? GENOMICS SHARED RESOURCE The Genomics Shared Resource is managed by the Cancer Center and provides full nucleic acid-to-data services, from library preparation to basic data analysis, focused primarily on next-generation sequencing (NGS) applications. Most of the services currently offered by the Core have been added in the last 5 years following the recruitment of Dr. Brian James as the Facility Director in 2013. The Core upgrades in the past funding period include Illumina-based sequencing on the NextSeq 500, automated library preparation using the Eppendorf epMotion 5075, single-cell sequencing on the 10x Genomics Chromium and Bio-Rad ddSeq platforms, and human cell line authentication using the Promega GenePrint 10 system. In addition to RNA-seq, services offered include ChIP-seq, ATAC-seq, single-cell RNA-seq, exome-seq, CRISPR libraries, and phage display libraries. Since the Genomics Core began offering NGS service, it has worked with the majority of Cancer Center member labs. In many cases, this was the lab's first experience with high-throughput sequencing technology, and the Core was instrumental in helping the investigators to design, execute, and interpret these experiments. Integrated basic NGS bioinformatic analysis is included as part of the service. This is a critical component in assuring the quality of the data produced and facilitating the eventual scientific success of the Center members. The Genomics Core provides broad support, with 41 Center labs having used the Core in the last 5 years, and it has supported at least 46 cancer-related publications.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
Project #
Application #
Study Section
Special Emphasis Panel (ZCA1)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Sanford Burnham Prebys Medical Discovery Institute
La Jolla
United States
Zip Code
Ekanayake, Vindana; Nisan, Danielle; Ryzhov, Pavel et al. (2018) Lipoprotein Particle Formation by Proapoptotic tBid. Biophys J 115:533-542
Diez-Cuñado, Marta; Wei, Ke; Bushway, Paul J et al. (2018) miRNAs that Induce Human Cardiomyocyte Proliferation Converge on the Hippo Pathway. Cell Rep 23:2168-2174
Wang, Yang; Li, Yue; Yue, Minghui et al. (2018) N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. Nat Neurosci 21:195-206
Lundquist, Mark R; Goncalves, Marcus D; Loughran, Ryan M et al. (2018) Phosphatidylinositol-5-Phosphate 4-Kinases Regulate Cellular Lipid Metabolism By Facilitating Autophagy. Mol Cell 70:531-544.e9
Ramirez, Monica L Gonzalez; Poreba, Marcin; Snipas, Scott J et al. (2018) Extensive peptide and natural protein substrate screens reveal that mouse caspase-11 has much narrower substrate specificity than caspase-1. J Biol Chem 293:7058-7067
Wei, Yang; Toth, Julia I; Blanco, Gabrielle A et al. (2018) Adapted ATPase domain communication overcomes the cytotoxicity of p97 inhibitors. J Biol Chem 293:20169-20180
Tinoco, Roberto; Carrette, Florent; Henriquez, Monique L et al. (2018) Fucosyltransferase Induction during Influenza Virus Infection Is Required for the Generation of Functional Memory CD4+ T Cells. J Immunol 200:2690-2702
Wonder, Emily; Simón-Gracia, Lorena; Scodeller, Pablo et al. (2018) Competition of charge-mediated and specific binding by peptide-tagged cationic liposome-DNA nanoparticles in vitro and in vivo. Biomaterials 166:52-63
Limpert, Allison S; Lambert, Lester J; Bakas, Nicole A et al. (2018) Autophagy in Cancer: Regulation by Small Molecules. Trends Pharmacol Sci 39:1021-1032
Fujita, Yu; Khateb, Ali; Li, Yan et al. (2018) Regulation of S100A8 Stability by RNF5 in Intestinal Epithelial Cells Determines Intestinal Inflammation and Severity of Colitis. Cell Rep 24:3296-3311.e6

Showing the most recent 10 out of 599 publications