TY - JOUR T1 - Tissue Resolved, Gene Structure Refined Equine Transcriptome JF - bioRxiv DO - 10.1101/061952 SP - 061952 AU - T.A. Mansour AU - E.Y. Scott AU - C.J. Finno AU - R.R. Bellone AU - M.J. Mienaltowski AU - M.C. Penedo AU - P.J. Ross AU - S.J. Valberg AU - J.D. Murray AU - C.T. Brown Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/07/08/061952.abstract N2 - Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of single nucleotide polymorphisms (SNPs). The current annotation of the horse genome lacks the specificity and sensitivity necessary to distinguish differential isoform expression, untranslated region (UTR) usage and, to some extent, sensitive differential gene expression. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome. This equine transcriptome integrates eight different tissues from over fifty individuals and improves gene structure, isoform resolution while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome. We have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date. We encourage the integration of further transcriptomes with our annotation pipeline. ER -