Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing of exogenous RNAi mutants under CPL-1* expression

ABSTRACT: The goal of this experiment was to identify RNAs that are regulated by the exogenous RNAi pathway under ER stress conditions.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE202291 | GEO | 2022/09/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA sequencing of exogenous RNAi mutants under CPL-1* expression

Project description:RNA sequencing of exogenous RNAi mutants under CPL-1* expression

| PRJNA835407 | ENA

meg-3 meg-4 mutants are defective in exogenous RNAi signal amplification

Project description:Worms were fed a dsRNA trigger against the pos-1 gene and subjected to sRNAseq to see if they could amplify the exogenous RNAi trigger. meg-3 meg-4 were not able to amplify the signal as robustly as wild-type.

2019-07-23 | GSE134627 | GEO

meg-3 meg-4 mutants are defective in exogenous RNAi signal amplification

Project description:meg-3 meg-4 mutants are defective in exogenous RNAi signal amplification

| PRJNA555887 | ENA

RNA sequencing of AGO2 -/- Mouse embryonic fibroblast under ER stress conditions

Project description:The goal of this experiment was to identify RNAs regulated by AGO2 under ER stress conditions.

2022-09-23 | GSE161121 | GEO

dsGFP as exogenous control on RNAi assays and its effects on gene expression in Apis mellifera

Project description:Double stranded RNAs are used to induce gene silencing in functional studies. In Apis mellifera green fluorescent protein (GFP) dsRNA (dsGFP) has been used as an exogenous control as its sequence has no homology in honeybee genome. However, some undesirable effects are observed after dsGFP treatment. A microarray approach comparing gene expression differences between untreated and dsGFP treated groups, containing honeybees workers in two different developmental stages, pre-pupae and light-brown eyed pupae, were used to test the reliability of dsGFP as a control for RNAi experiments. According to these microarrays results dsGFP can be used as a control in RNAi assays as long as the affected genes are taken into account in the analysis.

2013-01-10 | GSE43193 | GEO

dsGFP as exogenous control on RNAi assays and its effects on gene expression in Apis mellifera

2013-01-10 | E-GEOD-43193 | biostudies-arrayexpress

Effects of dsRNA-GFP as exogenous control on honey bee RNAi assays: gene expression changes in workers

Project description:A green fluorescence protein (GFP)-derived dsRNA (dsRNA-GFP) has been used as an exogenous control for Apis mellifera RNAi assays by multiple research groups. Its sequence does not share any significant homology with any known honey bee genes. Although dsRNA-GFP is not expected to trigger an RNAi response in treated bees, undesirable effects on gene expression, pupal pigmentation or developmental timing have been routinely observed. To better understand the multiple molecular and phenotypic effects of dsRNA-GFP in honey bees and to evaluate its use as a control for RNAi studies, we examined the impact of dsRNA-GFP on global gene expression patterns in developing workers. We found that dsRNA-GFP causes large-scale changes in gene expression associated with multiple biological processes. Furthermore, dsRNA-GFP exposure tended to preferentially decrease, rather than increase, expression of genes compared to controls.

2013-01-10 | GSE41004 | GEO

The Caenorhabditis elegans RDE-10/RDE-11 complex regulates RNAi by promoting secondary siRNA amplification

Project description:From a forward genetic screen for C. elegans genes required for RNAi, we identified rde-10 and through proteomic analysis of RDE-10-interacting proteins, we identified a protein complex containing the new RNAi factor RDE-11, the known RNAi factors RSD-2 and ERGO-1, as well as other candidate RNAi factors. The newly identified RNAi defective genes rde-10 and rde-11 encode a novel protein and a RING-type zinc finger domain protein, respectively. Mutations in rde-10 and rde-11 genes cause dosage-sensitive RNAi deficiencies: these mutants are resistant to low dosage, but sensitive to high dosage of double-stranded RNAs. We assessed the roles of rde-10, rde-11, and the dosage-sensitive RNAi defective genes rsd-2, rsd-6 and haf-6 in both exogenous and endogenous small RNA pathways using high-throughput sequencing and qRT-PCR. These genes are required for the accumulation of secondary siRNAs in both exogenous and endogenous RNAi pathways.

2012-04-07 | GSE37083 | GEO

Principles Governing Dicer-2 Substrate Selection are Revealed by Characterizing the RNAi Response to Virus Infection and Exogenous dsRNA

Project description:Background: RNA silencing pathways play critical roles in gene regulation, virus infection, and transposon control. RNA interference (RNAi) is mediated by small interfering RNAs (siRNAs), which are liberated from double stranded (ds) RNA precursors by Dicer and direct the RNA-induced silencing complex (RISC) to target transcripts. Recent efforts have uncovered important principles governing small RNA (smRNA) sorting into RISC, yet mechanisms defining substrate selection by Dicer proteins remain uncharacterized. Methodology: To better characterize Dicer-2 substrates in Drosophila, we examined the antiviral RNAi response, which generates virus-derived siRNAs from viral RNA. Using high-throughput sequencing, we found that diverse viruses were uniquely targeted; substrates included dsRNA replication intermediates and intramolecular RNA stem loops. smRNA distribution patterns from viral and synthetic dsRNA precursors were highly reproducible, and machine learning techniques identified characteristics of precursor molecules and smRNA duplexes important in determining relative smRNA abundance. Significance: To our knowledge, this study provides the first description of the rules governing Dicer-2 substrate selection, which has important implications for exogenous RNA silencing technologies and the development of smRNA-based antiviral therapeutics. virus-derived siRNA (vsiRNA) expression comparison between control and 4 different virus-infected cells in control as well as 5 different RNAi pathway protein knock-downs in Drosophila dl1 cells

2013-01-31 | E-GEOD-28957 | biostudies-arrayexpress

A cytoplasmic Argonaute protein promotes the inheritance of RNAi

Project description:RNAi-elicited gene silencing is heritable and can persist for multiple generations after its initial induction in C. elegans. However, the mechanism by which parental-acquired trait-specific information from RNAi is inherited by the progenies is not fully understood. Here, we identified a cytoplasmic Argonaute protein, WAGO-4, necessary for the inheritance of RNAi. WAGO-4 exhibits asymmetrical translocation to the germline during early embryogenesis, accumulates at the perinuclear foci in the germline, and is required for the inheritance of exogenous RNAi targeting both germline- and soma-expressed genes. WAGO-4 binds to 22G-RNA and its mRNA targets. Interestingly, WAGO-4-associated endogenous 22G-RNA targets the same cohort of germline genes as CSR-1 and similarly contains untemplated addition of uracil at the 3' ends. The poly(U) polymerase CDE-1 is required for the untemplated polyuridylation of WAGO-4-associated 22G-RNAs and inheritance of RNAi. Therefore, we conclude that the cytoplasmic Argonaute protein WAGO-4 also promotes the inheritance of RNAi in addition to the nuclear RNAi pathway.

2018-04-28 | GSE112475 | 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