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High-throughput genomic assays: Applications and analysis of DSL technology and next-generation sequencing.

机译：高通量基因组测定：DSL技术和下一代测序的应用和分析。

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摘要

Determining DNA sequence has been a principle tool for several methods in biology research. From whole genome sequencing to RNA expression assays to several types of immunoprecipitation experiments, sequencing DNA has been a staple detection technique. Recent advances in sequencing and detection of DNA has revealed many new possibilities, and problems, with regards to data analysis. Here, I present a study analyzing a novel detection technology and sequencing method. These are both important contributions for not only providing new insights for utilizing a more sensitive detection technique, but also creating a method which enables any researcher to quickly analyze the unheralded amount of sequence data now being produced, soon be available to everyone.;Chapter 2 focuses on the current uses and analysis of a novel DNA detection technique called DNA Selection and Ligation (DSL). By taking advantage of the more sensitive and specific DSL strategy, any assay that is dependent on DNA detection is improved. In this chapter, I show how DSL can be used to modify the standard chromatin immunoprecipitation (ChIP)-on-chip assay (termed ChIP-DSL), in both the promoter-specific and tiling cases. Additionally, I show how the ChIP-DSL method gives promising results for a high-throughput version of the chromatin conformation capture (3C) assay, which is used to measure if two regions of DNA are interacting.;Chapter 3 concentrates on next-generation sequencing, more specifically on the Illumina Genome Analyzer (GA). After describing the details of how the sequencing is performed and analyzed, I discuss the current flaw in these datasets, and propose a solution to the problem, the Genome Ontology. I then give several examples where the Genome Ontology is helpful in extracting knowledge from these incredibly large datasets.;Chapter 4 describes numerous future directions of my own work as well as several of my observations that resulted from working with these next-generation sequencing datasets.
机译：确定DNA序列已成为生物学研究中几种方法的主要工具。从全基因组测序到RNA表达测定再到几种免疫沉淀实验，DNA测序已成为一种重要的检测技术。 DNA测序和检测的最新进展揭示了有关数据分析的许多新可能性和问题。在这里，我介绍了一项分析新型检测技术和测序方法的研究。这些都是重要的贡献，不仅为利用更灵敏的检测技术提供新见解，而且还为创建一种方法，使任何研究人员能够快速分析目前正在产生的未预料的序列数据量，很快便对所有人开放。重点介绍了一种称为DNA选择和连接（DSL）的新型DNA检测技术的当前使用和分析。通过利用更敏感和更具体的DSL策略，任何依赖于DNA检测的检测方法都会得到改善。在本章中，我将展示在启动子特定和平铺情况下，如何使用DSL修改标准的芯片染色质免疫沉淀（ChIP）芯片测定（称为ChIP-DSL）。此外，我展示了ChIP-DSL方法如何为染色质构象捕获（3C）分析的高通量版本提供有希望的结果，该方法用于测量两个DNA区域是否相互作用。;第3章着重于下一代测序，尤其是在Illumina基因组分析仪（GA）上进行测序。在描述了如何执行和分析测序的细节之后，我讨论了这些数据集中的当前缺陷，并提出了该问题的解决方案，即基因组本体论。然后，我给出几个例子，其中基因组本体论有助于从这些难以置信的大型数据集中提取知识。第4章介绍了我自己工作的许多未来方向以及我与这些下一代测序数据集一起工作所得到的一些观察结果。

著录项

  • 作者

    Hutt, Kasey Robert.;

  • 作者单位

    University of California, San Diego.;

  • 授予单位 University of California, San Diego.;
  • 学科 Biology Bioinformatics.
  • 学位 Ph.D.
  • 年度 2009
  • 页码 150 p.
  • 总页数 150
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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