Genetics, Bioinformatics and Systems Biology Colloquium
Thursdays, 12:00 pm – 1:00 pm
UC San Diego, Powell-Focht Bioengineering Hall, Fung Auditorium
Complete schedule here
The Torrey Pines Mesa features a wide range of world-class core facilities for performing comprehensive, system-wide experiments and subsequent bioinformatic analysis.
UCSD Center for Computational Biology & Bioinformatics
The UCSD Center for Computational Biology & Bioinformatics (CCBB) is a collaborative center that provides investigators with bioinformatics expertise to analyze large molecular datasets and develop novel algorithms. We have expertise in genomics, transcriptomics, epigenomics, systems biology and translational medicine. Our services include data analysis, biological interpretation, grant writing and training. Please contact the Center’s Executive Director, Dr. Kathleen Fisch, for more information.
UCSD IGM Genomics Center
The UCSD IGM Genomics Center offers full services in next generation sequencing, whole-genome genotyping and copy number variation analysis, and bioinformatics support for data analysis (see Services). The IGM Genomics Center offers assay design consultation, sequencing library preparation (DNA/RNA/smallRNA/targeted sequencing), single cell RNA sequencing (10X Genomics), llumina platform sequencing (MiSeq, HiSeq2500 (Rapid, V3 and V4 Chemistry), and HiSeq4000), PacBio SMRT sequencing and Illumina genotyping and methylation arrays. Please contact the Center’s Director, Dr. Kristen Jepsen, for more information.
TSRI Scripps Center for Metabolomics
The Scripps Research Institute’s Scripps Center fro Metabolomics targets and untargets metabolomics. Using a cloud-based XCMS systems biology and metabolomics platform allows users to dig deeper into their data simply by clicking on a heat maps, cloud plots or multi group analyses to obtain information. Please contact the Center’s Director, Dr. Gary Siuzdak, for more information.
TSRI NGS & Microarray Core
The Scripps Research Institute’s NGS and Microarray Core offers NGS library prep and sequencing (NextSeq500 and MiSeq); custom microarray fabrication and confocal scanning (primarily glycan and peptide arrays). Please contact the Core Directors, Dr. Steven Head or Dr. Phillip Ordoukhanian, for more information.
SBPMDI Bioinformatics Core
Sanford Burnham Prebys Medical Discovery Institute’s Bioinformatics Core can help with: (i) Cancer driver gene discovery using VIPER algorithm from Califano group and other machine learning techniques, (ii) Next-Gen Sequencing, metabolomics and proteomics data integration and analysis aiming to generate testable hypotheses, (iii) Systems Biology support and pathway analysis (including via IPA and MetaCore). Other areas of activity include biostatistics, grant and paper preparation, website and database development, education and training. Pre-computed models of cancer progression in 23 major cancer types are now available for community at our Regulattice portal http://regulattice.burnham.org/ (Username: demo; Password: demo1). Please contact the Core’s Director, Dr. Alexey Eroshkin, for more information.
SBPMDI Cancer Metabolism
Cancer Metabolism is a developing Shared Resource within the SBP Cancer Center. The scientific focus of the core is to investigate the role of metabolism in cancer on both the cellular and organismal level, combining in vitro and in vivo analysis. By using GC-MS analysis of small metabolites: quantification and stable isotope (13C, 15N) tracing; Enzyme analyzer for glucose, lactate and glutamine in medium (high throughput) an overall model of cellular metabolism is built. All of the instruments and approaches are available on a fee-for-service basis to Cancer Center scientists, but also (as capacity permits) to outside users. Samples for most services can be shipped, but Seahorse users need to be local so they can bring live cells for analysis. Please contact the Core’s Director, Dr. David Scott, for more information.
SBPMDI Flow Cytometry Shared Resource
Sanford Burnham Prebys Medical Discovery Institute’s Flow Cytometry Resource provides access to high-speed cell sorting and analytical flow cytometry in two locations on the SBP La Jolla campus. Trained investigators have 24-hr/day access to a variety of analytical flow cytometers available for independent use. Core staff provide technical expertise, hardware and software training, operate the facility’s cell sorters and are available to assist with analysis experiments for those who prefer to have their samples run by an expert cytometrist. Scientists planning a flow cytometry experiment are encouraged to consult facility staff for assistance with protocols, fluorochrome selection or other aspects of experiment design. Please contact the Core’s Director, Dr. Yoav Altman, for more information.
