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 deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species. A consortium of primate biologists, molecular biologists, and bioinformatists participate in the development and extension of the NHPRTR. Michael Katze of the University of Washington (UW) and Chris Mason of Cornell University (CU) along with Gary Schroth of Illumina were the leaders of this initial phase of the project. Currently, the Washington National Primate Resource Center maintains this website. There are three main data set types available on the site as described below.
In 2012, we produced a raw data set containing 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).The RNASeq data was described in Pipes et al, 2013. Access these data here.
For this effort, we selected 11 of the original 15 NHP species/subspecies and collected RNA-Seq data from ~15 tissues from each species. The completed tissue-specific RNA-seq dataset consists of over 10 billion paired-end raw reads. The summary of the dataset and access to the data can be found here.
Additionally, tissue-specific small RNA data is available for rhesus macaque here
Upcoming domain specific NHP transcriptome analysis
- RNA-seq analysis of NHP immune cell specific transcriptomes. This upcoming RNA-seq dataset will cover sorted immune cell subsets (B cells, Monocytes, NK cells, total CD4+ T cells, naïve CD4+ T cells, CD4+ central memory T cells, CD4+ effector memory T cells, and CD8+ T cells) from rhesus macaque, African green monkey, sooty mangabey, and human peripheral blood mononuclear cells. More detailed description of this project is available here.
- RNA-seq analysis of NHP brain tissue transcriptomes. The Mason lab is collecting additional brain samples to parallel the human effort called BrainSpan (Brainspan.org), which will enable region-specific characterization of the functional elements of primate brains, catalog orthologous genes, and improve the annotation of these genomes.