Biological research is shifting paradigms from molecular reductionist approaches to include larger-scale investigations of the entire proteome or genome. High-throughput (HT) biology began in earnest with the Human Genome Project; increasingly HT tools are being exploited for protein research. Given the importance of proteins in disease etiology and treatment, a major challenge facing biology is the elucidation of the physiological role of every protein. Using HT approaches, functional proteomics will address this challenge by expressing proteins at a scale of thousands at a time, and by subsequently assaying their functional properties, such as subcellular location, interacting partners, biochemical activity and regulated modification. A prerequisite for all these studies is a comprehensive collection of full-length expression-ready (FLEX) clones. Such a collection is being built using recombinational cloning, which allows rapid transfer into any vector, in frame and without mutation. These FLEXGene clones provide researchers with a powerful resource that expresses proteins in all experimental formats and at any chosen scale. As a complement to the FLEX repository, a collection is being assembled of clones encoding small inhibitory RNAs (siRNAs), which specifically inhibit the expression of their cognate gene. Together with FLEXGene, these collections allow users to up- or down-regulate specific proteins to study their function in biology and disease. Furthermore, assaying sets of hundreds of clones enables investigators to conduct large-scale screens to identify key proteins or pathways. The overall objective of this project is to build a robust repository that makes these clones readily available to researchers. However, the number of collected clones (already >15,000) exceeds the ability to distribute, track and retrieve them manually. User-requested sets of 200 clones can be dispersed over 100 different plates. Without automation, the fulfillment of dozens of clone requests is untenable on a just-in-time basis. This application requests funds to obtain an automated storage unit. The BIOPHILE storage unit with individual vial retriever (IVR) uniquely combines the reliability of robotically controlled retrieval with the required clone stability of -80 x C. Bar-coded samples are robotically retrieved without opening a freezer door, thus maintaining a stable temperature. While manual distribution accommodates fewer than 100 clones per day, the BIOPHILE has a capacity of 1,200 clones per day.
| Zuo, Dongmei; Mohr, Stephanie E; Hu, Yanhui et al. (2007) PlasmID: a centralized repository for plasmid clone information and distribution. Nucleic Acids Res 35:D680-4 |
