A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

负责人：

University Of Edinburgh;;University Of Edinburgh

关键词：

FAANG Transcriptome genome functional annotation sheep Ovis aries ruminant gene expression atlas transcription network Biological Sciences::Genetics

DOI：

doi:10.7488/ds/2112

摘要：

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of guilt by association was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.;;This dataset contains three .txt files - S1_Dataset.txt, S2_Dataset.txt and S3_Dataset.txt - corresponding to three supplemental files published as Clark, et al. (2017) A high resolution atlas of gene expression in the domestic sheep (Ovis aries). These supplemental files are expression atlases, respectively listing the: (1) expression level per gene per tissue per replicate, (2) average expression level per tissue per developmental stage, and (3) female:male expression ratio per gene. In all cases, expression level is quantified as transcripts per million (TPM).