About: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome

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About: Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome
Creator	Feldmann, Heinz Safronetz, David Tchitchek, Nicolas Ebihara, Hideki Martens, Craig »more»
source	PMC
abstract	BACKGROUND: The Syrian hamster (golden hamster, Mesocricetus auratus) is gaining importance as a new experimental animal model for multiple pathogens, including emerging zoonotic diseases such as Ebola. Nevertheless there are currently no publicly available transcriptome reference sequences or genome for this species. RESULTS: A cDNA library derived from mRNA and snRNA isolated and pooled from the brains, lungs, spleens, kidneys, livers, and hearts of three adult female Syrian hamsters was sequenced. Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons). This combined contig/singleton dataset, designated as the Syrian hamster transcriptome, represents a total of 60,117,204 nucleotides. Our Mesocricetus auratus Syrian hamster transcriptome mapped to 11,648 mouse transcripts representing 9,562 distinct genes, and mapped to a similar number of transcripts and genes in the rat. We identified 214 quasi-complete transcripts based on mouse annotations. Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library. The Syrian hamster transcriptome was aligned to the current release of the Chinese hamster ovary (CHO) cell transcriptome and genome to improve the genomic annotation of this species. Finally, our Syrian hamster transcriptome was aligned against 14 other rodents, primate and laurasiatheria species to gain insights about the genetic relatedness and placement of this species. CONCLUSIONS: This Syrian hamster transcriptome dataset significantly improves our knowledge of the Syrian hamster's transcriptome, especially towards its future use in infectious disease research. Moreover, this library is an important resource for the wider scientific community to help improve genome annotation of the Syrian hamster and other closely related species. Furthermore, these data provide the basis for development of expression microarrays that can be used in functional genomics studies.
has issue date	2014-11-14(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0112617
bibo:pmid	25398096
has license	cc0
sha1sum (hex)	f11b19a9e1845ff5ab66a42d5409f8caed24faa1
schema:url	https://doi.org/10.1371/journal.pone.0112617
resource representing a document's title	Sequencing, Annotation and Analysis of the Syrian Hamster (Mesocricetus auratus) Transcriptome
has PubMed Central identifier	PMC4232415
has PubMed identifier	25398096
schema:publication	PLoS One
resource representing a document's body	covid:f11b19a9e1845ff5ab66a42d5409f8caed24faa1#body_text
is schema:about of	named entity 'HAMSTER' named entity 'EBOLA' named entity 'MULTIPLE' named entity 'NEW' named entity 'AVAILABLE' »more»

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