RNA-Seq Based Rat Transcriptome Annotation

Rat (Rattus norvegicus) is an important model organism in toxicological, neurological model and primary cell cultures for its short period and high similarity with human. The rat transcriptome is the most wildly concerned level in the various studies. For example, there are652toxicological data sets related with rat, ranking first in GEO database, while the second one is mouse with160records. However, the transcriptome annotation of rat is far from completed when comparing with the one of human or mouse. Some efforts have been made to improve Rat Genome Database (RGD) annotations by AceView based on cDNA and EST sequences, but a great gap between rat and mouse still exists.High-throughput RNA sequencing (RNA-Seq) promises a comprehensive picture of the transcriptome, and the complexity of the transcriptome were greatly illustrated in the past several years by RNA-Seq at the levels of genome coverage, junction, isoform and coding potential. Many species were documented in this topic, including Caenorhabditis elegans, Mus musculus and Homo sapiens, and it was shown an unprecedented number of transcripts that have been escaped from our observation for yearsThis study focuses on the data significance of RNA-Seq analysis and application, and reveals the importance of data resource on RNA-Seq analysis. By tuning reconstruction pipeline and sequencing extensively samples, my research provides a set of rat data for RNA-Seq based analysis, including junction database, gene models, and functional annotation with equivalent amount with that of mouse. Totally484,128junctions are included in the junction database,185,569transcripts were identified and more than10,000ones were annotated with significant GO terms.In addition, a set of isoform-only tissue enriched transcripts were identified as an example, which indicates the available of the multiple-isoform enriched resource for understanding tissue specific alternative splicing mechanism.