Fast, Flexible and Inexpensive Ink-Jet Array Printer

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项技术的几个新应用。完成后，这一独特系统的建造、维护和操作规范将向科学界发布，满足快速、灵活和廉价合成定制寡核苷酸阵列芯片的需求。对盐杆菌、酵母菌和小鼠T细胞受体模型系统的喷墨和针点微阵列的初步实验结果表明，ISB喷墨阵列的开发取得了重大进展。尽管有了相当大的改进，但在准备将该仪器引入基础研究实验室之前，还需要更好的一致性、密度和改进的原位寡核苷酸合成质量控制。与其他方法相比，原位喷墨阵列合成最有希望的优势是它的速度和灵活性；新的阵列可以在一夜之间设计和打印，而不需要对数千个PCR基因产物进行编目和排列。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，我们还将采用喷墨芯片来研究基因敲除和合成致命突变、遗传变异、体外转录因子结合以及体内蛋白质与天然染色质结合的影响。由于改进的寡核苷酸设计、数据采集、分析以及与其他实验室共享数据的能力在当今的后基因组研究环境中必须成为高度优先事项，我们正在开发能够快速找到成百上千个基因或DNA片段的独特寡核苷酸的软件。该软件正在利用新出现的微阵列数据的MIAME/MAGE标准集成到关系数据库包中。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，可以被移植到这个系统中，并将纳入到ISB或其他机构开发的分析软件的链接。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以图形方式显示阵列所产生的复杂数据集来增强系统的功能。

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.