The Genomics Shared Resource provides services in the following areas:

Next-generation sequencing technology is one of the most powerful genomics technologies to emerge in recent years and is accelerating the pace of advances in basic and translational research. The Genomics Shared Resource, or GSR, helps clients with samples at any point of the process, whether with already prepared sequencing libraries or in the early stages of a project. The GSR has robust data analysis pipelines in place and works closely with clients to get the most out of experiments.

Schedule a Free Consultation Sequencing Sample Submission Form

The GSR has extensive experience with the isolation of DNA and RNA from various sources (whole blood, buffy coat, plasma, frozen and FFPE tissue, virus, cell lines, and others). The GSR also has all the equipment necessary to perform spectrophotometric and fluorometric quantification and quality assessment of nucleic acids. The GSR’s nucleic acids services are an excellent option for any researcher, whether to provide the equipment, laboratory space, or personnel to work with nucleic acids, or to provide the experience and expertise to yield robust and consistent results in downstream applications.

Schedule a Free Consultation Nucleic Acids Sample Submission Form

The NanoString GeoMx Digital Spatial Profiler (DSP) system provides high-resolution genomics analyses of heterogeneous tissue and tumor samples, i.e., those consisting of multiple cell types, different states of the same cell type, or molecularly diverse cancer cell populations. It is this cellular heterogeneity that confounds the interpretation of results from typical “bulk” gene expression profiling and proteomics analyses. The GeoMx DSP system solves this problem by enabling spatially resolved gene and protein expression profiling in tissue sections by preserving morphological context. In essence, the benefits of single cell genomic profiling are combined with that of the spatial preserving property of histological tissue analysis.

The GeoMx DSP instrument accomplishes spatial profiling by integrating several key steps in the procedure: high-magnification (20X) brightfield and fluorescence slide scanning, selection of regions of interest (ROIs) in the tissue section for analysis, ultraviolet light (UV) light-mediated photocleavage of transcript-specific oligonucleotide barcodes from bound antibodies or RNA probes within each ROI, and then microfluidics-based collection of the released barcodes. The DSP technology performs whole slide imaging with up to four fluorescent stains to capture tissue morphology, which guide in the selection of ROIs for high plex profiling with up to 20,000 barcoded reagents.

The DSP chemistry enables spatially resolved high plex profiling of RNA and protein targets on two serial sample sections. In addition to frozen sections, this system is optimal for analysis of clinical formaldehyde-fixed paraffin-embedded (FFPE) specimens and therefore valuable for translational research. In addition to its application in dissecting the heterogeneity of human cancers and mouse tumor models, this spatial transcriptomics and proteomics technology can be applied to all model systems in order to define fundamental aspects of biology including differentiation, morphogenesis, cell-cell interactions, neovascularization, and neuroanatomy. It is anticipated that this resolution enhancing technology will greatly benefit researchers at the UC Davis Cancer Center as well as the entire UC Davis community of basic and translational researchers, and will add an essential dimension to our research capabilities. This new cutting-edge technology will provide new opportunities for discovery and hypothesis generation.   

Consultation is provided at an hourly rate for assistance with experimental design, troubleshooting, data analysis, results interpretation, and manuscript/grant proposal preparation.

The data processing and analysis capabilities of the GSR are supported by an infrastructure of servers and computational workstations, as well as licenses for several commercial bioinformatic software packages.

Appointments for consultation and bioinformatics can be made online here.
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