Project description:Purpose: We performed an NGS study on the circadian changes in Rhesus Macaque retina and pineal gland transcriptome in order to elucidate novel elements in the primate circadian clock. Methods: Total RNA from retina and pineaal glands of Rhesus Macauqes euthanized at 4 timepoints (Dawn, Day, Dusk and Night) was deep sequenced, in triplicate, using Illumina HiSeq2000. Reads were aligned using STAR aligner and differential expression was asssessed using DESeq2. Results: We discover a variety of novel genes that show circadian activivty in both retina and pineal gland of the Rhesus Macaque. A particular set of genes involved in the production of N-acetyltryptamine in Rhesus Macaque retina appears to be responsible for the circadian oscillations of the concentrations of N-acetyltriptamine in the plasma, thereby accentuating N-acetyltriptamine as a retina derived signaling molecule in primates. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
Project description:The purpose of the experiment was to compare placental transcriptome of rhesus macaque at approximately 80% completed gestation to human placental transcriptomes.
Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 7,631 nuclei in macaque adult testis. This dataset includes two samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
