MRI: Acquisition of an Illumina GAIIx for Genomics and Microbial Ecology

该提案描述了Illumina GAIIx核酸测序仪和相关仪器的收购，以加强海洋生物实验室和更广泛的伍兹霍尔科学界的微生物生态学和基因组学研究计划。该仪器将大大降低微生物分析、基因组测序和RNA-Seq分析的成本，同时利用先进DNA测序平台的现有经验。所要求的设备将提供约50亿nt/天的日吞吐量，足以满足现有NSF和NIH资助计划下设备的主要和次要用户确定的约1755亿核苷酸（nt）测序需求;这些估计不包括MBL高中，本科和研究生水平课程的预计使用，如下所述。智力优势：大规模并行DNA测序仪和支持DNA样品制备仪器要求在这个MRI提案中共享使用，将服务于NSF资助的和其他研究人员在海洋生物实验室在伍兹霍尔和合作者在伍兹霍尔海洋研究所包括马萨诸塞州理工学院的科学家谁参加了伍兹霍尔中心的海洋和人类健康由NSF资助。拟购买的仪器包括Illumina GAIIx大规模并行DNA测序仪和Covaris S-2 DNA声学剪切仪。这些设备将满足至少八个资助项目的新的DNA测序要求，这些项目属于两大主题：微生物群落概况分析和基因组学/转录组学。微生物生态学项目包括分析人类影响的淡水供应，长期生态研究地点，受控的中生态系统和人类肠道;基因组学项目包括基因组进化的研究，重点是细菌共生体中有害进化的机制和后果，microRNA在无性轮虫中的作用，以及自然群落中的基因组变异，包括叶圈和海底。该设备将大大提高我们的大规模并行测序能力，同时将测序成本降低许多倍。收购Illumina GAIIx还将使研究人员能够增加其正在进行的研究的范围和深度，并考虑采用基于序列的方法来解决生态学和进化生物学中的新问题。该设备将在W. M.凯克生态和进化遗传学设施，位于海洋生物实验室（MBL）的约瑟芬湾保罗比较分子生物学和进化中心（BPC）内，自1997年以来，伍兹霍尔科学界的研究人员共享使用资源。更广泛的影响：新仪器将为各级学生和研究人员提供令人兴奋的机会。PI目前指导博士后学者和Brown-MBL研究生，他们将立即从我们的测序设施中增加GAIIx中受益。此外，MBL实验室将主办本科生在MBL？的NSF研究经验，本科生和学期在环境科学计划。这些学生将受益于一个新的课程模块的开发，从海水到序列，其中将纳入GAIIx数据的使用。该课程模块还将通过我们与伍兹霍尔当地非营利性海洋教育组织Zephyr教育基金会的合作为高年级高中学生提供服务。此外，通过将GAIIx测序设施整合到MBL夏季课程中，我们将扩大对研究生和博士后学生的多样化人群的培训，这些学生将对国家和国际产生影响。最后，访问和暑期教师谁通常可能外包他们的测序将有机会在居住期间使用仪器，学习第一手资料如何生成和处理序列数据集，什么协议是可能的，也许同样重要的是，下一代测序的局限性和错误来源。这种面向高中和本科生的新课程开发与夏季和访问教师，研究生和博士后的严格培训相结合，将使GAIIx与MBL的新的和现有的培训机会紧密结合。

This proposal describes the acquisition of an Illumina GAIIx nucleic acid sequencer and related instrumentation to enhance microbial ecology and genomics research programs at the Marine Biological Laboratory and the broader Woods Hole scientific community. The instrumentation will dramatically reduce the cost of microbial profiling, genome sequencing and RNA-Seq profiles while leveraging existing experience with advanced DNA sequencing platforms. The requested equipment would provide a daily throughput capacity of ~5 billion nt/day, sufficient for the ~1755 billion nucleotides (nt) of sequencing needs identified by major and minor users of the equipment under existing NSF and NIH funded programs; these estimates do not include projected use by MBL high school, undergraduate, and graduate level courses as described below. Intellectual Merit: The massively parallel DNA sequencer and a supporting DNA sample preparation instrument requested for shared use in this MRI proposal will serve NSF-funded and other investigators at the Marine Biological Laboratory in Woods Hole and collaborators at the Woods Hole Oceanographic Institution inclusive of Massachusetts Institute of Technology scientists who participate in the Woods Hole Center for Oceans and Human Health funded by the NSF. The instruments to be purchased include an Illumina GAIIx massively parallel DNA sequencing machine plus an accessory Covaris S-2 DNA acoustic shearer. The equipment will accommodate new DNA sequencing requirements for at least eight funded projects falling within two major themes: microbial community profiling and genomics/transcriptomics. Microbial ecology projects include profiling of human-impacted fresh water supplies, long-term ecological research sites, controlled mesocosms, and the human gut; genomics projects include studies of genome evolution that focus on mechanisms and consequences of deleterious evolution in bacterial symbionts, the role of microRNAs in asexual rotifers, and genomic variation in natural communities, including the phyllosphere and the subseafloor. This equipment will dramatically increase our massively parallel sequencing capacity while at the same time reducing sequencing costs by many fold. Acquisition of an Illumina GAIIx will additionally enable investigators to increase the scope and depth of their ongoing research and consider sequence-based approaches to new questions in ecology and evolutionary biology. The equipment will operate within the W. M. Keck Ecological and Evolutionary Genetics Facility within the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution (BPC) at the Marine Biological Laboratory (MBL), a shared-use resource for investigators in the Woods Hole scientific community operational since 1997. Broader Impacts: The new instrumentation will provide exciting opportunities for students and researchers at all levels. The PIs currently mentor postdoctoral scholars and Brown-MBL graduate students who will immediately benefit from the addition of a GAIIx to our sequencing facility. Additionally, MBL laboratories will host undergraduates in the MBL?s NSF Research Experience for Undergraduates and Semester in Environmental Sciences programs. These students will benefit from the development of a new curriculum module, From Seawater to Sequences, which will incorporate use of the GAIIx data. This curriculum module will also serve upper-level high school students through our collaboration with the Zephyr Education Foundation, a local non-profit marine education group in Woods Hole. In addition, through the integration of the GAIIx sequencing facility into MBL summer courses, we will extend the training of a diverse population of graduate and postdoctoral students next generation sequencing methods that will have national and international impact. Finally, visiting and summer faculty who might usually outsource their sequencing will have access to the instrument while in residence, learning first hand how sequence datasets are generated and processed, what protocols are possible, and perhaps equally importantly, the limitations and sources of error in next-generation sequencing. This combination of new curriculum development geared towards high school and undergraduate students with rigorous training for summer and visiting faculty, graduate students, and postdocs will allow for a strong integration of the GAIIx with both new and established training opportunities at the MBL.