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

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 (+4 others)
2014 Nucleic Acids Research  
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  ...  Together, these comprehensive reference transcriptomes from multiple primates serve as a valuable community resource for genome annotation, gene dynamics and comparative functional analysis.  ...  To develop a reference gene expression resource, the Non-Human Primate Reference Transcriptome Resource (NHPRTR, http://nhprtr.org) was initiated to deeply sequence RNA from multiple primates using next-generation  ... 
doi:10.1093/nar/gku1110 pmid:25392405 pmcid:PMC4383927 fatcat:sy53zpxbbjexjcagogmrgfku44

The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics

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 (+3 others)
2012 Nucleic Acids Research  
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  ...  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).  ...  ACKNOWLEDGEMENTS We would like to thank Illumina, Inc. for contributing almost all of the resources and reagents needed for completing the sample preps, sequencing and primary data analysis.  ... 
doi:10.1093/nar/gks1268 pmid:23203872 pmcid:PMC3531109 fatcat:op3ttl5v6ndslfsvd45suvcnq4

Analysis Of Rna Editing In Non-Human Primates

Marjan Bozinoski, Chris Mason
2015 Zenodo  
Expanding the analysis in tissue-specific manner, we observe distinct conservation of RNA editing sites throughout the different brain regions, with ones phylogenetically closest to human showing more  ...  Additionally, we analyze RNA editing in tissue specific manner, using data from 14 separate sequenced tissues from each of the species.  ...  dozen non-human primates 8 as part of the Non-Human Primate Reference Transcriptome Resource (NHPRTR).  ... 
doi:10.5281/zenodo.31145 fatcat:vzitv2adnjbbbpfc3pz2wxj5ii

Old World Monkeys and New Age Science: The Evolution of Nonhuman Primate Systems Virology

R. E. Palermo, J. Tisoncik-Go, M. J. Korth, M. G. Katze
2013 ILAR journal  
oligonucleotide microarray, paving the way for further resource development and additional primate sequencing projects.  ...  Against this backdrop of both expanding sequence data and the early application of sequence-derived DNA microarrays tools, we will contextualize the development of these community resources and their application  ...  Funding was also provided by the NIAID Reagent Resource Support Program for AIDS Vaccine Development (Division of AIDS contract N01-A30018).  ... 
doi:10.1093/ilar/ilt039 pmid:24174440 pmcid:PMC3814399 fatcat:keiexb64pnacxo5syyahzpny7q

Immune System Promiscuity in Human and Nonhuman Primate Evolution

Brinkworth, Babbitt
2018 Human Biology: The Official Publication of the American Association of Anthropological Genetics  
An assessment of genetic sequences also found positive selection in the coding regions of differentially expressed genes between tissues functionally associated with immunity.  ...  Individual comparisons of immune and nonimmune tissues in primates revealed low divergence in gene expression between tissues, with the exception of whole blood.  ...  Visit http://digitalcommons.wayne.edu/humbiol/ after publication to acquire the final version. provided by the National Science Foundation (JFB) through grant BCS-1750675 and NSF BCS-  ... 
doi:10.13110/humanbiology.90.4.01 pmid:31714693 fatcat:6xopiwc4rvfnhaiywnlaozrcdy

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

Margherita Francescatto, Marina Lizio, Ingrid Philippens, Ronald Bontrop, Mizuho Sakai, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa (+7 others)
2017 Scientific Data  
Rhesus macaque was the second non-human primate whose genome has been fully sequenced and is one of the most used model organisms to study human biology and disease, thanks to the close evolutionary relationship  ...  But compared to human, where several previously unknown RNAs have been uncovered, the macaque transcriptome is less studied.  ...  Acknowledgements We thank the BPRC for providing the material and the GeNAS facility for data production. We also thank Dr Cornelis Blauwendraat for critically reading the manuscript.  ... 
doi:10.1038/sdata.2017.163 pmid:29087374 pmcid:PMC5663209 fatcat:7dzt764oybd67bd56ojq3sh7rm

Novel brain expressed RNA identified at the MIR137 schizophrenia-associated locus

Olympia Gianfrancesco, Alix Warburton, David A. Collier, Vivien J. Bubb, John P. Quinn
2017 Schizophrenia Research  
As we observed for MIR137, EU358092 expression was modulated in response to psychoactive drug treatment in the human SH-SY5Y neuroblastoma cell line.  ...  Bioinformatic analysis of publically available CNS expression data indicates that MIR137 and EU358092 are often coexpressed in vivo.  ...  Acknowledgment Olympia Gianfrancesco was the recipient of BBSRC Case Studentship ID 119131.  ... 
doi:10.1016/j.schres.2016.11.034 pmid:27913161 pmcid:PMC5477099 fatcat:zofcd3mgtzaa3aaqm23o4pny6e

Comparative primate genomics: emerging patterns of genome content and dynamics

Jeffrey Rogers, Richard A. Gibbs
2014 Nature reviews genetics  
Whole genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved.  ...  Preface Advances in genome sequencing technologies have created new opportunities for comparative primate genomics.  ...  Acknowledgments The authors thank Kim Worley, Stephen Richards, Muthuswamy Raveendran, Gloria Fawcett, David Rio Deiros and Fuli Yu for valuable discussion, and three anonymous reviewers for their comments  ... 
doi:10.1038/nrg3707 pmid:24709753 pmcid:PMC4113315 fatcat:isjnpmoxtzed5nrnbpnzvic2s4

