Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CMV 2b immunoprecipitated small RNAs data set

ABSTRACT: We report that CMV2b exist in a complex of sRNAs in arabidopsis, with significant preference to repeat-associated AGO4-related 24nt siRNAs. This differential selection of siRNAs in vivo helps CMV 2b to perturb host epigenetic defense in the form of transposons activation and severeal repeat associated loci hypomethylation.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE23771 | GEO | 2013/01/18

SECONDARY ACCESSION(S): PRJNA130833

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CMV 2b immunoprecipitated small RNAs data set

Project description:We report that CMV2b exist in a complex of sRNAs in arabidopsis, with significant preference to repeat-associated AGO4-related 24nt siRNAs. This differential selection of siRNAs in vivo helps CMV 2b to perturb host epigenetic defense in the form of transposons activation and severeal repeat associated loci hypomethylation. Examination of CMV 2b presence in sRNAs complex in vivo

2013-01-18 | E-GEOD-23771 | biostudies-arrayexpress

Small RNAs from Arabidopsis plants infected with CMV-?2b

Project description:We focused our analyses on the description of viral (CMV-?2b) and, based on genetic and molecular evidence, classified them and discussed their relevance in antiviral defense. Small RNAs from Arabidopsis plants from different genetic backgrounds infected with (CMV-?2b) were sequenced before or after immunoprecipitation with antibodies against key proteins involved in antiviral defense.

2012-03-01 | E-GEOD-27477 | biostudies-arrayexpress

Small RNAs from Arabidopsis plants infected with CMV-∆2b

Project description:We focused our analyses on the description of viral (CMV-∆2b) and, based on genetic and molecular evidence, classified them and discussed their relevance in antiviral defense.

2012-03-01 | GSE27477 | GEO

Virus-derived siRNAs in Arabidopsis thaliana

Project description:We investigated the role of A. thaliana RDRs in the RNAi-mediated viral immunity by using a mutant of cucumber mosaic virus (CMV) that does not express the VSR protein 2b. CMV contains three positive-strand genomic RNAs and the 2b protein encoded by RNA2 is essential for infection by suppressing antiviral silencing initiated by either DCL4 or DCL2. Our results demonstrate an essential role for the amplification of viral siRNAs by either RDR1 or RDR6 in antiviral silencing. Further analyses, including Illumina sequencing of more than 3.5 million viral siRNAs, indicated target specificity of the two antiviral RDRs.

2010-01-20 | GSE19965 | GEO

Small RNAs from dcl3 and rdr6 mutants of Physcomitrella

Project description:Endogenous 24nt short interfering RNAs (siRNAs) derived mostly from intergenic and repetitive genomic regions constitute a major class of endogenous small RNAs in Arabidopsis thaliana. Accumulation of A. thaliana 24nt siRNAs requires the Dicer family member DCL3, and clear homologs of DCL3 exist in both flowering and non-flowering plants. However, the absence of a conspicuous 24nt peak in the total RNA populations of several non-flowering plants has raised the question of whether this class of siRNAs might, in contrast to the ancient 21nt microRNAs (miRNAs) and 21-22nt trans-acting siRNAs (tasiRNAs), be an angiosperm-specific innovation. Analysis of non-miRNA, non-tasiRNA hotspots of small RNA production within the genome of the moss Physcomitrella patens revealed multiple loci which consistently produced a mixture of 21-24nt siRNAs with a peak at 23nts. These Pp23SR loci were significantly enriched in transposon content, depleted in overlap with annotated genes, and typified by dense concentrations of the 5-methyl cytosine (5mC) DNA modification. Deep sequencing of small RNAs from two independent Ppdcl3 mutants showed that the P. patens DCL3 homolog is required for the accumulation of 22-24nt siRNAs, but not 21nt siRNAs, at Pp23SR loci. The 21nt component of Pp23SR-derived siRNAs was also unaffected by a mutation in the RNA-dependent RNA polymerase mutant Pprdr6. Transcriptome-wide, Ppdcl3 mutants specifically failed to accumulate 23 and 24nt small RNAs from repetitive regions. We conclude that intergenic/repeat-derived siRNAs are indeed a broadly conserved, distinct class of small regulatory RNAs within land plants. Our results also suggest that Pp DCL3 produces siRNAs of heterogenous size, unlike its A. thaliana homolog which generates exclusively 24nt siRNAs.

2008-12-19 | GSE12468 | GEO

Deep sequencing and analysis of small RNAs from Nt-Xanthi and CMV delta 2b-infected Nt-Xanthi

Project description:To investigate if CMV infection might affect the accumulation of sat-like RNAs, sRNA isolated from Nt-Xanthi and Nt-Xanthi infected with SD-CMVdeltasatRNA were sequenced.

2014-12-01 | GSE63586 | GEO

Methylomonas sp. 2B strain:2B

Project description:Methylomonas sp. 2B strain:2B Genome sequencing

| PRJNA1169796 | ENA

Pol IV-RDR2 protein interaction study

Project description:Protein-protein interaction between DNA dependent RNA polymerase IV and RNA dependent RNA polymerase2. The coupled activities of the physically associated polymerases lead to the biogenesis of dsRNAs that serve as precursors of 24nt siRNAs.

2020-09-14 | PXD020170 | Pride

CMV-CTLs scVDJ-RNAseq

Project description:We conducted immune- and RNA-sequencing of HLA-A24-restricted CMVpp65-specific CTLs to better understand the immune reconstitution of CMV-CTLs after allo-HCT. To the best of our knowledge, this is the first report on the features of TCRβ-CDR3, diversity, and GEP of HLA-A24 CMV-CTLs according to the CMV-reactivation pattern among recipients after allo-HCT. In addition, we further sought to demonstrate homogeneity or heterogeneity according to individual CTL clones using single-cell RNA-sequencing technology.

2021-01-01 | GSE156841 | GEO

PERFORMANCE OF STOOL AND SERUM CYTOMEGALOVIRUS REAL-TIME POLYMERASE CHAIN REACTION AND THEIR COMBINATION IN DIAGNOSING CMV COLITIS

Project description:Interventions: Patients with the detection of either cytomegalic cells or IHC-CMV cells were diagnosed with CMV colitis.,Patients older than 18 years with clinical suspicion of CMV colitis but negative biopsy for CMV.,Asymptomatic patients underwent colonoscopy for screening.;Diagnostic,Diagnostic,Diagnostic;CMV colitis,Non-CMV colitis ,Healthy volunteers Primary outcome(s): Diagnostic performance After colonoscopy Sensitivity, Specificity

| 2756739 | ecrin-mdr-crc

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