Project Details
Projekt
Generation of the iBeetle templates, development of the iBeetle-base to a central gene function database and mining the data for new relationships by clustering
Applicant
Professor Dr. Gregor Bucher
Subject Area
General Genetics and Functional Genome Biology
Term
from 2010 to 2017
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 102336348
As prerequisite for the genome wide RNAi screen, the so called iBeetle-Library will be established that aims at representing all genes of the Tribolium genome in one copy, respectively. We want to base the first round of template production on an EST approach, where randomly cloned cDNAs are sequenced. By bioinformatics sequence analysis, one sequence per cluster will be selected and the respective plasmid integrated into the iBeetle-Library. The reason for the EST based approach is that we want to work with confirmed transcripts as far as possible. Moreover, we do not want to select against genes with unusual structure that might be missed in automatic annotations. Finally, the current version of the genomic sequence has not yet reached the quality of the Drosophila or C.elegans counterparts. Therefore, an entirely PCR based approach - as was performed in these species - would miss important genes, would lead to duplicate injections of the same gene (because many genes are erroneously predicted as two) and would be prone to technical problems when primers are located in erroneously predicted exons. In order to also include genes with low expression level that are not covered by the ESTs, we will further expand the iBeetle-Library by a PCR based approach. As prerequisite for this, we will enhance the annotation of the genomic sequence (in collaboration with others in the community) by producing transcriptome data by state of the art sequencing methods. Based on the iBeetle-Library, double stranded RNAs are produced for the genome wide knock-down of genes. Furthermore, this wili bc the first comprehensive collection of Tribolium genes that is likely to be the basis for further projects and the enhancement of the genome annotation will enhance the research on Tribolium beyond this project.In addition, a database will be generated that serves several aims: I) Screening: During the screen, the data will be collected via web interface and stored in the central database located al Göttingen. The data will be collected in form of buttons, drop-down menus with a predefined vocabulary, free text fields and pictures. Moreover, the progress and efficiency of the screen can be monitored by using the entered data. 2) Analysis of genome wide phenotypic information. 3) Publication and linking with other resources: The data will be linked lo other databases (BeetleBase, FlyBase etc) and an extensive online search tool will allow identifying phenotypes for the consortium and - upon publication - for the entire community.
DFG Programme
Research Units
