Illumina Sequencer to Facilitate Functional Genomics at Berkeley

Illumina 测序仪促进伯克利功能基因组学的发展

• 批准号: 7795092
• 负责人: JOHN W. TAYLOR
• 金额: $ 49.95万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7795092
• 关键词: Affinity; Alleles; Alternative Splicing; Animals; Bacteria; Base Sequence; Binding; Biological Models; Biology; California; Cataloging; Catalogs; Communities; Complex; Computer software; DNA; DNA Microarray Chip; DNA Sequence; DNA-Binding Proteins; Data Analyses; Data Quality; Epigenetic Process; Experimental Designs; Faculty; Frequencies; Funding; Generations; Genome; Genomics; Genotype; Human Cell Line; In Vitro; Individual; Laboratories; Length; Location; Maps; Measures; Messenger RNA; Methods; Modeling; Mus; Nucleic Acids; Preparation; Process; Proteins; Protocols documentation; RNA Binding; RNA-Binding Proteins; Reading; Research; Research Personnel; Running; Sampling; Techniques; Technology; Time; Tissues; Training; Universities; abstracting; base; cost; distributed data; functional genomics; genome-wide; high throughput analysis; human stem cells; innovation; mutant; plant fungi; research study; transcription factor

DESCRIPTION (provided by applicant): 6. Project Summary/Abstract. Second generation DNA sequencing machines capable of generating tens to hundreds of million sequence reads in a single run at a modest cost have transformed functional genomics. It is now simpler, more accurate and in many cases less expensive to analyze the composition of complex nucleic acid mixtures directly, by sequencing, than indirectly by hybridization to a DNA microarray, as had been the norm for the last decade. High-throughput sequencing has also enabled new functional genomic experiments that could not be efficiently carried out with microarrays. The Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley has catalyzed this shift by providing Berkeley faculty with access to next-gen sequencing, along with training and assistance in experimental design, sample preparation and data analysis. The center's two Illumina Genome Analyzers have been in constant use since they came online (one 15 months ago, a second 9 months ago). During that time, 23 NIH-funded (and 27 total) laboratories have used these machines to carry out a wide variety of functional genomic experiments, including: quantifying mRNA abundance, measuring mRNA synthesis and decay rates, identifying alternative splice forms and the frequency of their utilization, comparing the expression of different alleles, mapping the locations of regions bound by transcription factors and other DNA interacting proteins, determining the genome-wide distribution of epigenetic marks, cataloging the RNAs bound by RNA binding proteins, pinpointing mutants and genotyping individuals from large crosses. Analyzed samples have come from multiple species of bacteria, protists, plants, fungi and animals, including both model and non-model systems, mouse and human stem cells, and normal and diseased human cell-lines and tissues. In addition, Berkeley investigators have developed new sequencing-based techniques to characterize the in vitro affinity of DNA binding proteins to their targets, and to rationally evolve proteins to have desired functions. The center has been used to sequence several bacterial, fungal and animal genomes. Supporting this flurry of activity is a talented group of computational biologists at Berkeley developing innovative methods for base-calling, read mapping, assembly and analysis of this high-throughput sequencing data, and distributing and supporting software implementation of their methods that are actively used at Berkeley and elsewhere. With reasonably stable experimental protocols and analysis methods, the major factor limiting the wider utilization of this technology at Berkeley is sequencing capacity. Our two machines operate continuously and produce an average of 10 runs per month per machine (the length of a run depends on the desired read length and paired end status). Nonetheless, the queue of samples gets longer and longer, and there is currently a delay of nearly two months to have samples processed. We are requesting funds to purchase an additional Illumina Genome Analyzer IIx DNA sequencer to serve the demonstrated need of the Berkeley biology community. We have a fully operational facility, with an outstanding director, that has been producing high-quality data from Illumina sequencers for over a year. A new machine would be put to immediate use, and would have a significant positive impact on NIH-funded research in our community.

描述（由申请人提供）： 6。项目摘要/摘要。 第二代DNA测序机能够以适度的成本在一次运行中产生数十亿至数百万个序列的读数已改变了功能基因组学。现在，它更简单，更准确，在许多情况下，与过去十年的常态一样，通过测序，与DNA微阵列的杂交直接分析复合核酸混合物的组成比间接地分析复合核酸混合物的组成。高通量测序还实现了无法通过微阵列有效进行的新功能基因组实验。 伯克利分校的Vincent J. Coates基因组测序实验室通过为伯克利教师提供了下一代测序，以及实验设计，样本准备和数据分析的培训和帮助，从而促进了这一转变。自上网以来，该中心的两个Illumina基因组分析仪一直在不断使用（一个15个月前，第二个9个月前）。 在此期间，NIH资助（和27个总共）实验室已经使用这些机器进行了多种功能性基因组实验，包括：量化mRNA丰度，测量mRNA的合成和衰减率，确定替代性剪接形式，识别其替代性剪接形式及其频率及其利用的频率，并比较了不同的等级的范围，并绘制了其他范围的范围，并绘制了概括的范围，并确定了概括的范围，并绘制了概括的范围，并确定了概括的范围，并确定了概括性的范围，并构图了概括的范围，并构图了概括的范围，概括了概括的范围。表观遗传标记的分布，通过RNA结合蛋白结合的RNA分类，指出突变体和来自大十字的基因分型个体。经过分析的样品来自多种细菌，生物，植物，真菌和动物，包括模型和非模型系统，小鼠和人类干细胞，以及正常和患病的人类细胞线和组织。此外，伯克利研究人员已经开发了新的基于测序的技术，以表征DNA结合蛋白与目标的体外亲和力，并合理地进化蛋白质以具有所需的功能。该中心已用于对几种细菌，真菌和动物基因组进行测序。 支持这一活动的是伯克利的一组才华横溢的计算生物学家群体，开发了用于基础接听，读取映射，组装和分析此高通量测序数据的创新方法，并分发和支持在伯克利和其他地方积极使用的方法的软件实施和支持其方法。 借助合理稳定的实验方案和分析方法，限制伯克利该技术更广泛利用的主要因素是测序能力。我们的两台机器连续运行，平均每月每台机器10次运行（运行的长度取决于所需的读取长度和配对的最终状态）。尽管如此，样品队列的排队越来越长，目前延迟了将近两个月的样品处理样品。 我们要求资金购买额外的Illumina Genome Analyzer IIX DNA Sequencer，以满足伯克利生物学社区的需求。我们拥有一家全面运营的设施，并拥有一位出色的董事，该设施已经从Illumina测序仪中生产了一年多的高质量数据。新机器将立即使用，并将对我们社区中的NIH资助研究产生重大积极影响。