RNASeqMetaDB – a database and web server for navigating metadata of publicly available mouse RNA-Seq data sets

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 data sets.

To facilitate the reuse of these data sets, researchers from Texas A&M University collected the associated metadata and organized them in a database called RNASeqMetaDB. The metadata was manually curated to ensure annotation consistency. They 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 data sets that match their interests. Summary statistics of the metadata is also presented on the web server showing interesting global patterns of RNA-Seq studies.

Availability – Freely available on the web at: http://rnaseqmetadb.ece.tamu.edu

Contact: pengyu.bio@gmail.com

Guo Z, Tzvetkova B, Bassik JM, Bodziak T, Wojnar BM, Qiao W, Obaida MA, Nelson SB, Hu BH, Yu P. (2015) RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq data sets. Bioinformatics [Epub ahead of print]. [abstract]

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