PROJECT SUMMARY/ABSTRACT
We are requesting funds for a Vizgen MERSCOPE high throughput imaging system to enhance spatial
transcriptomics research at the University of California, San Diego (UC San Diego). The MERSCOPE is the first
and only commercial platform for Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH)
technology, which enable simultaneous imaging of hundreds of mRNA species at single molecule resolution in
tens of thousands of cells. The MERSCOPE will be placed in the UC San Diego Center for Epigenomics, a
collaborative research center serving both spatial epigenomics and single-cell genomics technologies for the
broad research community at the university. The highly trained staff of the Center are experienced with both
spatial epigenomics technologies and single cell genomics technologies. Launched in 2019, the Spatial and
Functional Genomics Platform of the Center has accumulated extensive expertise in MERFISH and high
throughput multiplexed FISH techniques with two home-built microscope systems. However, to meet a sharp
increase in the demand for spatial transcriptomics research and better serve the research community, it is
necessary for us to acquire a MERSCOPE. This instrument combined with our experience with spatial genomics
technologies, proven track record of collaboration, and fee-for-service work using bulk and single cell genomics
technologies, will enable the Center to fulfil the large demand, dramatically improving the spatial transcriptomics
(MERFISH) capabilities, shortening turnaround time, and significantly reducing the cost of spatial genomics
assays.
The Center for Epigenomics has supported epigenomics research in the laboratories of hundreds of NIH-
supported investigators in UC San Diego, as well as neighboring institutions in the areas of basic, translational,
and clinical biomedical research. For the proposal, we have identified 11 Major and Minor Users across the UC
San Diego and surrounding research community, including investigators from the School of Engineering, Division
of Biological Sciences, and from multiple departments within the School of Medicine as well as Sanford Burnham
Prebys Medical Discovery Institute. The projects of our users encompass the areas of genetics, epigenetics,
single cell genomics, and metagenomics that all rely on high throughput spatial and single cell technologies to
drive discovery. The spatial transcriptomics data generated on the MERSCOPE will positively impact studies in a
variety of disease areas, including aging, neurological diseases, cardiac disease, liver diseases, diabetes, cancer,
drug abuse/addiction and birth defects.
UC San Diego is strongly committed to creating a healthier world by advancing science, technology and medicine
and the Center for Epigenomics is determined to continue to provide cutting edge spatial epigenomics and single
cell epigenomic technologies as well as technical expertise to the local research community. With the support of
our institution and our qualified staff, we will ensure that the MERSCOPE will be maintained and used to its full
potential.