SBPMDI Functional Genomics
The Functional Genomics Core facility at Sanford Burnham Prebys Medical Discovery Institute provides infrastructure for unbiased Target Discovery by means of genome-wide genetic screening in cultured cells. The Core’s primary effort is dedicated to loss-of-function screening via RNAi and CRISPR-CAS9 technologies although other services such as micro-RNA (miR) screening and cell population barcoding for clonal analysis are also available. Our range of expertise covers from project feasibility assessment, all the way through verification of identified targets. In addition to screens, the Core produces CRISPR-engineered cell lines to serve as models for screening or to aid the follow-up process, and can provide reagents tailored to the needs of each project such as sh/siRNAs, ORF clones, CRISPR reagent aliquots. Our personnel develop both plate reader and image-based cellular assays, and adapt them to high-throughput screening in arrayed format in conjunction with the High Content Screening Core. CRISPR-CAS9 screens are performed in pooled format using either off-the shelf or custom made lentiviral libraries, and results are de-convoluted in our Genome Analysis shared resource. Please contact the Core’s Director, Dr. Pedro Aza-Blanc, for more information.
The Genomics Core at Sanford Burnham Prebys Medical Discovery Institute in La Jolla provides next-generation sequencing services, providing assistance with experimental design, sample QC, library preparation, sequencing, and data analysis through Illumina BaseSpace. The facility primarily provides high throughput sequencing on the Illumina NextSeq 500. The Core also provides full-service Quantitative real-time PCR (Q-PCR) analysis, predominantly utilizing SYBR green, as well as amplification-free analysis of RNA expression using the NanoString nCounter. Additional Core services include full service Human cell line authentication, utilizing short tandem repeat analysis (STR), as well mycoplasma testing. The Core provides a variety of shared genomics-related analytical instruments and training in their use, for SBP investigators. The Genomics Core also provides its services to investigators outside of SBP. Please contact the Core’s Director, Dr. Brian James, for more information.
The Sanford Burnham Prebys Medical Discovery Institute’s Proteomics Shared Resource provides state-of-the-art mass spectrometry-based proteomics services including identification, quantification and characterization of proteins and their post-translational modifications. We provide proteomics services to SBP scientists as well as outside non-profit and for-profits organization on a fee-for-service basis. The Proteomics Shared Resources is located on SBP main campus in La Jolla and currently houses five mass spectrometry platforms. The facility is run by four highly committed proteomics experts, including two faculty members as scientific advisors. Please contact the Core’s Director, Dr. Alex Rosa Campos, for more information.
SBPMDI Tumor Analysis
The Tumor Analysis Service of the Animal Facility at Sanford Burnham Prebys Medical Discovery Institute in La Jolla provides experienced, dedicated expertise in analyzing animal models of human cancer and other diseases. It provides investigators access to a wide variety of human cancer cell lines for xenograft studies, some primary human xenograft models and additional transgenic mouse solid tumors and leukemia models. Solid tumors are typically initiated by subcutaneous or orthotopic transplantation of cultured cells, frozen viable tumors or fresh transplanted tumor tissue. Experimental compounds or other host manipulations are administered and tumor size, metastases, histopathology and blood chemistry are evaluated. The core also offers serial passaging of tumors and derivation of 2D and 3D cultures from xenograft tumors, including patient-derived xenograft (PDX) models. Please contact the Core’s Director, Dr. Darren (Ben) Finlay, for more information.
SBPMDI Viral Vectors
The goal of the Viral Vector Core Facility at Sanford Burnham Prebys Medical Discovery Institute is to assist Institute investigators, as well as outside laboratories, with cost-effective production of high-quality, high-titer lentiviral, retroviral and adenoviral vector. The Viral Vector Core offers a variety of services including ready-to-transduce lentiviral and adenoviral particles, and custom lentiviral, retroviral, and adenoviral production and titrations. Packaging, concentrating, and titration of user-supplied lentiviral constructs are the major activities of the core. Our most recent “The Works” service includes custom lentiviral vector construction for constitutive or inducible cDNA/shRNA expression as well as promoter/enhancer reporter, viral packaging, and titration (ready-to-transduce control particles provided). Please contact the Core’s Director, Dr. Chun-Teng Huang, for more information.
SBPMDI Other Resources
Dr. Piotr Cieplak of Sanford Burnham Prebys Medical Discovery Institute offers computational chemistry, structural modeling, simulations, bioinformatics, and computational algorithms.