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. 项目总结/摘要。 第二代 DNA 测序机能够以适度的成本在单次运行中生成数千万至数亿个序列读数，已经彻底改变了功能基因组学。现在，通过测序直接分析复杂核酸混合物的组成比通过与 DNA 微阵列杂交间接分析更简单、更准确，并且在许多情况下更便宜，这在过去十年中已成为常态。高通量测序还使得新的功能基因组实验成为可能，而这是微阵列无法有效进行的。 加州大学伯克利分校的 Vincent J. Coates 基因组测序实验室为伯克利分校的教员提供下一代测序技术，以及实验设计、样品制备和数据分析方面的培训和帮助，从而促进了这一转变。该中心的两台 Illumina 基因组分析仪自上线以来一直在持续使用（一台 15 个月前，另一台 9 个月前）。 在此期间，23 个 NIH 资助的（总共 27 个）实验室使用这些机器进行了各种功能基因组实验，包括：量化 mRNA 丰度、测量 mRNA 合成和衰减率、识别替代剪接形式及其使用频率、比较不同等位基因的表达、绘制转录因子和其他 DNA 相互作用蛋白结合区域的位置图、确定全基因组范围 表观遗传标记的分布、对 RNA 结合蛋白结合的 RNA 进行编目、精确定位突变体并对大杂交中的个体进行基因分型。分析的样品来自多种细菌、原生生物、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系和组织。此外，伯克利研究人员还开发了新的基于测序的技术来表征 DNA 结合蛋白与其靶标的体外亲和力，并合理地进化蛋白质以具有所需的功能。该中心已用于对多种细菌、真菌和动物基因组进行测序。 支持这一系列活动的是伯克利分校一群才华横溢的计算生物学家，他们开发了用于碱基识别、读图谱、组装和分析高通量测序数据的创新方法，并分发和支持伯克利和其他地方积极使用的方法的软件实施。 由于实验方案和分析方法相当稳定，限制该技术在伯克利得到更广泛应用的主要因素是测序能力。我们的两台机器连续运行，每台机器每月平均产生 10 次运行（运行的长度取决于所需的读取长度和配对末端状态）。尽管如此，样本队列却越来越长，目前样本处理延迟了近两个月。 我们正在申请资金购买额外的 Illumina Genome Analyzer IIx DNA 测序仪，以满足伯克利生物学界的实际需求。我们拥有一个全面运营的设施，并拥有一位出色的主管，一年多来一直在通过 Illumina 测序仪生成高质量的数据。一台新机器将立即投入使用，并对我们社区中由 NIH 资助的研究产生重大的积极影响。