This proposal is aimed at expanding the goals of the """"""""Program for Rat EST Sequencing and Mapping"""""""". In the initial phase of this project, the applicant used a highly efficient strategy called serial subtraction of normalized cDNA libraries (SSNL) to identify nearly 25,000 non-redundant rat ESTs. These ESTs along with the ESTs identified by The Institute of Genome Research (TIGR) make up the rat UniGene set consisting of over 30,000 members. By the beginning of the renewal phase of this project, 5'EST sequences will have been generated on 24,289 members of the UniGene set. In addition, 10,000 rat ESTs will have been mapped using radiation hybrids. In the renewal phase of this project, SSNL will be used to identify an additional 30,000 rat ESTs to bring the UniGene set to a minimum of 60,000 ESTs. Generation of 5' sequence will be completed on all 60,000 members of the UniGene set. Furthermore, in collaboration with Dr. Howard Jacob at the Medical College of Wisconsin, the applicants will radiation hybrid map an additional 27,000 ESTs towards developing a map of 37,000 ESTs. Finally, they will continue to develop algorithms and software for EST clustering, expression analysis and mapping, and continue to maintain an informatics processing and management system for rat gene discovery and mapping. Progress during the initial phase of this project resulted in unprecedented efficiency in gene discovery.
| Kwitek, Anne E; Gullings-Handley, Jo; Yu, Jiaming et al. (2004) High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Genome Res 14:750-7 |
| Laffin, Jennifer J S; Scheetz, Todd E; Bonaldo, Maria de Fatima et al. (2004) A comprehensive nonredundant expressed sequence tag collection for the developing Rattus norvegicus heart. Physiol Genomics 17:245-52 |
| Gavin, A J; Scheetz, T E; Roberts, C A et al. (2002) Pooled library tissue tags for EST-based gene discovery. Bioinformatics 18:1162-6 |
| Scheetz, T E; Raymond, M R; Nishimura, D Y et al. (2001) Generation of a high-density rat EST map. Genome Res 11:497-502 |
| Kwitek, A E; Tonellato, P J; Chen, D et al. (2001) Automated construction of high-density comparative maps between rat, human, and mouse. Genome Res 11:1935-43 |
