Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Caenorhabditis elegans (at Late L4 stage) of rrf-3(pk1426) rde-1(ne219) unc-62p::rde-1 and daf-2(e1370) rrf-3(pk1426) rde-1(ne219) unc-62p::rde-1 grown on control RNAi or cyd-1 RNAi.

ABSTRACT: RNA-seq of Caenorhabditis elegans (at Late L4 stage) of rrf-3(pk1426) rde-1(ne219) unc-62p::rde-1 and daf-2(e1370) rrf-3(pk1426) rde-1(ne219) unc-62p::rde-1 grown on control RNAi or cyd-1 RNAi.

PROVIDER: PRJEB64540 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR11758000_1.fastq.gz	Fastqsanger.gz
	ERR11758000_2.fastq.gz	Fastqsanger.gz
	ERR11758001_1.fastq.gz	Fastqsanger.gz
	ERR11758001_2.fastq.gz	Fastqsanger.gz
	ERR11758002_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

RNA-seq of Caenorhabditis elegans at Late L4 stage of WT, daf-2(e1370), daf-16(mgDf50) daf-2(e1370) on control RNAi and cdk-12 RNAi

Project description:RNA-seq of Caenorhabditis elegans at Late L4 stage of WT, daf-2(e1370), daf-16(mgDf50) daf-2(e1370) on control RNAi and cdk-12 RNAi

| PRJEB49003 | ENA

RNA-seq profile of two daf-2 (e1370);daf-12(m20) samples

Project description:RNA-seq profile of two daf-2 (e1370);daf-12(m20) samples

2019-12-03 | GSE68669 | GEO

Endogenous DAF-16 genome-wide recruitment under low Insulin signalling condition in Caenorhabditis elegans

Project description:In order to understand the complexity of gene regulation downstream of IIS, we did RNA-seq in mixed culture in wild-type, daf-2(e1370), daf-16(mgDf50);daf-2(e1370) and daf-2(e1370);daf-12(m20 and correlated it with ChIP-seq data

2016-03-01 | GSE67975 | GEO

C. elegans microarrays: daf-2(-) vs. daf-2(-) xbp-1(-)

Project description:Transcriptional profiling of day 1 animals comparing untreated daf-2(-) animals and daf-2(-) xbp-1(-) animals. Goal was to identify genes whose expression in daf-2 mutants is dependent (directly or indirectly) on xbp-1. Two-condition experiment, daf-2(-) animals and daf-2(-) xbp-1(-) animals. 4 Biological replicates in daf-2(e1370) background: 4 sets of daf-2(e1370) animals and their matching daf-2(e1370) xbp-1(zc12) animals. 4 Biological replicates in daf-2(e1368) background: 4 sets of daf-2(e1368) animals and their matching daf-2(e1368) xbp-1(zc12) animals.

2010-02-02 | E-GEOD-20148 | biostudies-arrayexpress

The RDE-10/RDE-11 complex triggers RNAi induced mRNA degradation by association with target mRNA in C. elegans

Project description:The molecular mechanisms for target mRNA degradation in C. elegans undergoing RNA interference (RNAi) are not fully understood. Using a combination of genetic, proteomic and biochemical approaches, we report a divergent RDE-10/RDE-11 complex that is required for RNAi in C. elegans. The RDE-10/RDE-11 complex acts in parallel of nuclear RNAi. Association of the complex with target mRNA is dependent on RDE-1 but not RRF-1, suggesting that target mRNA recognition depends on primary but not secondary siRNA. Furthermore, RDE-11 is required for mRNA degradation subsequent to target engagement. Deep sequencing reveals a 5-fold decrease in secondary siRNA abundance in rde-10 and rde-11 mutant animals, while primary siRNA and micro-RNA biogenesis is normal. Therefore, the RDE-10/RDE-11 complex is critical for amplifying the exogenous RNAi response. Our work uncovers an essential output of the RNAi pathway in C. elegans.

2012-04-26 | GSE36494 | GEO

Adult C. elegans: Control daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi

Project description:Transcriptional profiling of adult C. elegans comparing daf-16(-); daf-2(-) animals with adult daf-2(-) animals. Two-condition experiment, daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi. Biological replicates: 8 daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi, independently grown and harvested. One replicate per array.

