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

为少数群体服务的公共机构旧金山州立大学和专门从事生物多样性和进化研究的博物馆加州科学院(CAS)被授予一台Illumina MiSeq Benchtop测序仪，以便在这两个机构开发下一代测序(NGS)能力。MiSeq系统是一个可访问且具有成本效益的测序平台，学生、研究人员和教职员工将利用该平台培训学生并拓宽获奖机构科学家的研究范围。MiSeq测序仪将安置在旧金山州立大学生物系，并将补充共享分子核心设施中的现有设备。该仪器将使SF State(以及相关的Romberg Tiburon中心)、中科院和圣何塞州立大学的25个以上研究小组开展基于NGS的研究项目。使用MiSeq将使学生和教师研究人员能够扩展他们的研究中采用的方法，以解决包括生物体如何适应不断变化的环境、通过自然选择适应长期环境变化的机制以及确定疾病致病的关键机制等问题。MiSeq将是为SF State的学生和教职员工扩大生物多样性、信息学和基因组学培训的机构努力的基石，对于生物系的核心使命至关重要，即扩大传统上代表性不足的群体对科学的参与，使他们能够对最先进的仪器进行研究。作为这些目标的一部分，该仪器及其产生的数据将被纳入旧金山州立大学的研究生和本科生课程和培训经验。与科学院合作，将创建一个新的博物馆展览，展示两个机构的研究人员使用基因组和序列数据来探索生物多样性、气候变化和进化问题。这次展览将利用科学院的公共推广基础设施，并将直接让SF州立大学的学生使用所要求的工具展示他们自己的研究。所述研究目的的主要目标是改变SFSU和CAS的研究和培训，以开展最先进的基因组研究。在过去的两年里，SF State和CAS已经接触到了一大批具有尖端问题和生物信息学专业知识的科学家、博士后和研究生，以便在他们的研究中利用高通量基因组学技术。这些研究人员分为三个重叠的研究领域：微生物和疾病基因组学、比较基因组学、进化基因组学和种群基因组学，以及生态和保护基因组学。具体的研究应用包括：1)发现和组装微生物小基因组，2)转录组和RNA测序，3)微生物元基因组学，4)聚合酶链式反应扩增子测序，5)减少代表性文库测序和6)低覆盖率全基因组测序。NGS技术的提供将使中科院能够在国家认可的自然历史博物馆和推广中心(每年有100多万游客)创建一个新的展览，展示使用基因组数据来探索生物多样性、气候变化和进化的问题。收购这一仪器将使旧金山州立大学和中科院的不同学生群体获得知识、技能和经验，成为生物科学以及竞争激烈和不断扩大的基因组学领域的最佳候选人。通过将培训和推广与Illumina MiSeq实现的最先进的科学相结合，该奖项将对旧金山地区及其他地区的生物多样性研究和可持续发展科学产生广泛影响。

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.