Genomics Core | Gladstone Institutes

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block-page-title-block"> <div class="content"> <h1 class="title page-title"><span class="field field--name-title field--type-string field--label-hidden">Genomics Core</span> </h1> </div> </div> </div> </div> </div> </div> </div> </div> </div> <div class="clearfix main-content region--dark-typography region--white-background region--no-separator"> <div class="landing-page-container" > <div class="clearfix main-content__container"> <div class="row"> <section> <div class="clearfix main-content__section" > <div class="region region-content"> <div id="block-showcase-lite-content" class="clearfix block block-system block-system-main-block"> <div class="content"> <article data-history-node-id="3271" class="node node--type-core-mini-sites node--promoted node--view-mode-full clearfix"> <div class="node__container"> <div class="node__main-content clearfix"> <header class="node__header"> </header> <div id="mini-core-tabs" class="row"> <div id="subtabs" class="subtabs"> <ul class="sudonav"> <li class="tab"><a href="#overview"><span>Overview</span></a></li> <li class="tab"><a href="#capabilities"><span>Capabilities</span></a></li> <li class="tab"><a href="#fees-and-scheduling"><span>Fees and Scheduling</span></a></li> <li class="tab"><a href="#publications"><span>Publications</span></a></li> <li class="tab"><a href="#faqs"><span>FAQs</span></a></li> </ul> <div class="content-wrap"> <section id="overview"> <div id="intro"> <div class="container"> <p class="large">The Genomics Core provides state-of-the-art genomic and sequencing services to support basic and translational medical research for academic institutions and industry sectors. We strive to enable access to cost-effective, customized genomic analyses, as a functional extension of your lab.</p> <p>The core closely collaborates with other Gladstone core facilities, UC San Francisco Center for Advanced Technology, UC San Francisco Core Immunology Lab, and 10x Genomics. Our approach of providing consultation prior to experiment design as well as incorporating the latest techniques, makes our services a crucial resource for all researchers.</p> </div> </div> <div id="manager"> <div class="container"> <h2>Contact</h2> <div class="field field--name-field-core-contact field--type-entity-reference field--label-hidden field--entity-reference-target-type-user clearfix field__item"><article class="user user--coredirector"> <div class="user__compact"> <p> <b>Horng-Ru Lin, PhD </b><br> Core Director <br> <a class="cracked" href="mailto:horngru.lin@gladstone.ucsf.edu">Email</a> <a class="forflow" href="mailto:flow-core@gladstone.ucsf.edu">Email</a><br> </p> </div> <style> .forflow {display:none} </style> </article> </div> </div> </div> <div class="corebk1">   </div> <div class="services"> <div class="container"> <h2>Services Provided</h2> <ul> <li>10x Genomics Chromium single cell/nucleus solutions: 3’/5’ Gene Expression, V(D)J Profiling, ATAC and Multiome (ATAC + Gene Expression)</li> <li>Visium spatial transcriptomics for FFPE and fresh-frozen tissues</li> <li>Customized NGS library preparation: DNA/RNA-seq, SMART-seq, Amplicon seq, PacBio SMRT seq, CRISPR-based single-cell screens, etc.</li> <li>Sequencing on the Illumina platforms at the Gladstone Genomics Core and UC San Francisco CAT</li> <li>Sample preparation and QC: nucleic acid extraction, DNA/chromatin shearing, Bioanalyzer analysis, nucleic acid quantitation by Qubit and qPCR</li> <li>Bioanalyzer, Covaris S2, Qubit and Nanodrop available for use by researchers</li> <li>Consultations on genomics, epigenomics, and transcriptomics projects</li> </ul> </div> </div> <div class="core-equipment"> <div class="container"> <h2>Core Equipment</h2> <div class="views-element-container"><div class="view view-equipment view-id-equipment view-display-id-equip js-view-dom-id-3c4824c6fe8a98d3ba60b1d6cbc5943726578f9f57e9a69ef6bf43ceff1183dd"> <div