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The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics
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...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531109/ https://www.ncbi.nlm.nih.gov/pubmed/23203872 http://dx.doi.org/10.1093/nar/gks1268 |
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author | Pipes, Lenore Li, Sheng Bozinoski, Marjan Palermo, Robert Peng, Xinxia Blood, Phillip Kelly, Sara Weiss, Jeffrey M. Thierry-Mieg, Jean Thierry-Mieg, Danielle Zumbo, Paul Chen, Ronghua Schroth, Gary P. Mason, Christopher E. Katze, Michael G. |
author_facet | Pipes, Lenore Li, Sheng Bozinoski, Marjan Palermo, Robert Peng, Xinxia Blood, Phillip Kelly, Sara Weiss, Jeffrey M. Thierry-Mieg, Jean Thierry-Mieg, Danielle Zumbo, Paul Chen, Ronghua Schroth, Gary P. Mason, Christopher E. Katze, Michael G. |
author_sort | Pipes, Lenore |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3531109 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-35311092013-03-07 The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics Pipes, Lenore Li, Sheng Bozinoski, Marjan Palermo, Robert Peng, Xinxia Blood, Phillip Kelly, Sara Weiss, Jeffrey M. Thierry-Mieg, Jean Thierry-Mieg, Danielle Zumbo, Paul Chen, Ronghua Schroth, Gary P. Mason, Christopher E. Katze, Michael G. Nucleic Acids Res Articles 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. Oxford University Press 2013-01 2012-11-29 /pmc/articles/PMC3531109/ /pubmed/23203872 http://dx.doi.org/10.1093/nar/gks1268 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. |
spellingShingle | Articles Pipes, Lenore Li, Sheng Bozinoski, Marjan Palermo, Robert Peng, Xinxia Blood, Phillip Kelly, Sara Weiss, Jeffrey M. Thierry-Mieg, Jean Thierry-Mieg, Danielle Zumbo, Paul Chen, Ronghua Schroth, Gary P. Mason, Christopher E. Katze, Michael G. The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics |
title | The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics |
title_full | The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics |
title_fullStr | The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics |
title_full_unstemmed | The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics |
title_short | The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics |
title_sort | non-human primate reference transcriptome resource (nhprtr) for comparative functional genomics |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531109/ https://www.ncbi.nlm.nih.gov/pubmed/23203872 http://dx.doi.org/10.1093/nar/gks1268 |
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