Guo Zhengyu, Tzvetkova Boriana, Bassik Jennifer M, Bodziak Tara, Wojnar Brianna M, Qiao Wei, Obaida Md A, Nelson Sacha B, Hu Bo Hua, Yu Peng
Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77843, USA.
Department of Biology & Center for Behavioral Genomics, Brandeis University, Waltham, MA 02454, USA and.
Bioinformatics. 2015 Dec 15;31(24):4038-40. doi: 10.1093/bioinformatics/btv503. Epub 2015 Aug 30.
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.
Freely available on the web at http://rnaseqmetadb.ece.tamu.edu.
基因靶向是一种向生物体中的特定基因引入突变的方法。由于体内基因功能评估和人类疾病建模的重要性，该技术已被广泛用于生成大量突变小鼠模型。由于高通量测序技术的近期突破，已对许多此类小鼠模型进行了RNA测序实验，从而产生了数百个可公开获取的数据集。为便于这些数据集的重复使用，我们收集了相关元数据并将其组织在一个名为RNASeqMetaDB的数据库中。元数据经过人工整理以确保注释的一致性。我们开发了一个网络服务器，以便于数据库导航和数据查询。用户可以使用多个参数（如基因、疾病、组织类型、关键词和相关出版物）搜索数据库，以找到符合其兴趣的数据集。网络服务器上还展示了元数据的汇总统计信息，呈现了RNA测序研究有趣的全局模式。
