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. 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. Over the years NHPRTR has expanded into two major Phases.
In 2012, we produced a raw data set contains 40.5 billion 100nt reads from 21 tissues across thirteen primate organisms (Owl monkey and squirral monkey were added later?). 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.
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.