class="view-header"> <style> .view-display-id-confocal #3040 {visibility:hidden !important} </style> </div> <div class="view-content"> <div class="views-view-grid horizontal cols-2 clearfix"> <div class="views-row clearfix row-1"> <div class="views-col col-1" style="width: 50%;"><div class="views-field views-field-title"><span class="field-content"><p>NextSeq 500 Sequencing System</p></span></div></div> <div class="views-col col-2" style="width: 50%;"><div class="views-field views-field-title"><span class="field-content"><p>MiSeq Sequencing System</p></span></div></div> </div> <div class="views-row clearfix row-2"> <div class="views-col col-1" style="width: 50%;"><div class="views-field views-field-title"><span class="field-content"><p>Single Cell Analysis</p></span></div></div> <div class="views-col col-2" style="width: 50%;"><div class="views-field views-field-title"><span class="field-content"><p>CFX384 Touch Real-Time PCR Detection System</p></span></div></div> </div> <div class="views-row clearfix row-3"> <div class="views-col col-1" style="width: 50%;"><div class="views-field views-field-title"><span class="field-content"><p>iSeq 100 Sequencing System</p></span></div></div> <div class="views-col col-2" style="width: 50%;"><div class="views-field views-field-title"><span class="field-content"><p>NanoDrop One Spectrophotometer</p></span></div></div> </div> <div class="views-row clearfix row-4"> <div class="views-col col-1" style="width: 50%;"><div class="views-field views-field-title"><span class="field-content"><p>2100 Bioanalyzer Instrument</p></span></div></div> <div class="views-col col-2" style="width: 50%;"><div class="views-field views-field-title"><span class="field-content"><p>Chromium Controller</p></span></div></div> </div> </div> </div> </div> </div> </div> </div> <div class="core-members"> <div class="container"> <h2>Core Members</h2> <div class="views-element-container"><div class="view view-user-admin-people view-id-user_admin_people view-display-id-core_members js-view-dom-id-ab330b27d03148999faa9934a4cf51b84e5b2149c8c411009569cc899d21973d"> <div class="view-content"> <div class="views-view-grid horizontal cols-2 clearfix"> <div class="views-row clearfix row-1"> <div class="views-col col-1" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Mylinh Bernardi</b><br>Research Scientist<br></p> </div> </article> </div> <div class="views-col col-2" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Horng-Ru Lin</b><br>Core Director<br></p> </div> </article> </div> </div> <div class="views-row clearfix row-2"> <div class="views-col col-1" style="width: 50%;"><article class="user user--compnomail"> <div class="user__compact"> <p><b>Felicia Miller</b><br>Research Technologist II<br></p> </div> </article> </div> </div> </div> </div> </div> </div> </div> </div> <div id="events"> <div class="container"> <h2 class="text-align-center large">Events</h2> <p class="text-align-center large">The Genomics Core hosts a number of events from training to product demos.</p> <p class="text-align-center butncenter"><a class="button magenta" href="/events?search=genomics+core">Upcoming Events</a></p> </div> </div>  </section> <section id="capabilities"> <div id="capab-intro"> <div class="container"> <h2 class="tabtop">Capabilities</h2> <p>We are committed to developing a team of genomic professionals with diverse expertise to provide consultation and customized experimentation, implement emerging technologies, and deliver high quality data.</p> </div></div> <div class="alt-rows odd ar-1"> <div class="container"> <div class="row"> <div class="col-sm-6 capspacer">   </div> <div class="col-sm-6"> <p class="large">Consultation: We provide consultations on experiment design, sample preparation, experimentation, and data interpretation. We involve 10X Genomics and the <a href="https://gladstone.org/science/bioinformatics-core">Bioinformatics Core</a> in project discussions if necessary.