Acquisition for Illumina HiSeq 2500

收购 Illumina HiSeq 2500

• 批准号: 8247281
• 负责人: George S. Grills
• 金额: $ 59.01万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-07-01 至 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8247281
• 关键词: Bioinformatics; Biological Sciences; Core Facility; DNA Methylation; DNA Resequencing; DNA Sequence; Detection; Development; Funding; Future; Gene Expression; Generations; Genome; Genomics; Hybrids; Kinetics; Laboratories; Length; Macromolecular Complexes; Measures; Modification; Mutation; Polymerase; Preparation; RNA; RNA Sequences; RNA methylation; Reading; Research Personnel; Resolution; Resources; Ribosomes; Running; Sampling; Services; Spliceosomes; System; Technology; Technology Assessment; Time; Transcript; United States National Institutes of Health; Universities; Variant; cDNA Library; computerized data processing; cost; cost effective; epigenomics; experience; instrument; multidisciplinary; new technology; next generation; research study; single molecule

DESCRIPTION (provided by applicant): The introduction of new DNA sequencing technologies presents an exceptional opportunity for creative applications with potential for breakthrough discoveries. Funding is requested for a Pacific Biosystems (PacBio) sequencing instrument. The newly available PacBio third generation sequencing technology will be located in the Cornell University Life Sciences Core Laboratories Center (CLC). The CLC has extensive experience in running next generation sequencing instrument systems and in providing a wide range of next generation sequencing applications as core facility services. The CLC currently has a Roche 454 GS FLX, two Illumina GAIIx units and an Illumina HiSeq 2000 sequencing platform. There is a clear need for a PacBio instrument to be placed at Cornell. This application describes 24 projects from 21 NIH funded investigator groups that will utilize the instrument. The PacBio will be operated with a multidisciplinary, multi-core approach, including support from the CLC advanced technology assessment, genomics, epigenomics, bioinformatics, and bio-IT core resources. Implementation of the PacBio in a core facility as a university-wide shared research resource will enable cost effective access to this vital new technology. The PacBio instrument system allows single molecule real time sequencing. The system includes high throughput sample preparation, sequence detection, data processing, and assembly. There is no other instrument currently available that can sequence with a comparable combination of PacBio long read lengths, fast throughput, and low cost per run. PacBio applications include de novo assembly of smaller scale genomes, hybrid de novo and resequencing assembly of larger genomes that cannot be solved using short- read technologies alone, rare mutation (SNP) detection, characterization of structural variation, and gene expression and whole transcripts sequencing using cDNA libraries. PacBio applications under development include direct detection of DNA methylation by measuring polymerase kinetics, direct RNA sequencing, direct detection of RNA modifications such as RNA methylation, and high-resolution studies of macromolecular complexes like the ribosome and the spliceosome,. These applications are unique features of the PacBio technology. The PacBio technology will make possible experiments that are impractical or impossible with other available sequencing instruments. The instrument will facilitate a broad range of current and future NIH funded projects at Cornell University.

描述（由申请人提供）：新的DNA测序技术的引入为具有突破性发现潜力的创造性应用提供了一个特殊的机会。要求为太平洋生物系统公司（PacBio）的测序仪器提供资金。新推出的PacBio第三代测序技术将位于康奈尔大学生命科学核心实验室中心（CLC）。CLC在运行下一代测序仪器系统和提供广泛的下一代测序应用作为核心设施服务方面拥有丰富的经验。CLC目前有一个Roche 454 GS FLX，两个Illumina GAIIx单元和一个Illumina HiSeq 2000测序平台。有一个明确的需要PacBio仪器被放置在康奈尔大学。该应用程序描述了来自21个NIH资助的研究小组的24个项目，这些项目将使用该仪器。PacBio将采用多学科，多核心的方法进行操作，包括CLC先进技术评估，基因组学，表观基因组学，生物信息学和生物IT核心资源的支持。在核心设施中实施PacBio作为全校共享的研究资源，将使这一重要的新技术具有成本效益。PacBio仪器系统允许单分子真实的时间测序。该系统包括高通量样品制备、序列检测、数据处理和组装。目前没有其他仪器可以与PacBio长读取长度、快速通量和每次运行低成本的可比组合进行测序。PacBio应用包括较小规模基因组的从头组装、不能单独使用短读技术解决的较大基因组的杂交从头组装和重测序组装、罕见突变（SNP）检测、结构变异的表征以及使用cDNA文库的基因表达和全转录物测序。PacBio正在开发的应用包括通过测量聚合酶动力学直接检测DNA甲基化，直接RNA测序，直接检测RNA修饰（如RNA甲基化）以及高分辨率研究大分子复合物（如核糖体和剪接体）。这些应用是PacBio技术的独特功能。PacBio技术将使其他现有测序仪器不切实际或不可能的实验成为可能。该工具将促进康奈尔大学目前和未来NIH资助的广泛项目。

项目成果

Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P. humuli Using RNA Sequencing and Genotyping-By-Sequencing.

• DOI: 10.1371/journal.pone.0143665
• 发表时间: 2015
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Summers CF;Gulliford CM;Carlson CH;Lillis JA;Carlson MO;Cadle-Davidson L;Gent DH;Smart CD
• 通讯作者: Smart CD

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine.

• DOI: 10.1371/journal.pone.0134880
• 发表时间: 2015
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Hyma KE;Barba P;Wang M;Londo JP;Acharya CB;Mitchell SE;Sun Q;Reisch B;Cadle-Davidson L
• 通讯作者: Cadle-Davidson L

High-throughput discovery of post-transcriptional cis-regulatory elements.

转录后顺式调控元件的高通量发现。

• DOI: 10.1186/s12864-016-2479-7
• 发表时间: 2016
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Wissink,ErinM;Fogarty,ElizabethA;Grimson,Andrew
• 通讯作者: Grimson,Andrew

Digestive organ in the female reproductive tract borrows genes from multiple organ systems to adopt critical functions.

• DOI: 10.1093/molbev/msv048
• 发表时间: 2015-06
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Meslin C;Plakke MS;Deutsch AB;Small BS;Morehouse NI;Clark NL
• 通讯作者: Clark NL