Dr. Peng Yu creates new database and webserver for mouse RNASeq studies

Sep 21st, 2015 | By | Category: Bioinformatics, Call for Papers, FrontPage, In the News, News, Publications, Success
 Genomics - DNA - Gene - Genetics
RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets.

Guo Z, Tzvetkova B, Bassik JM, Bodziak T, Wojnar BM, Qiao W, Obaida MA, Nelson SB, Hu BH, Yu P

Abstract

Gene targeting is a protocol for introducing a mutation to a specific gene in an organism. Because of the importance of in vivo assessment of gene function and modeling of human diseases, this technique has been widely adopted to generate a large number of mutant mouse models. Due to the recent breakthroughs in high-throughput sequencing technologies, RNA-Seq experiments have been performed on many of these mouse models, leading to hundreds of publicly available datasets. To facilitate the reuse of these datasets, we collected the associated metadata and organized them in a database called RNASeqMetaDB. The metadata were manually curated to ensure annotation consistency. We developed a web server to allow easy database navigation and data querying. Users can search the database using multiple parameters like genes, diseases, tissue types, keywords and associated publications in order to find datasets that match their interests. Summary statistics of the metadata are also presented on the web server showing interesting global patterns of RNA-Seq studies.

Link to publication

Link to RNASeqMetaDB

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