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

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 - Nucleic Acids Res. (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.

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Summary of tissue-specific raw RNA-seq data (in millions of read pairs) for 11 NHP species and subspecies. All RNA-seq libraries were prepared with total RNAs with the strand-specific protocol and ribosomal RNA depletion (100 + 100 nt paired-end reads). Whole blood libraries were added a globin depletion step (50 + 50 nt paired-end reads). Additional tissue-specific RNA-seq data available from this NHPRTR update but not included in this table are: (i) testis (35.4 million read pairs) and ovary (33.1) from rhesus macaque Indian-origin; (ii) left (50.9) and right (69.5) brain hemispheres from marmoset; (iii) whole blood from ring tailed lemur (102.4), owl monkey (94.0) and rhesus macaque Chinese-origin (107.3); (iv) liver samples (50-nt single read reads) with polyA selection from Rhesus macaque Chinese-origin (26.2), cynomolgus macaque Mauritian-origin (20) and cynomolgus macaque Chinese-origin (16.9).
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Figure 1: Summary of tissue-specific raw RNA-seq data (in millions of read pairs) for 11 NHP species and subspecies. All RNA-seq libraries were prepared with total RNAs with the strand-specific protocol and ribosomal RNA depletion (100 + 100 nt paired-end reads). Whole blood libraries were added a globin depletion step (50 + 50 nt paired-end reads). Additional tissue-specific RNA-seq data available from this NHPRTR update but not included in this table are: (i) testis (35.4 million read pairs) and ovary (33.1) from rhesus macaque Indian-origin; (ii) left (50.9) and right (69.5) brain hemispheres from marmoset; (iii) whole blood from ring tailed lemur (102.4), owl monkey (94.0) and rhesus macaque Chinese-origin (107.3); (iv) liver samples (50-nt single read reads) with polyA selection from Rhesus macaque Chinese-origin (26.2), cynomolgus macaque Mauritian-origin (20) and cynomolgus macaque Chinese-origin (16.9).

Mentions: From the original collection of 21 tissues from 15 NHP species/subspecies, we selected 11 species/subspecies and 9 to 15 tissues from each species for extensive RNA-seq analysis (Figure 1). Besides the availability of sufficient amounts of good quality RNAs, the species and tissues were chosen to cover large evolutionary distances and to be most relevant to biomedical researchers. The tissues selected reflect the importance of particular primate models in the study of human diseases like AIDS pathogenesis and vaccine development, respiratory diseases, metabolic disorders and neurobiology. Specifically, we sampled five hematopoietic or immune system tissues (bone marrow, spleen, lymph node, thymus and whole blood), five central nervous system locations (cerebellum, frontal cortex, temporal lobe, global cortex and pituitary) and six main organs (kidney, liver, heart, skeletal muscle, lung and colon). We also sequenced ovaries and testes from Indian-origin rhesus macaque (RMI) and whole blood from ring tailed lemur, owl monkey and Chinese-origin rhesus macaque (RMC). Finally, as an internal control, liver samples from cynomolgus (Mauritian and Chinese, CMM and CMC) and Chinese-origin rhesus macaque were sequenced using a polyA selected protocol.


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

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 - Nucleic Acids Res. (2014)

Summary of tissue-specific raw RNA-seq data (in millions of read pairs) for 11 NHP species and subspecies. All RNA-seq libraries were prepared with total RNAs with the strand-specific protocol and ribosomal RNA depletion (100 + 100 nt paired-end reads). Whole blood libraries were added a globin depletion step (50 + 50 nt paired-end reads). Additional tissue-specific RNA-seq data available from this NHPRTR update but not included in this table are: (i) testis (35.4 million read pairs) and ovary (33.1) from rhesus macaque Indian-origin; (ii) left (50.9) and right (69.5) brain hemispheres from marmoset; (iii) whole blood from ring tailed lemur (102.4), owl monkey (94.0) and rhesus macaque Chinese-origin (107.3); (iv) liver samples (50-nt single read reads) with polyA selection from Rhesus macaque Chinese-origin (26.2), cynomolgus macaque Mauritian-origin (20) and cynomolgus macaque Chinese-origin (16.9).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4383927&req=5

Figure 1: Summary of tissue-specific raw RNA-seq data (in millions of read pairs) for 11 NHP species and subspecies. All RNA-seq libraries were prepared with total RNAs with the strand-specific protocol and ribosomal RNA depletion (100 + 100 nt paired-end reads). Whole blood libraries were added a globin depletion step (50 + 50 nt paired-end reads). Additional tissue-specific RNA-seq data available from this NHPRTR update but not included in this table are: (i) testis (35.4 million read pairs) and ovary (33.1) from rhesus macaque Indian-origin; (ii) left (50.9) and right (69.5) brain hemispheres from marmoset; (iii) whole blood from ring tailed lemur (102.4), owl monkey (94.0) and rhesus macaque Chinese-origin (107.3); (iv) liver samples (50-nt single read reads) with polyA selection from Rhesus macaque Chinese-origin (26.2), cynomolgus macaque Mauritian-origin (20) and cynomolgus macaque Chinese-origin (16.9).
Mentions: From the original collection of 21 tissues from 15 NHP species/subspecies, we selected 11 species/subspecies and 9 to 15 tissues from each species for extensive RNA-seq analysis (Figure 1). Besides the availability of sufficient amounts of good quality RNAs, the species and tissues were chosen to cover large evolutionary distances and to be most relevant to biomedical researchers. The tissues selected reflect the importance of particular primate models in the study of human diseases like AIDS pathogenesis and vaccine development, respiratory diseases, metabolic disorders and neurobiology. Specifically, we sampled five hematopoietic or immune system tissues (bone marrow, spleen, lymph node, thymus and whole blood), five central nervous system locations (cerebellum, frontal cortex, temporal lobe, global cortex and pituitary) and six main organs (kidney, liver, heart, skeletal muscle, lung and colon). We also sequenced ovaries and testes from Indian-origin rhesus macaque (RMI) and whole blood from ring tailed lemur, owl monkey and Chinese-origin rhesus macaque (RMC). Finally, as an internal control, liver samples from cynomolgus (Mauritian and Chinese, CMM and CMC) and Chinese-origin rhesus macaque were sequenced using a polyA selected protocol.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, WA 98109, USA Washington National Primate Research Center, Seattle, WA 98109, USA.

Show MeSH
Related in: MedlinePlus