Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Publications

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

Similar Datasets

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)

Project description:We describe here transcripts induced after infection of zebrafish with Spring Viremia Carp Virus (SVCV). Two days after infection, differentially expressed transcript levels from selected immune-related zebrafish genes were studied in internal organs (pooled spleen, head kidney). Also, transcripts from resistant fishes to viral infection one month after inoculation were studied. Three different experiments were performed to get three biological replicates. Fishes were divided into two groups in each experiment. First group was infected by immersion with SVCV 10^7 pfu/ml, second group was used as a control of non-infected fishes. 6 fishes per group were sacrificed two days post infection, whereas the rest of the infected fishes from the three experiments were maintained for 30 days in the aquariums and then survivors (six for experiment) were sacrificed. This submission includes three biological replicate groups for the non-infected fish and the two days post-infected fish, and two biological replicate groups for the 30 days post-infected fish.

2013-11-04 | E-GEOD-42263 | biostudies-arrayexpress

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

Project description:We applied high throughput sequencing technology to identify microRNA genes in bighead carp and silver carp. We identified 167 conserved miRNAs in bighead carp and 166 in silver carp. By two computational stragegies, we obtained 39 novel miRNAs in bighead carp and 54 in silver carp, for which, no homologs were found in other species. Several miRNA* sequences were found in our dataset as well, some particular ones might have gene regulation function. Gain and loss of family members were observed in several miRNA families, which partially reflected the fate of miRNA gene duplicates. Total RNA of juvenile bighead carp and silver carp were sequenced on one Solexa lane, respectively.

2010-09-01 | E-GEOD-22232 | biostudies-arrayexpress

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

2010-09-01 | GSE22232 | GEO

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

2013-11-04 | GSE42263 | GEO

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

Project description:As the fetal heart develops, cardiomyocyte proliferation potential decreases while fatty acid oxidative capacity increases, a highly regulated transition known as cardiac maturation. Small noncoding RNAs, such as microRNAs (miRNAs), contribute to the establishment and control of tissue-specific transcriptional programs. However, small RNA expression dynamics and genome wide miRNA regulatory networks controlling maturation of the human fetal heart remain poorly understood. Transcriptome profiling of small RNAs revealed the temporal expression patterns of miRNA, piRNA, circRNA, snoRNA, snRNA and tRNA in the developing human heart between 8 and 19 weeks of gestation. Our analysis revealed that miRNAs were the most dynamically expressed small RNA species throughout mid-gestation. Cross-referencing differentially expressed miRNAs and mRNAs predicted 6,200 mRNA targets, 2134 of which were upregulated and 4066 downregulated as gestation progresses. Moreover, we found that downregulated targets of upregulated miRNAs predominantly control cell cycle progression, while upregulated targets of downregulated miRNAs are linked to energy sensing and oxidative metabolism. Furthermore, integration of miRNA and mRNA profiles with proteomes and reporter metabolites revealed that proteins encoded in mRNA targets, and their associated metabolites, mediate fatty acid oxidation and are enriched as the heart develops.This study revealed the small RNAome of the maturing human fetal heart. Furthermore, our findings suggest that coordinated activation and repression of miRNA expression throughout mid-gestation is essential to establish a dynamic miRNA-mRNA-protein network that decreases cardiomyocyte proliferation potential while increasing the oxidative capacity of the maturing human fetal heart.

2024-01-26 | PXD044936 | Pride

Transcriptome Analysis of Common Carp (Cyprinus carpio) Fed with Animal and Plant Diets

Project description:purpose?To elucidate the relationship of utilization different type of diets in fish method?enzyme activity determination and transcriptome sequencing were performed in common carp fed with single animal diet group (group AD), plant diet group (group PD) and mix diets group (group MD). Group MD as control group results? 916 and 1296 differentially expressed genes were identified between group AD vs MD and PD vs MD. Protein digestion and absorption, bile secretion, hematopoietic cell lineage and intestinal immune network for IgA production pathways were significantly differentially expressed between common carp fed with single type of diet and mix diets. Conclusion?common carp fed with mix diets had stronger immunity than common carp fed with single type of diets.

2019-01-19 | GSE125366 | GEO

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

Project description:Because fin base is supposed to be the entry zone of some fish virus, we wanted to know which transcripts are induced after infection of zebrafish with Spring Viremia Carp Virus (SVCV). Two days after infection, differentially expressed transcript levels from selected immune-related zebrafish genes were studied in zebrafish fins. Also transcripts from resistant fishes to viral infection one month after inoculation were studied.

2017-06-10 | GSE58205 | GEO

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.

2011-01-29 | E-GEOD-26909 | biostudies-arrayexpress

Robust partitioning of microRNA targets from downstream regulatory changes [Ribo-seq]

Project description:MicroRNA’s function is defined by the targets it regulates. Despite miRNAs’ crucial role in various cellular processes and disease states, the identification of their targets remains challenging. Existing methods suffer from high false-positive rates and are inadequate in differentiating direct targets from downstream regulatory changes. Here, we introduce a simple approach involving combined analysis of RNA-seq and Precise RunOn-seq (PRO-seq) (CARP) to effectively measure post-transcriptional regulation. We apply this approach to seven different miRNAs and robustly distinguish their direct targets from downstream changes. We validate the efficacy of our approach using argonaute-CLIP-seq. We show using CARP and ribosome-profiling analyses that accelerated mRNA decay is the major mode of target regulation by miRNAs. Additionally, our comparative analyses reveal that CARP aids in discovery of complex regulatory mechanisms and in capturing false-negatives of existing approaches. Furthermore, post-transcriptional changes measured using CARP uncover miRNA-dependent regulation of coding sites. Lastly, we demonstrate that PRO-seq provides mechanistic explanation of indirect targeting, unraveling miRNA regulatory networks. Finally, we believe that CARP is particularly suitable to study in vivo functions of miRNAs in primary cells.

2020-08-07 | GSE140366 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data