Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).
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.
Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.
Xinxia
X
Peng
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA honey@uw.edu.
Jean
J
Thierry-Mieg
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA.
Danielle
D
Thierry-Mieg
Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.
Andrew
A
Nishida
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA Institute for Computational Biology (ICB), Weill Cornell Medical College, New York, NY 10065, USA.
Lenore
L
Pipes
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA Institute for Computational Biology (ICB), Weill Cornell Medical College, New York, NY 10065, USA.
Marjan
M
Bozinoski
Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.
Matthew J
MJ
Thomas
Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.
Sara
S
Kelly
Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.
Jeffrey M
JM
Weiss
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
Muthuswamy
M
Raveendran
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
Donna
D
Muzny
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
Richard A
RA
Gibbs
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
Jeffrey
J
Rogers
Illumina, Inc., San Diego, CA 92122, USA.
Gary P
GP
Schroth
Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA honey@uw.edu.
Michael G
MG
Katze
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA Institute for Computational Biology (ICB), Weill Cornell Medical College, New York, NY 10065, USA Feil Family Brain and Mind Research Institute (BMRI), Weill Cornell Medical College, New York, NY 10065, USA honey@uw.edu.
Christopher E
CE
Mason
D000818:Animals; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D020407:Internet; D008251:Macaca; D058977:Molecular Sequence Annotation; D009928:Organ Specificity; D011323:Primates / Q000235:genetics*; D012015:Reference Standards; D016415:Sequence Alignment / Q000592:standards; D017423:Sequence Analysis, RNA