NHPRTR.org

Welcome to the NHPRTR

Announcements

February 2018 - Alternative Splicing Patterns in Rhesus Macaque Transcriptomes

Final processed isoform data from Iso-seq analysis of multiple rhesus macaque tissues are available here.

April 2015 - Small RNA Tissue Specific RNA-seq Data for Rhesus Macaque

Tissue specific small RNA sequence data is now available for rhesus macaque here. Tissue specific data for NHP species is additionally now integrated with AceView.

November 2014 - Publication on the Tissue Specific RNA-seq Data

The tissue specific data is published by Nucleic Acid Research, and is accessible here.

September 2014 – mRNA-seq dataset of macaque rectal samples from SIV acute infection model.

Data available from NCBI GEO (GSE56845). Please see Barrenas et al. 2014 for more details.

June, 2014 – Updated Macaque Genome Annotation

We have processed the RNAseq data for Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque, and generated updated genome annotations for both macaques. The work was detailed in Peng et al, 2014. The updated annotation can be downloaded from here.

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. Chris Mason of Cornell University (CU) along with Gary Schroth of Illumina were the leaders of this initial phase of the project. The Division of NHP Systems Biology at the Washington National Primate Resource Center (Deborah Fuller and Michael Gale, Jr.) maintains this website. Currently, there are four comprehensive data sets available as described below.

Set I. RNAseq analysis of tissue pools for individual NHP species

We have generated 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.

Set II. RNA-seq analysis of NHP tissue-specific transcriptomes

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.

Set III. Tissue-specific small RNA data for rhesus macaque

Tissue-specific small RNA data is available for rhesus macaque here

Set IV. Full-length Indian-origin rhesus macaque transcriptome using PacBio Iso-Seq technology

Uing PacBio Iso-Seq technology, we generated high quality full-length transcriptome sequencing reads using four sample types from rhesus macaque: lymph node tissue, peripheral blood mononuclear cells (PBMC), whole blood, and rectal tissue. The summary of this dataset and access to the data can be found here.

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