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）： 系统生物学研究所（ISB）正在开发一种新的喷墨寡核苷酸阵列合成器和这种技术的几种新应用。完成后，该独特系统的构建、维护和操作规范将发布给科学界，满足快速、灵活和廉价合成定制寡核苷酸阵列芯片的需求。初步实验比较结果从喷墨和针点微阵列的嗜盐菌，酵母，和小鼠T细胞受体模型系统揭示了显着的进步，在发展中的ISB喷墨阵列。尽管有相当大的改进，更好的一致性，密度和改进的质量控制，在原位寡核苷酸合成的仪器是准备引入基础研究实验室之前，需要。与其他方法相比，原位喷墨阵列合成最有前途的优势是它的速度和灵活性;新阵列可以在一夜之间设计和打印，而不需要对数千个PCR基因产物进行分类和阵列。我们打算利用这种灵活性来应对新的挑战。 除了基因表达分析，我们将采用喷墨芯片研究基因敲除和合成致死突变，遗传变异，体外转录因子结合和体内蛋白质结合天然染色质的影响。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改进集成必须在当今的后基因组研究环境中占据高度优先地位，因此我们正在开发能够同时快速找到数百或数千个基因或DNA片段的独特寡核苷酸的软件。该软件正在整合到一个关系数据库包中，利用新兴的MIAME/法师标准的微阵列数据。来自其他高通量技术的数据，如DNA测序、基因分型和蛋白质组学，可以移植到这个系统中，并与ISB或其他机构开发的分析软件相连接。该项目的目标是向科学界提供一种快速、灵活的喷墨阵列系统，并提供软件，通过质量控制、数据收集和分析以及阵列器生成的复杂数据集的图形可视化来增强该系统的功能。