The Gladstone Genomics Core offers a full range of services to support next-generation sequencing (NGS) and to meet the needs of the scientific research community. NGS experiments enable cutting-edge genomics, transcriptomics, and epigenomics studies. We offer several types of library preparations for NGS, including quality control steps and sequencing, and are constantly looking to expand our range of services with the latest techniques.

Our latest focus has been on single cell and nuclei library preparation using the 10X Genomics platform. Spatial Transcriptomics has recently been added to menu of services. The core also provides expert consultation, customized support, access to state-of-the-art technologies, and the highest quality data.

Contact

Horng-Ru Lin, PhD
Staff Research Scientist III

 

Services Provided

  • Sequencing: The core provides Illumina NextSeq 500, iSeq, MiSeq, HiSeq, and NovaSeq
  • Single cell analysis: the core provides 10x Genomics Single Cell 3’ and 5’ Gene Expression, Single Cell V(D)J, and Visium Spatial Gene Expression
  • NGS library preparation (RNA-seq, small RNA-seq, ChIP-seq, Amplicon seq)
  • QC and sample preparation: the core provides RNA/DNA quality checks, nucleic acid quantitation, NGS library quantitation, real-Time PCR, and DNA and chromatin shearing

Core Members

Mylinh Bernardi
Research Scientist

Horng-Ru Lin
Staff Research Scientist III

Jim McGuire
Research Scientist

FAQs

How Do I Get My Project Started?

If you need help entering a request in iLab, email genomics-core@gladstone.ucsf.edu and we would be happy to initiate a request under your name.

What if I Need to Cancel or Edit My Request?

All projects in iLab can be edited or cancelled any time before the project is started. We'll contact you to confirm details before we get started. 

I'm Not Sure the Best Way to Analyze My Data or How Many Samples to Submit. What Should I Do?

Email us with questions at genomics-core@gladstone.ucsf.edu if you need help getting started. We can answer most questions over email or schedule a Zoom meeting to discuss your project.

When Can I Expect My Results?

Samples are placed in a queue at the time they are dropped off at the core and are processed on a first-come, first-served basis. Bioanalyzer results are usually returned within one week. A rush service is available.

NGS library prep and sequencing projects are typically completed in two to four weeks. Sequencing at the UCSF CAT core depends on their queue.

Expedited NextSeq sequencing is also available.

How Do You Calculate Your Fees?

Most of our fees derive from the cost of reagents, in addition to consumables, labor, instrument service contracts, and indirect costs (for external researchers). Gladstone is a nonprofit and operates without outside funding, so we make every effort to keep our costs low.

Events

The Behavioral Core hosts a number of events from training to product demos.

Upcoming Events

Capabilities

Gladstone’s Genomics Core offers services to researchers at UC San Francisco, external nonprofits, and for-profit companies. Experimental design consultations, close interactions with Gladstone’s Bioinformatics Core, and a willingness to explore non-routine work and ad-hoc techniques, make the Gladstone Genomics Core a crucial resource for all researchers.

 

We accept projects that range from a few samples to >50 samples. Biological triplicates are strongly recommended.

We can accept samples at various stages of library preparation (total RNA, cDNA, PCR products, and ready-to-sequence libraries).

 
 

We’re aware that sometimes it is not possible to attain high quality RNA/ DNA, and we’re willing to work with researchers to process difficult samples. We have had considerable success with generating sequencing data from less-than-ideal samples.

Fees and Scheduling

Register and log into iLab to:

  • Schedule access to instruments (prior training is required).
  • Drop off samples and reagents.
  • View a list of our services and fees.

Getting Started and Scheduling

All of our services are listed and ordered through our iLab website. You will need to create a free account to get started. Learn how to sign up for iLab. We are aware of the complexity of our services and of the iLab system.

Contact us directly at genomics-core@gladstone.ucsf.edu if you have questions or need help getting started.

Publications

Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation. 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

Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis. 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.

Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. 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.

Single-cell analysis of cardiogenesis reveals basis for organ level developmental defects. 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.

Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics During Cardiac Reprogramming. 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.

Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. 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.

Differential effects of partial and complete loss of TREM2 on microglial injury response and tauopathy. 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.

Cardiac-enriched BAF chromatin-remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function. 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.

 Ketogenic diet reduces mid-life mortality and improves memory in aging mice. John C Newman, Anthony J Covarrubias, Minghao Zhao, Xinxing Yu, Philipp Gut, Che-Ping Ng, Yu Huang, Saptarsi Haldar, and Eric Verdin.

Chemical Enhancement of In Vitro and In Vivo Direct Cardiac Reprogramming. 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. 

Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis. 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. 

KMT2D regulates specific programs in heart development via histone H3 lysine 4 di-methylation. Siang-Yun Ang, Alec Uebersohn, C. Ian Spencer, Yu Huang, Ji-Eun Lee, Kai Ge, and Benoit G. Bruneau.

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. 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.

More Publications