</p> </div> </div> </div> </div> <div class="alt-rows even ar-2"> <div class="container"> <div class="row"> <div class="col-sm-6"> <p class="large">10x Genomics Single Cell Solutions: We provide assays to profile gene expression and open chromatin regions at the single cell level. Our services include cell/nucleus partitioning through library construction to sequencing with all necessary QC checks.</p> </div> <div class="col-sm-6 capspacer">   </div> </div> </div> </div> <div class="alt-rows odd ar-3"> <div class="container"> <div class="row"> <div class="col-sm-6 capspacer">   </div> <div class="col-sm-6"> <p class="large">Visium Spatial Transcriptomics: Spatial transcriptomics is a next-generation molecular profiling solution that allows the researcher to gain a holistic understanding of gene expression in the tissue microenvironment. Visium projects are processed as a joint collaboration between the <a href="https://gladstone.org/science/histology-and-light-microscopy-core">Histology and Light Microscopy Core</a> and Genomics Core.</p> </div> </div> </div> </div> <div class="alt-rows even ar-4"> <div class="container"> <div class="row"> <div class="col-sm-6"> <p class="large">Library Construction and Sequencing: Our core is experienced in constructing libraries from a diverse set of biological systems using varied methods. We offer customized library preparation based on your project goals. Sequencing on the Illumina platforms is carried out at Gladstone and UCSF CAT.</p> </div> <div class="col-sm-6 capspacer">   </div> </div> </div> </div> </section> <section id="fees-and-scheduling"> <div class="container"> <h2 class="tabtop">Fees and Scheduling</h2> <h2>Fees</h2><p><a href="https://my.ilabsolutions.com/account/login">You can view our services and fees in iLab.</a></p><h2>Scheduling</h2><p>You can access these instruments with prior training from Genomics Core staff.</p><ul><li>Agilent 2100 Bioanalyzer</li><li>Covaris S2 Focused-Ultrasonicator</li><li>Invitrogen Qubit 2.0 Fluorometer</li></ul><p>To schedule time with one of these instruments, <a href="https://my.ilabsolutions.com/sc/2991/gladstone-genomics-core/?tab=equipment">visit the iLab Equipment Calendar.</a></p><p><a href="mailto:genomics-core@gladstone.ucsf.edu">Contact us to schedule equipment training, schedule a consultation, or to arrange sample drop offs.</a></p><p> </p> </div> </section> <section id="publications"> <div class="container"> <h2 class="tabtop">Publications</h2> <p><a href="https://www.nature.com/articles/s41590-020-0654-0">Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation.</a> Andrew S. Mendiola, Jae Kyu Ryu, Sophia Bardehle, Anke Meyer-Franke, Kenny Kean-Hooi Ang, Chris Wilson, Kim M. Baeten, Kristina Hanspers, Mario Merlini, Sean Thomas, Mark A. Petersen, Alexander Williams, Reuben Thomas, Victoria A. Rafalski, Rosa Meza-Acevedo, Reshmi Tognatta, Zhaoqi Yan, Samuel J. Pfaff, Michael R. Machado, Catherine Bedard, Pamela E. Rios Coronado, Xiqian Jiang, Jin Wang, Michael A. Pleiss, Ari J. Green, Scott S. Zamvil, Alexander R. Pico, Benoit G. Bruneau, Michelle R. Arkin, Katerina Akassoglou</p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6803373/">Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis.</a> Swetansu K. Hota, Jeffrey R. Johnson, Erik Verschueren, Reuben Thomas, Aaron M. Blotnick, Yiwen Zhu, Xin Sun, Len A. Pennacchio, Nevan J. Krogan, and Benoit G. Bruneau.</p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668926/">Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards.</a> Abigail L. Lind, Yvonne Y.Y. Lai, Yulia Mostovoy, Alisha K. Holloway, Alessio Iannucci, Angel C.Y. Mak, Marco Fondi, Valerio Orlandini, Walter L. Eckalbar, Massimo Milan, Michail Rovatsos, Ilya G. Kichigin, Alex I. Makunin, Martina Johnson Pokorná, Marie Altmanová, Vladimir A. Trifonov, Elio Schijlen, Lukáš Kratochvíl, Renato Fani, Petr Velenský, Ivan Rehák, Tomaso Patarnello, Tim S. Jessop, James W. Hicks, Oliver A. Ryder, Joseph R. Mendelson III, Claudio Ciofi, Pui-Yan Kwok, Katherine S. Pollard, Benoit G. Bruneau.