2010-05-16 | E-GEOD-18561 | biostudies-arrayexpress

The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic foci in C. elegans

Project description:RNA interference (RNAi) is a potent mechanism for down-regulating gene expression. Conserved RNAi pathway components are found in animals, plants, fungi and other eukaryotes. In C. elegans, the RNAi response is greatly amplified by the synthesis of abundant secondary siRNAs. Exogenous double stranded RNA is processed by Dicer and RDE-1/Argonaute into primary siRNA that guides target mRNA recognition. The RDE-10/RDE-11 complex and the RNA dependent RNA polymerase RRF-1 then engage the target mRNA for secondary siRNA synthesis. However, the molecular link between primary siRNA production and secondary siRNA synthesis remains largely unknown. Furthermore, it is unclear if the sub-cellular sites for target mRNA recognition and degradation coincide with sites where siRNA synthesis and amplification occur. In the C. elegans germline, cytoplasmic P granules at the nuclear pores and perinuclear Mutator foci contribute to target mRNA surveillance and siRNA amplification, respectively. We report that RDE-12, a conserved FG domain containing DEAD-box helicase, localizes in P-granules and cytoplasmic foci that are enriched in RSD-6 but are excluded from the Mutator foci. Our results suggest that RDE-12 promotes secondary siRNA synthesis by orchestrating the recruitment of RDE-10 and RRF-1 to primary siRNA targeted mRNA in distinct cytoplasmic compartments.

2014-03-27 | GSE53830 | GEO

Analysis of nonsense-mediated mRNA decay in daf-2 mutants

Project description:To exmine the role of nonsense-mediated mRNA decay process in the longevity regulation of daf-2 mutants, we sequenced transcriptomes from day 1 adult Caenorhabditis elegans: Bristol N2 (wild-type), and smg-2(qd101), daf-2(e1370) and smg-2(qd101); daf-2(e1370) mutants.

2017-03-17 | GSE94077 | GEO

RNA-seq analysis comparing gene expression of unc-43(gf), unc-43(-) and egl-8(-) to the corresponding control strain in daf-2(+) and daf-2(-) background

Project description:To identify genes whose expression in Caenorhabditis elegans is regulated by unc-43/CamKII or egl-8/PLCbeta during adulthood, we performed an exploratory whole transcriptome RNA-sequencing (RNA-seq) study on unc-43(gf), unc-43(-), egl-8(-) and corresponding unc-43(+)/egl-8(+) control worms. To further account for potential influences of genetic background on unc-43/egl-8 function, these experiments were conducted in long-lived insulin-receptor defective [daf-2(-)], as well as in otherwise wildtype [i.e daf-2(+)] strains.

2022-10-01 | E-MTAB-11045 | biostudies-arrayexpress

Transcriptome analysis of C. elegans embryos lacking ADARs and the 26G pathway

Project description:Adenosine deaminases that act on RNA (ADARs) catalyze the conversion of adenosine to inosine in dsRNA. C. elegans ADARs, ADR-1 and ADR-2, promote the expression of genes containing dsRNA structures by preventing their processing into siRNAs and silencing by RNAi. The 26G endogenous siRNA (endo-siRNA) pathway generates a subset of siRNAs distinct from those made in adr-1;adr-2 mutants, but using many of the same factors. We found that adr-1;adr-2;rrf-3 mutants, lacking both ADARs and the RNA-dependent RNA polymerase RRF-3 required for the 26G pathway, display a bursting phenotype rescued by the RNAi factors RDE-1 and RDE-4. To determine what gene expression changes underlie the synthetic phenotype of adr-1;adr-2;rrf-3 mutants, we sequenced poly(A)+ RNA from adr-1;adr-2;rrf-3 embryos, their parent strains, and strains rescued with mutations in rde-1 and rde-4. We found that genes associated with edited structures were robustly downregulated in adr-1;adr-2;rrf-3 mutants in a manner partially dependent on rde-1 and rde-4. Additionally, genes induced during Orsay virus infections were induced in rrf-3 mutants and further upregulated in adr-1;adr-2;rrf-3 mutants, again dependent in part on rde-1 and rde-4.

2018-02-23 | GSE106647 | 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