MRI: Acquisition of a Next-Generation Sequencer for a Shared Genomics Core Facility at San Francisco State University and the California Academy of Sciences

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An award is made to San Francisco State University, a public minority-serving institution, and the California Academy of Sciences (CAS), a museum specializing in biodiversity and evolution research, to acquire an Illumina MiSeq Benchtop Sequencer in order to develop capability for next generation sequencing (NGS) at both institutions. The MiSeq system is an accessible and cost-effective sequencing platform that will be utilized by students, researchers, and faculty members to train students and broaden the research scope of scientists at the awarded institutions. The MiSeq Sequencer will be housed in the Department of Biology at SF State and will complement existing equipment in a shared molecular core facility. The instrument will enable NGS-based research projects by more than 25 research groups at SF State (and the associated Romberg Tiburon Center), CAS and San Jose State University. Access to the MiSeq will enable student and faculty researchers to expand the methodology employed in their research to address questions including how organisms adapt to changing environments, determining the mechanisms of adaptation by natural selection to long-term environmental change, and identifying critical mechanisms of disease pathogenicity. The MiSeq will be the cornerstone of institutional efforts to expand biodiversity, informatics and genomics training for students and faculty at SF State and is critical to the Department of Biology's core mission of broadening participation in science by traditionally underrepresented groups enabling them to conduct research on state-of the art instrumentation. As part of these goals, the instrument and the data it produces will be incorporated into SF State graduate and undergraduate courses and training experiences. In partnership with the Academy, a new museum exhibit will be created showcasing the use of genomic and sequence data by researchers at both institutions to explore questions of biodiversity, climate change and evolution. This exhibit will capitalize on the public outreach infrastructure of the Academy and will directly involve SF State students presenting their own research using the requested instrumentation.The primary goal of the described research aims is to transform research and training at SFSU and CAS to carry out state-of-the-art genomic research. Over the last two years SF State and CAS have reached a critical mass of scientists, post-docs and graduate students with cutting edge questions and bioinformatics expertise to utilize high-throughput genomics technology in their research. These researchers fall into three overlapping research areas: Microbial and disease genomics, Comparative, evolutionary and population genomics, and Ecological and conservation genomics. Specific research applications include the following: 1) Discovery and assembly of small microbial genomes, 2) Transcriptome and RNA sequencing, 3) Microbial metagenomics, 4) PCR amplicon sequencing, 5) Reduced-representation library sequencing and 6) Low-coverage whole-genome sequencing. Availability of NGS technology will allow CAS to create a new exhibit showcasing the use of genomic data to explore questions of biodiversity, climate change and evolution at a nationally-recognized natural history museum and outreach center (with more than 1 million visitors each year). Acquisition of this instrumentation will allow the diverse student body at SFSU and CAS to acquire the knowledge, skills and experience to be top candidates for careers in the biological sciences and in the competitive and expanding field of genomics. By combining training and outreach with state-of-the-art science enabled with the Illumina MiSeq, this award will have a broad impact on biodiversity research and sustainability science in the San Francisco area and beyond.