Evolutionary dynamics of circular RNAs in primates [article]

Gabriela Santos-Rodriguez, Irina Voineagu, Robert J Weatheritt
2021 bioRxiv   pre-print
By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related  ...  AbstractMany primate genes produce non-coding circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear.  ...  Transcriptome Resource (NHPRTR) resource (http://www.nhprtr.org/; (Peng et al., 2015)).  ... 
doi:10.1101/2021.05.01.442284 fatcat:dz4dxfnecnfvdeutq5d4cytnru

The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection

Michael Y. Galperin, Daniel J. Rigden, Xosé M. Fernández-Suárez
2015 Nucleic Acids Research  
The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77  ...  The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd and Caoimhe Ní Dhónaill for their help in compiling this issue.  ... 
doi:10.1093/nar/gku1241 pmid:25593347 pmcid:PMC4383995 fatcat:rpqeohyapre5rijy7vfn7r2p7a

Evolutionary dynamics of circular RNAs in primates

Gabriela Santos-Rodriguez, Irina Voineagu, Robert James Weatheritt
2021 eLife  
By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related  ...  Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.  ...  This provides a pool of evolutionary potential that could contribute 302 to the evolutionary rewiring of the cell. 310 ence 310 Transcriptome Resource (NHPRTR) resource (http://www.nhprtr.org/; (Peng  ... 
doi:10.7554/elife.69148 pmid:34542404 pmcid:PMC8516421 fatcat:g5lj3o3ny5fk5c2cmkhlibsh7a

A quantitative model for characterizing the evolutionary history of mammalian gene expression [article]

Jenny Chen, Ross Swofford, Jeremy Johnson, Beryl B Cummings, Noga Rogel, Kerstin Lindblad-Toh, Wilfried Haerty, Federica di Palma, Aviv Regev
2017 bioRxiv   pre-print
Here, we use RNA-seq across 7 tissues from 17 mammalian species to show that expression evolution across mammals is accurately modeled by the Ornstein- Uhlenbeck (OU) process.  ...  Characterizing the evolutionary history of a gene's expression profile is a critical component for understanding the relationship between genotype, expression, and phenotype.  ...  ., Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). Nucleic Acids Res. 43, D737-42 (2015). 32. D.  ... 
doi:10.1101/229096 fatcat:eo34mpdz7jeinmoyl2rijjawdu

Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes

Majid Mehravar, Fatemeh Ghaemimanesh, Ensieh M Poursani
2021 BMC Genomics  
However, the advantage and biological significance of overlapping genes is still unclear. Expressed sequence tags (ESTs) analysis enabled us to uncover an overlapping gene pair in the human genome.  ...  By using in silico analysis of previous experimental documentations, we reveal a new form of overlapping genes in the human genome, in which two genes found on opposite strands (Pou5f1 and Tcf19), share  ...  , testis, Kidney, Liver, Heart, Skeletal Muscle, Lung, Colon, Lymph Node, and Whole Blood) obtained from the Non-Human Primates Reference Transcriptome Resource (NHPRTR).  ... 
doi:10.1186/s12864-021-08039-6 pmid:34610795 pmcid:PMC8493703 fatcat:bwivtuacnbduvdigkwf5u5ufui

Dynamic landscape and regulation of RNA editing in mammals

Meng How Tan, Qin Li, Raghuvaran Shanmugam, Robert Piskol, Jennefer Kohler, Amy N. Young, Kaiwen Ivy Liu, Rui Zhang, Gokul Ramaswami, Kentaro Ariyoshi, Ankita Gupte, Liam P. Keegan (+256 others)
2017 Nature  
Pipes for help with non-human primate RNA-seq data, Y. Hu, P. Sahbaie, A. Chang, K.  ...  Subsequently, we performed cross-species comparisons using datasets from the Non-human Primate Reference Transcriptome Resource (NHPRTR) (Extended Data Fig. 6a, Methods) .  ...  of AIMP2 in various non-human primate tissues from the NHPRTR RNA-seq datasets. h, Replications of Fig. 4i with independent shRNAs.  ... 
doi:10.1038/nature24041 pmid:29022589 pmcid:PMC5723435 fatcat:l5pujkurerfbvoqxvguj6rvs2m

Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host

David Palesch, Steven E. Bosinger, Gregory K. Tharp, Thomas H. Vanderford, Mirko Paiardini, Ann Chahroudi, Zachary P. Johnson, Frank Kirchhoff, Beatrice H. Hahn, Robert B. Norgren, Nirav B. Patel, Donald L. Sodora (+18 others)
2018 Nature  
We identified several immune-related genes in the genome of C. atys that show substantial sequence divergence from macaques or humans.  ...  Here we sequenced and assembled the genome of a captive sooty mangabey.  ...  by the Nonhuman Primate Reference Transcriptome Resource (NHPRTR; http://www.nhprtr.org/) 27 and the Human Genome Sequencing Center (HGSC) of Baylor College of Medicine.  ... 
doi:10.1038/nature25140 pmid:29300007 pmcid:PMC5843367 fatcat:j45ytjsgqndzlkveqfwtgbojve
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