</p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6719697/">Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects.</a> T. Yvanka de Soysa, Sanjeev S. Ranade, Satoshi Okawa, Srikanth Ravichandran, Yu Huang, Hazel T. Salunga, Amelia Schricker, Antonio Del Sol4, Casey A. Gifford, Deepak Srivastava.</p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6632093/">Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics During Cardiac Reprogramming.</a> Nicole R. Stone1,2,3, Casey A. Gifford1,2,4, Reuben Thomas2, Karishma J. B. Pratt2, Kaitlen Samse-Knapp2, Tamer M. A. Mohamed2,4, Ethan M. Radzinsky2, Amelia Schricker2, Lin Ye2, Pengzhi Yu2,4, Joke G. van Bemmel2, Kathryn N. Ivey2,3,4, Katherine S. Pollard2,5,6,7, and Deepak Srivastava.</p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588463/">Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins.</a> Ibraheem Ali, Diego Garrido Ruiz, Zuyao Ni, Jeffrey R. Johnson, Heng Zhang, PaoChen Li, Mir M. Khalid, Ryan J. Conrad, Xinghua Guo, Jinrong Min, Jack Greenblatt, Matthew Jacobson, Nevan J. Krogan, and Melanie Ott.</p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6176614/">Differential effects of partial and complete loss of TREM2 on microglial injury response and tauopathy.</a> Faten A. Sayed, Maria Telpoukhovskaia, Lay Kodama, Yaqiao Li, Yungui Zhou, David Le, Axel Hauduc, Connor Ludwig, Fuying Gao, Claire Clelland, Lihong Zhan, Yonatan A. Cooper, Dimitrios Davalos, Katerina Akassoglou, Giovanni Coppola, and Li Gan.</p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829499/">Cardiac-enriched BAF chromatin-remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function.</a> Xin Sun, Swetansu K. Hota, Yu-Qing Zhou, Stefanie Novak, Dario Miguel-Perez, Danos Christodoulou, Christine E. Seidman, J. G. Seidman, Carol C. Gregorio, R. Mark Henkelman, Janet Rossant, and Benoit G. Bruneau.</p><p> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605815/ ">Ketogenic diet reduces mid-life mortality and improves memory in aging mice.</a> John C Newman, Anthony J Covarrubias, Minghao Zhao, Xinxing Yu, Philipp Gut, Che-Ping Ng, Yu Huang, Saptarsi Haldar, and Eric Verdin.</p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340593/ ">Chemical Enhancement of In Vitro and In Vivo Direct Cardiac Reprogramming.</a> Tamer M. A. Mohamed, PhD, Nicole R. Stone, MSc, Emily C. Berry, PhD, Ethan Radzinsky, BSc, Yu Huang, MD, Karishma Pratt, BSc, Yen-Sin Ang, PhD, Pengzhi Yu, PhD, Haixia Wang, PhD, Shibing Tang, PhD, Sergey Magnitsky, PhD, Sheng Ding, PhD, Kathryn N. Ivey, PhD, and Deepak Srivastava, MD. </p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180611/ ">Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis.</a> Yen-Sin Ang, Renee N. Rivas, Alexandre J. S. Ribeiro, Rohith Srivas, Janell Rivera, Nicole R. Stone, Karishma Pratt, Tamer M. A. Mohamed, Ji-Dong Fu, C. Ian Spencer, Nathaniel D. Tippens, Molong Li, Anil Narasimha, Ethan Radzinsky, Anita MoonGrady, Haiyuan Yu, Beth L. Pruitt, Michael Snyder, and Deepak Srivastava. </p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813342/ ">KMT2D regulates specific programs in heart development via histone H3 lysine 4 di-methylation.</a> Siang-Yun Ang, Alec Uebersohn, C. Ian Spencer, Yu Huang, Ji-Eun Lee, Kai Ge, and Benoit G. Bruneau.</p><p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769693/">Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.</a> Luis Luna-Zurita, Christian U. Stirnimann, Sebastian Glatt, Bogac L. Kaynak, Sean Thomas, Florence Baudin, Md Abul Hassan Samee, Daniel He, Eric M. Small, Maria Mileikovsky, Andras Nagy, Alisha K. Holloway, Katherine S. Pollard, Christoph W. Müller, and Benoit G. Bruneau.