Fast, Flexible and Inexpensive Ink-Jet Array Printer

快速、灵活且廉价的喷墨阵列打印机

• 批准号: 6744073
• 负责人: STEPHEN R LASKY
• 金额: $ 55.55万
• 依托单位: INSTITUTE FOR SYSTEMS BIOLOGY
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-05-05 至 2006-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6744073
• 关键词: biotechnology; computer data analysis; computer graphics /printing; computer program /software; gene expression; gene targeting; genetic polymorphism; genotype; high throughput technology; lethal genes; mass spectrometry; matrix assisted laser desorption ionization; microarray technology; nucleic acid sequence; oligonucleotides; protein binding; proteomics; surface plasmon resonance; technology /technique development; transcription factor

DESCRIPTION (provided by applicant): A new ink-jet oligonucleotide array synthesizer and several novel applications of this technology are being developed by the Institution for Systems Biology (ISB). When completed, specifications for construction, maintenance, and operation of this unique system will be released to the scientific community, satisfying the need for fast, flexible, and inexpensive synthesis of custom oligonucleotide array chips. Preliminary experiments comparing the results from ink-jet and pin-spotted microarrays for halobacterium, yeast, and murine T-cell receptor model systems reveal significant progress in the development of the ISB ink-jet arrayer. Despite considerable improvements, better consistency, density, and improved quality controls of in situ oligonucleotide synthesis are needed before this instrument is ready to be introduced into basic research laboratories. The most promising advantage of in situ ink-jet array synthesis over alternative methods is its speed and flexibility; new arrays can be designed and printed overnight without the need to catalog and array thousands of PCR gene products. We intend to take advantage of this flexibility to approach new challenges. In addition to gene expression analysis, we will adapt ink-jet chips to study the effects of gene knock-outs and synthetic lethal mutations, genetic variation, in vitro transcription factor binding, and in vivo protein binding to native chromatin. Because improved integration of oligonucleotide design, data acquisition, analysis, and the ability to share data with other laboratories must assume a high priority in today's post-genomic research setting, we are developing software that can quickly find unique oligonucleotides for hundreds or thousands of genes or DNA segments simultaneously. This software is being integrated into a relational database package utilizing emerging MIAME/MAGE standards for microarray data. Data from other high-throughput techniques, such as DNA sequencing, genotyping, and proteomics, can be ported into this system, and links to analysis software developed at the ISB or at other institutions will be incorporated. The goal of this project is to make a fast, flexible ink-jet array system available to the scientific community and to provide software that enhances the functionalities of the system through quality control, data collection and analysis, and graphic visualization of the complex data-sets generated by the arrayer.

描述（由申请人提供）： 系统生物学机构（ISB）开发了一种新的喷墨寡核苷酸阵列合成器和该技术的几种新颖应用。完成后，该独特系统的构建，维护和操作规格将发布给科学界，满足对自定义寡核苷酸阵列芯片的快速，灵活和廉价合成的需求。比较大杆菌，酵母和鼠T细胞受体模型系统的墨水和销斑微阵列的结果的初步实验揭示了ISB墨水喷射阵列的开发中的显着进展。尽管有很大的改进，但仍需要在将该仪器引入基础研究实验室之前，需要更好的一致性，密度和改善原位寡核苷酸合成的质量控制。与替代方法相比，原位墨水阵列合成的最有希望的优势是其速度和灵活性。可以在一夜之间设计和印刷新阵列，而无需对数千种PCR基因产品进行编目和阵列。我们打算利用这种灵活性来应对新的挑战。 除基因表达分析外，我们还将适应喷墨芯片，以研究基因敲除和合成致死突变，遗传变异，体外转录因子结合以及体内蛋白与天然染色质的结合的影响。由于寡核苷酸设计，数据采集，分析以及与其他实验室共享数据的能力的整合得以改善，必须在当今的基因组后研究环境中高度优先考虑，因此我们正在开发软件，这些软件可以快速为数百或数千个基因或DNA片段而迅速找到独特的寡核苷酸。该软件正在集成到使用新兴迈阿密/法师标准的微阵列数据的关系数据库软件包中。可以将来自其他高通量技术的数据（例如DNA测序，基因分型和蛋白质组学）移植到该系统中，并将合并到ISB或其他机构开发的分析软件的链接。该项目的目的是使科学界可以使用快速，灵活的喷墨阵列系统，并提供通过质量控制，数据收集和分析以及对数组生成的复杂数据集的图形可视化来增强系统功能的软件。