- Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). [PMID: 25392405]
Xinxia Peng, Jean Thierry-Mieg, Danielle Thierry-Mieg, Andrew Nishida, Lenore Pipes, Marjan Bozinoski, Matthew J Thomas, Sara Kelly, Jeffrey M Weiss, Muthuswamy Raveendran, Donna Muzny, Richard A Gibbs, Jeffrey Rogers, Gary P Schroth, Michael G Katze, Christopher E Mason
Nucleic acids research 2015:43(Database issue)
7 Citations (Google Scholar as of 2016-03-28)
Abstract: The non-human primate reference transcriptome resource (NHPRTR, available online at http://nhprtr.org/) aims to generate comprehensive RNA-seq data from a wide variety of non-human primates (NHPs), from lemurs to hominids. In the 2012 Phase I of the NHPRTR project, 19 billion fragments or 3.8 terabases of transcriptome sequences were collected from pools of ? 20 tissues in 15 species and subspecies. Here we describe a major expansion of NHPRTR by adding 10.1 billion fragments of tissue-specific RNA-seq data. For this effort, we selected 11 of the original 15 NHP species and subspecies and constructed total RNA libraries for the same ? 15 tissues in each. The sequence quality is such that 88% of the reads align to human reference sequences, allowing us to compute the full list of expression abundance across all tissues for each species, using the reads mapped to human genes. This update also includes improved transcript annotations derived from RNA-seq data for rhesus and cynomolgus macaques, two of the most commonly used NHP models and additional RNA-seq data compiled from related projects. Together, these comprehensive reference transcriptomes from multiple primates serve as a valuable community resource for genome annotation, gene dynamics and comparative functional analysis. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
- The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. [PMID: 23203872]
Lenore Pipes, Sheng Li, Marjan Bozinoski, Robert Palermo, Xinxia Peng, Phillip Blood, Sara Kelly, Jeffrey M Weiss, Jean Thierry-Mieg, Danielle Thierry-Mieg, Paul Zumbo, Ronghua Chen, Gary P Schroth, Christopher E Mason, Michael G Katze
Nucleic acids research 2013:41(Database issue)
24 Citations (Google Scholar as of 2016-02-28)
Abstract: RNA-based next-generation sequencing (RNA-Seq) provides a tremendous amount of new information regarding gene and transcript structure, expression and regulation. This is particularly true for non-coding RNAs where whole transcriptome analyses have revealed that the much of the genome is transcribed and that many non-coding transcripts have widespread functionality. However, uniform resources for raw, cleaned and processed RNA-Seq data are sparse for most organisms and this is especially true for non-human primates (NHPs). Here, we describe a large-scale RNA-Seq data and analysis infrastructure, the NHP reference transcriptome resource (http://nhprtr.org); it presently hosts data from12 species of primates, to be expanded to 15 species/subspecies spanning great apes, old world monkeys, new world monkeys and prosimians. Data are collected for each species using pools of RNA from comparable tissues. We provide data access in advance of its deposition at NCBI, as well as browsable tracks of alignments against the human genome using the UCSC genome browser. This resource will continue to host additional RNA-Seq data, alignments and assemblies as they are generated over the coming years and provide a key resource for the annotation of NHP genomes as well as informing primate studies on evolution, reproduction, infection, immunity and pharmacology.