</p> <p class="cntrbutt"><a class="morepub button outline">More Publications</a></p> </div> </section> <section id="faqs"> <div class="accordion-wrapper"> <div class="container"> <h2>FAQs</h2> <div class="accordion accord1"><h3>How Do I Submit Samples to Your Core?</h3></div> <div class="panel"> <p>To submit samples, <a href="https://my.ilabsolutions.com/account/login">register and submit a request in our online system, iLab.</a> Once we receive and approve your request, we will contact you to coordinate sample drop off.</p> </div> <div class="accordion"><h3>What Are Your Sample Submission Requirements?</h3></div> <div class="panel"> <p>You can find our <a href="https://my.ilabsolutions.com/account/login">sample submission requirements in iLab.</a></p> </div> <div class="accordion"><h3>What Is Your Turnaround Time?</h3></div> <div class="panel"> <p>Turnaround times may vary, depending on the queue at the time of submission but this is our general timeline.  </p><table style="width:500px;" border="1" cellpadding="1" cellspacing="1"><thead><tr><th scope="col">Service</th><th scope="col">Turnaround Time</th></tr></thead><tbody><tr><td>RNA extraction, Bioanalyzer, Quantitation</td><td>1 Week</td></tr><tr><td>Library Preparation</td><td>2–3 Weeks</td></tr><tr><td>Sequencing (NextSeq and iSeq)</td><td>1 Week</td></tr></tbody></table><p>Note: For NovaSeq sequencing, the turnaround time will vary depending on the queue at UCSF CAT.</p> </div> <div class="accordion"><h3>How Do I Acknowledge the Core in My Publications?</h3></div> <div class="panel"> <p>In publications, we ask that you include an acknowledgment to the Gladstone Genomics Core, e.g., <em>We thank [NAME] of the Gladstone Genomics Core for their assistance with [ASSAY/PROJECT].</em></p><p>In addition, <a href="mailto:genomics-core@gladstone.ucsf.edu">send us an email</a> to let let us know when your Gladstone-supported work is published.</p><p> </p> </div> </div> </div> </section> </div> </div> </div> <script src="/libraries/easytabs/jquery-1.7.1.min.js" type="text/javascript"></script> <script src="/libraries/easytabs/jquery.hashchange.min.js" type="text/javascript"></script> <script src="/libraries/easytabs/jquery.easytabs.min.js" type="text/javascript"></script> <script type="text/javascript"> $(function( $ ){ $('#subtabs').easytabs(); }); </script> <script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.0/jquery.min.js"></script> <script src="/libraries/owl-carousel2/owl.carousel.js"></script> <script> var owl = $('.owl-carousel'); owl.owlCarousel({ margin: 10, lazyLoad:true, lazyLoadEager: 1, loop: true, dots: false, responsive: { 0: { items: 1 }, 600: { items: 2 }, 1000: { items: 3, nav: true } } }) // disable scroll owl.on('drag.owl.carousel', function(event) { document.ontouchmove = function (e) { e.preventDefault() } }) // enable scroll owl.on('dragged.owl.carousel', function(event) { document.ontouchmove = function (e) { return true } }) </script> <script> if ($('#datalist li').length <= 15) { $('a.morepub ').hide(); } if ($('p.firstWord').length <= 15) { $('a.moreawards ').hide(); } $(function () { $('a.morepub').click(function () { $('#datalist li:hidden').slice(0, 15).show(); if ($('#datalist li').length == $('#datalist li:visible').length) { $('a.morepub ').hide(); } }); }); </script> <script> var acc = document.getElementsByClassName("accordion"); var i; for (i = 0; i < acc.length; i++) { acc[i].addEventListener("click", function() { this.classList.toggle("active"); var panel = this.nextElementSibling; if (panel.style.maxHeight){ panel.style.maxHeight = null; } else { panel.style.maxHeight = panel.scrollHeight + "px"; } }); }</script> <script> // This prevents the page from scrolling down to where it was previously. if ('scrollRestoration' in history) { history.scrollRestoration = 'manual'; } // This is needed if the user scrolls down during page load and you want to make sure the page is scrolled to the top once it's fully loaded. 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