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: From the original collection of 21 tissues from 15 NHP species/subspecies, we selected 11 species/subspecies and 9 to 15 tissues from each species for extensive RNA-seq analysis (Figure 1). Besides the availability of sufficient amounts of good quality RNAs, the species and tissues were chosen to cover large evolutionary distances and to be most relevant to biomedical researchers. The tissues selected reflect the importance of particular primate models in the study of human diseases like AIDS pathogenesis and vaccine development, respiratory diseases, metabolic disorders and neurobiology. Specifically, we sampled five hematopoietic or immune system tissues (bone marrow, spleen, lymph node, thymus and whole blood), five central nervous system locations (cerebellum, frontal cortex, temporal lobe, global cortex and pituitary) and six main organs (kidney, liver, heart, skeletal muscle, lung and colon). We also sequenced ovaries and testes from Indian-origin rhesus macaque (RMI) and whole blood from ring tailed lemur, owl monkey and Chinese-origin rhesus macaque (RMC). Finally, as an internal control, liver samples from cynomolgus (Mauritian and Chinese, CMM and CMC) and Chinese-origin rhesus macaque were sequenced using a polyA selected protocol.
Affiliation: Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.