RT Journal Article
SR Electronic
T1 Tissue Resolved, Gene Structure Refined Equine Transcriptome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 061952
DO 10.1101/061952
A1 T. A. Mansour
A1 E. Y. Scott
A1 C. J. Finno
A1 R. R. Bellone
A1 M. J. Mienaltowski
A1 M. C. Penedo
A1 P. J. Ross
A1 S. J. Valberg
A1 J. D. Murray
A1 C. T. Brown
YR 2016
UL http://biorxiv.org/content/early/2016/09/23/061952.abstract
AB Background Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR). 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.Results This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and 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.Conclusions 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 and can serve several types of downstream analyses.List of Abbreviations:(SNP)Single Nucleotide polymorphism(UTR)Untranslated region(CNS)Central nervous system(ICM)Inner cell mass(TE)Trophectoderm(RNA-seq)RNA sequencing