Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV

ABSTRACT: Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV

PROVIDER: PRJNA300560 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2862232.fastq.gz	Fastqsanger.gz
	SRR2862233.fastq.gz	Fastqsanger.gz
	SRR2862363.fastq.gz	Fastqsanger.gz
	SRR2862234.fastq.gz	Fastqsanger.gz
	SRR2862364.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV (miRNA-Seq)

Project description:To investigate how rice responds to RSV infection, we integrated miRNA expression with parallel mRNA transcription profiling by deep sequencing. A total of 570 miRNAs were identified of which 69 miRNAs (56 up-regulated and 13 down-regulated) were significantly modified by RSV infection. Digital gene expression (DGE) analysis showed that 1274 mRNAs (431 up-regulated and 843 down-regulated genes) were differentially expressed by RSV infection. The differential expression of selected miRNAs and mRNAs was confirmed by qRT-PCR. Gene ontology (GO) and pathway enrichment analysis showed that a complex set of miRNA and mRNA networks were selectively regulated by RSV infection. In particular, 63 differentially expressed miRNAs were found to be significantly and negatively correlated with 160 target mRNAs. Interestingly, 22 up-regulated miRNAs were negatively correlated with 24 down-regulated mRNAs encoding disease resistance-related proteins, indicating that the host defense responses were selectively suppressed by RSV infection. The suppression of both osa-miR1423-5p- and osa-miR1870-5p-mediated resistance pathways was further confirmed by qRT-PCR. Chloroplast functions were also targeted by RSV, especially the zeaxanthin cycle, which would affect the stability of thylakoid membranes and the biosynthesis of ABA. All these modifications may contribute to viral symptom development and provide new insights into the pathogenicity mechanisms of RSV.

2017-09-01 | GSE74498 | GEO

Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV (RNA-Seq)

2017-09-01 | GSE74497 | GEO

Transcriptome analysis of rice stripe virus-infected rice

Project description:Rice stripe virus (RSV) is one of the major virus diseases of rice in East Asia. Rice plants infected with RSV usually show symptoms such as chlorotic leaf stripes, weakness and senescence of leaves, and dwarfism. In order to characterize the host response to RSV infection at the gene expression level, the changes in transcriptome profiles of RSV-infected rice were monitored at three, six, nine, twelve, and fifteen days after inoculation by a rice oligomicroarray. The microarray data indicated that 1. transcription, translation and protein processing machineries were activated, 2. chloroplasts were disintegrated, and mitochondrion function was activated, 3. genes for transporters and cell wall synthesis were suppressed, and 4. the expression levels of pathogenesis-related genes were changed by RSV infection. Concurrent observation of symptom development, virus accumulation and transcriptome profiles in RSV-infected plants indicates that RSV symptoms are caused by unbalanced activities of organelles, suppression of cell elongation, and uncontrolled water transport, while translation activity of host cells may be increased in correlation with RSV propagation. Keywords: time course, virus infection, disease response Comparison between RSV- and mock-infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested; 4 time points (3, 6, 9, 12 days after inoculation (DAI)). Biological replicate: 1 control, 1 infected, independently grown and harvested; 1 time point (15 DAI). 1 sample derived from 5 plants grown under the same conditons.

2009-09-01 | E-GEOD-12681 | biostudies-arrayexpress

Transcriptome analysis of rice stripe virus-infected rice

2009-09-01 | GSE12681 | GEO

Transcription profiling of rice genotypes in response to rice stripe virus infection

Project description:During the pathogenesis of virus disease, lots of changes occur in plant hosts including the altered gene expression profiles. Rice stripe virus (RSV) is the type member of Tenuivirus, transmitted by Laodelphax striatellus in a circulative propagative man; To investigate the molecular differences in two japonica rice genotypes WuYun3 and KT95-418 in response to RSV infection, Affymetrix rice genome array were used to analyze and compare their transcriptional profiles. Experiment Overall Design: Nine-day old 20 rice seedlings were exposed to approximately 100 viruliferous small brown planthoppers (Laodelphax striatellus Fall) for two days to be innoculated by RSV. Then they were transplanted in insect-free greenhouse at 25Â±3C with a daily photope

2009-04-11 | E-GEOD-11025 | biostudies-arrayexpress

Comparative transcriptional profiling of two contrasting rice genotypes in response to rice stripe virus infection

2009-04-02 | GSE11025 | GEO

Rice stripe tenuivirus

Project description:Rice, Rice stripe virus, planthopper Raw sequence reads

| PRJNA388142 | ENA

Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-09-01 | GSE74499 | GEO

Comparative gene expression analysis between virus-susceptible and -resistant rice lines (NIL37 and NIL22)

Project description:Near-isogenic lines NIL37 and NIL22 were developed from the cross between Ilpum (recurrent parent susceptible to rice stripe virus (RSV)) and Shinkwang (donor parent resistant to RSV). NIL37 is susceptible to RSV, whereas NIL22 is resistant to RSV. In order to identify genes which are constitutively differentially expressed between NIL37 and NIL22, the gene expression in the two lines were compared at two different conditions (healthy, and RSV-inoculated). Keywords: Constitutive differential expression

2007-10-25 | GSE6126 | GEO

Oryza sativa Transcriptome or Gene expression

Project description:In this study, we analyzed the early response of two rice cultivars to infection by RSV (Rice stripe virus) and its carrier at the transcriptome level using next-generation deep-sequencing techniques. We investigated the alteration in gene expression between a disease-resistant cultivar and a susceptible cultivar before and after inoculation with RSV by co-culturing with Laodelphax striatellus for 48 h. Our study provides insight at the molecular level into the mechanism of development of rice stripe disease, which contributes to our understanding of the rice-RSV interaction.

2013-08-21 | E-MTAB-4392 | biostudies-arrayexpress

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