Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).
Bottom Line: The sequence quality is such that 88% of the reads align to human reference sequences, allowing us to compute the full list of expression abundance across all tissues for each species, using the reads mapped to human genes.This update also includes improved transcript annotations derived from RNA-seq data for rhesus and cynomolgus macaques, two of the most commonly used NHP models and additional RNA-seq data compiled from related projects.Together, these comprehensive reference transcriptomes from multiple primates serve as a valuable community resource for genome annotation, gene dynamics and comparative functional analysis.
Affiliation: Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.Show MeSH
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Mentions: The species assignment of each library was verified by analyzing over 5 million positions which appear as homozygous variant relative to human in at least one species. The analysis was facilitated by the fact that in most cases, all tissues in a species were coming from a single individual. We observed that each library was overwhelmingly sharing its homozygous SNPs only with the other libraries of the same species (average 99.987% identical SNPs, range: 99.56 to 100.00%). Therefore, all species and subspecies are consistently annotated. The correct assignment of tissues was verified using the covariance analysis of the expression patterns provided by the Magic pipeline (Supplementary Methods). Examples of tissue-specific genes are shown in Figure 3.
Affiliation: Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.