Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).

TitleTissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).
Publication TypeJournal Article
Year of Publication2015
AuthorsPeng, X, Thierry-Mieg, J, Thierry-Mieg, D, Nishida, A, Pipes, L, Bozinoski, M, Thomas, MJ, Kelly, S, Weiss, JM, Raveendran, M, Muzny, DM, Gibbs, RA, Rogers, J, Schroth, GP, Katze, MG, Mason, CE
JournalNucleic Acids Res
Volume43
IssueDatabase issue
PaginationD737-42
Date Published2015 Jan
ISSN1362-4962
KeywordsAnimals, Databases, Genetic, Gene Expression Profiling, Internet, Macaca, Molecular Sequence Annotation, Organ Specificity, Primates, Reference Standards, Sequence Alignment, Sequence Analysis, RNA
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.

DOI10.1093/nar/gku1110
Alternate JournalNucleic Acids Res.
PubMed ID25392405
PubMed Central IDPMC4383927
Grant ListU54-HG003273 / HG / NHGRI NIH HHS / United States
P51OD010425 / OD / NIH HHS / United States
HHSN272201300010C / / PHS HHS / United States
P51 OD010425 / OD / NIH HHS / United States
R24OD010445 / OD / NIH HHS / United States
P51 RR000166 / RR / NCRR NIH HHS / United States
R24OD011172 / OD / NIH HHS / United States
T32 GM083937 / GM / NIGMS NIH HHS / United States
/ / Intramural NIH HHS / United States
1R01NS076465-02 / NS / NINDS NIH HHS / United States
R24 OD011172 / OD / NIH HHS / United States