Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

NHPRTR (Nonhuman Primate Reference Transcriptome Resource)

General information

Description: 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.NHPRTR aims to generate comprehensive RNA-seq data from a wide variety of non-human primates (NHPs),from lemurs to hominids.
Year founded: 2013
Last update: 2015-4
Version: v1.0
Accessibility:
Manual:
Accessible
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Country/Region: United States
Data type:
RNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: University of Washington
Address: Seattle,WA 98109,USA
City: Seattle
Province/State: WA
Country/Region: United States
Contact name (PI/Team): Michael G. Katze
Contact email (PI/Helpdesk): honey@u.washington.edu

Related Database

Record metadata

Created on: 2015-06-20
Curated by:
Lin Liu [2016-03-28]
Li Yang [2015-11-24]
Li Yang [2015-06-26]

Ranking

All databases:
782/4549 (82.831%)
Expression:
132/799 (83.605%)
782
Total Rank
61
Citations
8.714
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Publications

25392405
Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). [PMID: 25392405]
Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE.

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.

Nucleic Acids Res. 2015:43(Database issue) | 26 Citations (from Europe PMC, 2020-05-30)
23203872
The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. [PMID: 23203872]
Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG.

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.

Nucleic Acids Res. 2013:41(Database issue) | 35 Citations (from Europe PMC, 2020-05-30)