Welcome to the NHPRTR

 

The Nonhuman Primate Reference Transcriptome Resource (NHPRTR) is a project that was initiated in mid 2010. The concept was to develop a NHP reference transcriptome resource consisting of Next Generation Sequence complete transcriptomes from multiple NHP species. A consortium of primate biologists, molecular biologists, and bioinformatists participate in the development and extension of the NHPRTR. The Steering Committee overseeing the collection, processing, sequencing and assemblies within the resource is composed of Michael Katze of the University of Washington (UW) and Chris Mason of Cornell University (CU) along with Gary Schroth of Illumina. Our current raw data set contains 40.5 billion 100nt reads from 21 tissues across thirteen primate organisms. The data comes from three types of RNA library preparation methods: non-directional mRNA-sequencing (RNA), non-directional mRNA-sequencing and Uracil-DNA Glycosolase (UDG), and total RNA (TOT). Data for RNA-seq was described in:

Pipes, L., S. Li, M. Bozinoski, R. Palermo, X. Peng, P. Blood, S. Kelly, J. M. Weiss, J. Thierry-Mieg, D. Thierry-Mieg, P. Zumbo, R. Chen, G. P. Schroth, C. E. Mason, and M. G. Katze. 2013. The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. Nucleic Acids Res 41:D906-D914.

Access these data here.

February 28, 2014

We have processed the RNAseq data for Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque, and generated updated genome annotations for both macaques. A manuscript detailing the work has been submitted to the 2014 special AIDS issue in the Journal of Medical Primatology. Please email us for an early access to the annotations.

In brief, for both macaque species we uncovered thousands of novel isoforms for annotated genes and thousands of un-annotated intergenic transcripts enriched with non-coding RNAs. We also identified thousands of transcript sequences which are partially or completely ‘missing’ from current macaque genome assemblies. Many newly identified transcripts were differentially expressed during SIV infection of rhesus macaques or during Ebola virus infection of cynomolgus macaques.