About: The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq

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About: The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.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	The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq
Creator	Yin, Jun Liu, Zhongchun Han, Song Chen, Xiong Zhang, Yingying Chen, Liujun He, Xiaohua Liu, Wanhong Peng, Biwen Sheng, Jiqun Shi, Yingying Tu, Huilin
source	PMC
abstract	Coxsackievirus A16 (CVA16) is one of major pathogens of hand, foot and mouth disease (HFMD) in children. Long non-coding RNAs (IncRNAs) have been implicated in various biological processes, but they have not been associated with CVA16 infection. In this study, we comprehensively characterized the landscape of IncRNAs of normal and CVA16 infected rhabdomyosarcoma (RD) cells using RNA-Seq to investigate the functional relevance of IncRNAs. We showed that a total of 760 IncRNAs were upregulated and 1210 IncRNAs were downregulated. Out of these dysregulated IncRNAs, 43.64% were intergenic, 22.31% were sense, 15.89% were intronic, 8.67% were bidirectional, 5.59% were antisense, 3.85% were sRNA host IncRNAs and 0.05% were enhancer. Six dysregulated IncRNAs were validated by quantitative PCR assays and the secondary structures of these IncRNAs were projected. Moreover, we conducted a bioinformatics analysis of an IncRNAs (ENST00000602478) to elucidate the diversity of modification and functions of IncRNAs. In summary, the current study compared the dysregulated IncRNAs profile upon CVA16 challenge and illustrated the intricate relationship between coding and IncRNAs transcripts. These results may not only provide a complete picture of transcription in CVA16 infected cells but also provide novel molecular targets for treatments of HFMD. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at 10.1007/s12250-015-3693-1 and is accessible for authorized users.
has issue date	2016-03-31(xsd:dateTime)
bibo:doi	10.1007/s12250-015-3693-1
bibo:pmid	27060091
has license	no-cc
sha1sum (hex)	59039af45c67a02cf8ee55fad292f90cf48d1fe7
schema:url	https://doi.org/10.1007/s12250-015-3693-1
resource representing a document's title	The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq
has PubMed Central identifier	PMC7090472
has PubMed identifier	27060091
schema:publication	Virol Sin
resource representing a document's body	covid:59039af45c67a02cf8ee55fad292f90cf48d1fe7#body_text
is schema:about of	named entity 'validated' named entity 'landscape' named entity 'THESE' named entity 'SECONDARY' named entity 'INFECTED' named entity 'PATHOGENS' named entity 'MAJOR' named entity 'VALIDATED' named entity 'CHARACTERIZED' named entity 'STRUCTURES' named entity 'COMPLETE' named entity 'MODIFICATION' named entity 'PROVIDE' named entity 'STUDY' named entity 'SUMMARY' named entity 'PROFILE' named entity 'pathogens' named entity 'coding' named entity 'sRNA' named entity 'HFMD' named entity 'rhabdomyosarcoma' named entity 'Coxsackievirus' named entity 'infected' named entity 'HFMD' named entity 'bidirectional' named entity 'bioinformatics' named entity 'total' named entity 'infected' named entity 'HFMD' named entity 'enhancer' named entity 'infection' named entity 'bioinformatics' named entity 'RNA-seq' named entity 'Exon' named entity 'messenger RNAs' named entity 'eukaryotic translation' named entity 'intracellular' named entity 'heterocyclic compound' named entity 'Gene ontology' named entity 'apoptosis' named entity 'sRNA' named entity 'cDNA' named entity 'FBS' named entity 'mRNA' named entity 'Cytochrome-b5 reductase' named entity 'histone modifications' named entity 'chromosome 22' named entity 'quality control' named entity 'HFMD' named entity 'hybrids' named entity 'Kornienko' named entity 'Gene ontology' named entity 'regulation of transcription' named entity 'antisense' named entity 'down-regulated' named entity 'intergenic' named entity 'cDNA' named entity 'cis' named entity 'exons' named entity 'downregulated' named entity 'KEGG' named entity 'chromosome' named entity 'co-repressor' named entity 'promoter region' named entity 'NOD-like receptor' named entity 'DNase I hypersensitivity' named entity 'mRNAs' named entity 'Hippo signaling pathway' named entity 'inflammation' named entity 'RNA'

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