> <p><strong>DNA or RNA quantification</strong>: ThermoFisher Qubit (low-throughput) or Quant-iT (high-throughput), broad range or high sensitivity kits</p> </li> <li> <p><strong>RNA fragment analysis</strong>: Agilent TapeStation HS RNA ScreenTape or Bioanalyzer RNA Pico Chip</p> </li> <li> <p><strong>Library distribution analysis</strong>: Agilent TapeStation HS D1000 ScreenTape or BioAnalyzer HS DNA Chip</p> </li> <li> <p><strong>Library quantification</strong>: NEBNext Library Quant qPCR</p> </li> <li> <p><strong>Bead cleanups and size selection</strong>: MagBio HighPrep beads (Ampure XP equivalent)</p> </li> </ul> <p><a href="mailto:dseqcentre@utoronto.ca">Contact us</a> about making use of other basic pieces of lab equipment (e.g. thermocycler, heating block, tube or plate centrifuge).</p></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </main> <footer class="l-page__footer"> <div class="o-site-footer"> <div 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Donnelly</a> </li> <li class="m-menu-mobile__item--level-2 has-submenu"> <a href="/built-21st-century-science" class="m-menu-mobile__link--level-2 is-toggle" data-drupal-link-system-path="node/285">History of the Donnelly Centre</a> <ul class="m-menu-mobile__list--level-3"> <li class="m-menu-mobile__item--level-3"> <a href="/banting-and-best-department-medical-research-timeline" class="m-menu-mobile__link--level-3" data-drupal-link-system-path="node/347">Get to know our history through this interactive timeline</a> </li> <li class="m-menu-mobile__item--level-3"> <a href="/banting-and-best-department-medical-research" class="m-menu-mobile__link--level-3" data-drupal-link-system-path="node/344">Banting and Best Department of Medical Research</a> </li> <li class="m-menu-mobile__item--level-3"> <a href="/brenda-andrews-founding-director-donnelly-centre" class="m-menu-mobile__link--level-3" data-drupal-link-system-path="node/476">Brenda Andrews, Founding Director of Donnelly Centre</a> </li> <li class="m-menu-mobile__item--level-3"> <a href="/james-friesen-co-founder-donnelly-centre" class="m-menu-mobile__link--level-3" data-drupal-link-system-path="node/348">James Friesen, Co-Founder of Donnelly Centre</a> </li> <li class="m-menu-mobile__item--level-3"> <a href="/cecil-yip-co-founder-donnelly-centre" class="m-menu-mobile__link--level-3" data-drupal-link-system-path="node/346">Cecil Yip, Co-Founder of Donnelly Centre</a> </li> </ul> </li> <li class="m-menu-mobile__item--level-2"> <a href="/staff" class="m-menu-mobile__link--level-2" data-drupal-link-system-path="node/305">Staff</a> </li> <li class="m-menu-mobile__item--level-2"> <a href="/image-gallery" class="m-menu-mobile__link--level-2" data-drupal-link-system-path="node/328">Image Gallery</a> </li> <li class="m-menu-mobile__item--level-2"> <a href="/contact-us" class="m-menu-mobile__link--level-2" data-drupal-link-system-path="node/311">Contact Us</a> </li> </ul> </li> <div id="menu-mobile-header-content"> <div class="m-menu-mobile__header-content"> </div> </div> </ul> </nav> </div> <script>window.dataLayer = window.dataLayer || []; window.dataLayer.push({"drupalLanguage":"en","drupalCountry":null,"siteName":"Donnelly Centre for Cellular and Biomolecular Research","entityName":"migrate","entityType":"node","entityBundle":"ed_page","entityId":"365","entityTitle":"What We Offer","userUid":0,"breadcrumbLevel1":"Platforms","breadcrumbLevel2":"Donnelly Sequencing Centre","breadcrumbLevel3":"What We Offer"});</script> <link rel="stylesheet" href="https://use.typekit.net/zls1oah.css"> <script type="application/json" data-drupal-selector="drupal-settings-json">{"path":{"baseUrl":"\/","pathPrefix":"","currentPath":"node\/365","currentPathIsAdmin":false,"isFront":false,"currentLanguage":"en"},"pluralDelimiter":"\u0003","suppressDeprecationErrors":true,"ajaxPageState":{"libraries":"eJx9kFEKAyEQQy8keiSJOlWpzoijXfb2XUqhpR_9eySBhITtwraxULzTNBEX3drW4j5oO_E2ceuS7pF6ZddReRGDI3mWVSOpSVhoOGm6QAWPKlPNTXjhIJVO7outPrINE5z-R1RaTSaL5EYejHZeVep-BTMwkSdGUZfmHmj2o9jNY4dWtVAyeuqi7gKUzEFhIF6dm6_pVdinKSPJwX8s__ri7ecmAe0Jwbd-_A","theme":"webpac","theme_token":null},"ajaxTrustedUrl":[],"bu":{"_core":{"default_config_hash":"AblkqYHezKA1TuKStbuiQqvACikY5ElI-bHxMy-C25U"},"notify_ie":11,"notify_firefox":-2,"notify_opera":-2,"notify_safari":-2,"notify_chrome":-2,"insecure":false,"unsupported":false,"mobile":false,"visibility_type":"hide","visibility_pages":"admin\/*","source":"\/\/browser-update.org\/update.min.js","show_source":"","position":"top","text_override":"","reminder":4380,"reminder_closed":4380,"new_window":true,"url":"","no_close":false,"test_mode":false},"dataLayer":{"defaultLang":"en","languages":{"en":{"id":"en","name":"English","direction":"ltr","weight":0}}},"google_analytics":{"account":"UA-34496632-11","trackOutbound":true,"trackMailto":true,"trackTel":true,"trackDownload":true,"trackDownloadExtensions":"7z|aac|arc|arj|asf|asx|avi|bin|csv|doc(x|m)?|dot(x|m)?|exe|flv|gif|gz|gzip|hqx|jar|jpe?g|js|mp(2|3|4|e?g)|mov(ie)?|msi|msp|pdf|phps|png|ppt(x|m)?|pot(x|m)?|pps(x|m)?|ppam|sld(x|m)?|thmx|qtm?|ra(m|r)?|sea|sit|tar|tgz|torrent|txt|wav|wma|wmv|wpd|xls(x|m|b)?|xlt(x|m)|xlam|xml|z|zip"},"user":{"uid":0,"permissionsHash":"e5117ae9e1952bc666f6f6eded612e9062e3e550f37a6e73234d0ebf81dbff34"}}</script> <script src="/sites/default/files/js/js_vMSEPHDskVi_p9TfdYxNiqFwZ_jUvnuiJNwO6MCW38g.js?scope=footer&delta=0&language=en&theme=webpac&include=eJx9jkEOwyAMBD-E4EnIxg5BdewIQ1B-314qVT3ktjs7h8WZcMayc3lxDwQDBG7uCXmHq1n3sJkOWOx2cPrJ0a8a3aTRo4EdlDxUsyqcQUHu0YqnfxAW4wklVTEE-bbNpn4-NdNM3U6ypQ9TPljnG5FMUo4"></script> </body> </html>