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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identification of miRNA from Cyprinus carpio by high-throughput sequencing and bioinformatics analysis

ABSTRACT: Common carp is one of the main commercial fishes captured and cultured worldwide. Although common carp genome is not finished yet, this study provides a first large scale cloning and characterization of common carp miRNAs and their potential targets. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in gene regulation of common carp. We constructed a small RNA library from 17 Cyprinus carpio samples.

ORGANISM(S): Cyprinus carpio

SUBMITTER: J Li

PROVIDER: E-GEOD-35131 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs.

Zhu Ya-Ping YP Xue Wei W Wang Jin-Tu JT Wan Yu-Mei YM Wang Shao-Lin SL Xu Peng P Zhang Yan Y Li Jiong-Tang JT Sun Xiao-Wen XW

BMC genomics 20120821

<h4>Background</h4>MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. In model species, single-nucleotide polymorphisms (SNPs) have been reported to impair or enhance miRNA regulation as well as to alter miRNA biogenesis. SNPs are often associated with diseases or traits. To date, no studies into the effects of SNPs on miRNA biogenesis and r ...[more]

PMID: 22908890

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Identification of miRNA from Cyprinus carpio by high-throughput sequencing and bioinformatics analysis

Project description:Common carp is one of the main commercial fishes captured and cultured worldwide. Although common carp genome is not finished yet, this study provides a first large scale cloning and characterization of common carp miRNAs and their potential targets. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in gene regulation of common carp.

2012-07-16 | GSE35131 | GEO

Gene expression profiles after infection of zebrafish with Spring Viremia Carp Virus (SVCV)

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Characterization and comparative profiling of microRNA transcriptomes in bighead carp and silver carp

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Integrated small RNA, mRNA and protein omics reveal a miRNA network orchestrating metabolic maturation of the developing human heart

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Gene expression profiles in fins after infection of zebrafish with Spring Viremia Carp Virus (SVCV)

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Project description:Caspian common carp

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Solexa sequencing of small RNAs in Singapore grouper iridovirus (SGIV)-infected grouper cells

Project description:We applied Solexa sequencing technology to identify Singapore grouper iridovirus (SGIV) encoded microRNAs during its infection. A small RNA library arising from SGIV infected grouper cells (GP) was constructed and sequenced. We recovered 6,802,977 usable reads, of which 34,400 reads represented the small RNA sequences encoded by SGIV. Among them, 16 novel SGIV encoded miRNAs were identified by a computational pipeline. Generally, these 16 miRNAs are dispersed throughout the SGIV genome, while three of them are located within open reading frame 057L (ORF057L) region. Meanwhile, We identified 138 conserved microRNA genes between grouper fish and zebrafish. 18-30 nt small RNAs from SGIV-infected GP cells were sequenced in one Solexa lane.

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