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Items: 20

1.

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

(Submitter supplied) 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. more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13657
8 Samples
Download data: TXT
Series
Accession:
GSE53830
ID:
200053830
2.

The Vasa homolog RDE-12 engages target mRNA and a secondary-Argonaute WAGO-1 to promote RNAi in C. elegans

(Submitter supplied) Argonaute proteins (AGOs) are key nuclease effectors of RNA interference (RNAi) [1]. Although purified AGOs can mediate a single round of target-RNA cleavage in vitro, accessory factors are required for siRNA loading and to achieve multiple-target turnover [2, 3]. To identify AGO co-factors we immunoprecipitated the C. elegans AGO WAGO-1, which engages amplified small RNAs during RNAi [4]. These studies identified a robust association between WAGO-1 and a conserved Vasa ATPase-related protein RDE-12. more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13776
4 Samples
Download data: TXT
Series
Accession:
GSE54396
ID:
200054396
3.

MUT-14 and SMUT-1 DEAD box RNA helicases have overlapping roles in germline RNAi and endogenous siRNA formation in C. elegans

(Submitter supplied) This data series contains small RNA high-throughput sequencing data for each of the mutator class genes. Samples are from stage-matched adult C. elegans grown at 20˚C.
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13657
19 Samples
Download data: TXT
Series
Accession:
GSE54320
ID:
200054320
4.

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

(Submitter supplied) 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. more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL13657 GPL9269
19 Samples
Download data: TXT
Series
Accession:
GSE37083
ID:
200037083
5.

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

(Submitter supplied) 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. more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13657
12 Samples
Download data: TXT
Series
Accession:
GSE36494
ID:
200036494
6.

A Ribonuclease Coordinates siRNA Amplification and mRNA Cleavage during RNAi

(Submitter supplied) Effective silencing by RNA-interference (RNAi) depends on mechanisms that amplify and propagate the silencing signal. In some organisms, small-interfering (si) RNAs are amplified from target mRNAs by RNA-dependent RNA polymerase (RdRP). Both RdRP recruitment and mRNA silencing require Argonaute proteins, which are generally thought to degrade RNAi targets by directly cleaving them. However in C. elegans, the enzymatic activity of the primary Argonaute, RDE-1, is not required for silencing activity. more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL13657 GPL9269
33 Samples
Download data: TXT
Series
Accession:
GSE59300
ID:
200059300
7.

A Tudor-domain containing protein, SIMR-1, mediates silencing of piRNA target mRNAs by the Mutator Complex

(Submitter supplied) piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, silencing of piRNA target genes is mediated by the Mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, how mRNAs recognized by the piRNA pathway are handed off to the Mutator pathway is unclear. Here, we identify the Tudor domain-containing protein, SIMR-1, as a key mediator of this handoff. more...
Organism:
Caenorhabditis elegans
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL19757
64 Samples
Download data: TXT
Series
Accession:
GSE138220
ID:
200138220
8.

MicroRNA-Directed siRNA Biogenesis in Caenorhabditis elegans

(Submitter supplied) C.elegans small RNAs from HA::ALG-1, HA::ALG-2 and HA::RDE-1 IP and rde-1 mutants
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL9269 GPL9085
5 Samples
Download data: TXT
Series
Accession:
GSE20649
ID:
200020649
9.

Adult Caenorhabditis elegans: wild-type (N2) and mir-243 mutant worms

(Submitter supplied) Transcriptional profiling of N2 vs. mir-243 worms, aiming to identify direct and indirect targets of the microRNA.
Organism:
Caenorhabditis elegans
Type:
Expression profiling by array
Platform:
GPL8209
6 Samples
Download data: TXT
Series
Accession:
GSE20558
ID:
200020558
10.

elli-1 gene expression array

(Submitter supplied) Germ cells contain non-membrane bound cytoplasmic organelles that help maintain germline integrity. In C. elegans they are called P granules; without them, the germline undergoes partial masculinization or aberrant differentiation. One key P-granule component is the Argonaute CSR-1, a small-RNA binding protein that antagonizes accumulation of sperm-specific transcripts in developing oocytes. Loss of CSR-1 or components of its pathway results in a very specific, enlarged P-granule phenotype. more...
Organism:
Caenorhabditis elegans
Type:
Expression profiling by array
Platform:
GPL21109
8 Samples
Download data: TXT
Series
Accession:
GSE82322
ID:
200082322
11.

Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma

(Submitter supplied) Endogenous RNA-directed RNA polymerases (RdRPs) are cellular components capable of synthesizing new complementary RNAs from existing RNA templates. We present evidence for successive engagement of two different RdRPs in an endogenous siRNA-based mechanism targeting specific mRNAs in C. elegans soma. In the initiation stage of this process, a group of mRNA species are chosen as targets for downregulation, leading to accumulation of rare 26-nt 5'-phosphorylated antisense RNAs that depend on the RdRP homolog RRF-3, the argonaute ERGO-1, DICER, and a series of associated (ERI) factors. more...
Organism:
Caenorhabditis elegans
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9269
26 Samples
Download data: FA
Series
Accession:
GSE19414
ID:
200019414
12.

Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in ERGO-1/Argonaute pathway

(Submitter supplied) Argonaute (AGO) proteins interact with distinct classes of small RNAs to direct multiple regulatory outcomes. In many organisms, including plants, fungi and nematodes, cellular RNAdependent RNA polymerases (RdRPs) utilize AGO targets as templates for amplification of silencing signals. Here, we show that distinct RdRPs function sequentially to produce small RNAs that target endogenous loci in C. elegans. more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9269
8 Samples
Download data: GFF
Series
Accession:
GSE18714
ID:
200018714
13.

Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Caenorhabditis elegans
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL13657
40 Samples
Download data
Series
Accession:
GSE86517
ID:
200086517
14.

Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans [pre-mRNA-seq]

(Submitter supplied) Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to the H3K9 trimethylation (H3K9me3) response and transcriptional repression of target genes. The H3K9me3 response induced either by exogenous dsRNA or endogenous siRNA (endo-siRNA) is highly specific to the target loci and transgenerationally heritable. Despite these features, the role of H3K9me3 in transcriptional repression and heritable gene silencing at native target genes has not been tested. more...
Organism:
Caenorhabditis elegans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13657
5 Samples
Download data: XLSX
Series
Accession:
GSE86516
ID:
200086516
15.

Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans [RNA-seq]

(Submitter supplied) Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to the H3K9 trimethylation (H3K9me3) response and transcriptional repression of target genes. The H3K9me3 response induced either by exogenous dsRNA or endogenous siRNA (endo-siRNA) is highly specific to the target loci and transgenerationally heritable. Despite these features, the role of H3K9me3 in transcriptional repression and heritable gene silencing at native target genes has not been tested. more...
Organism:
Caenorhabditis elegans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13657
5 Samples
Download data: XLSX
Series
Accession:
GSE86515
ID:
200086515
16.

Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans [ChIP-seq]

(Submitter supplied) Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to the H3K9 trimethylation (H3K9me3) response and transcriptional repression of target genes. The H3K9me3 response induced either by exogenous dsRNA or endogenous siRNA (endo-siRNA) is highly specific to the target loci and transgenerationally heritable. Despite these features, the role of H3K9me3 in transcriptional repression and heritable gene silencing at native target genes has not been tested. more...
Organism:
Caenorhabditis elegans
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13657
30 Samples
Download data: XLSX
Series
Accession:
GSE86513
ID:
200086513
17.

C. elegans small RNA sequences from wild type animals fed on sel-1 dsRNA producing bacteria

(Submitter supplied) RNA interference (RNAi) is a phylogenetically widespread gene silencing process triggered by doublestranded RNA (dsRNA). In plants and C. elegans, two distinct populations of small RNAs have been proposed to participate in RNAi : "Primary siRNAs" (derived from Dicer nuclease-mediated cleavage of the original trigger) and "Secondary siRNAs" (additional small RNAs whose synthesis requires an RNA-directed RNA polymerase [RdRP]). more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL4569
1 Sample
Download data: TXT
Series
Accession:
GSE6282
ID:
200006282
18.

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

(Submitter supplied) 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. more...
Organism:
Caenorhabditis elegans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18245
24 Samples
Download data: TXT
Series
Accession:
GSE106647
ID:
200106647
19.

Gene regulation by small RNAs and ADAR RNA editing

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Caenorhabditis elegans
Type:
Expression profiling by high throughput sequencing; Third-party reanalysis; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL13657 GPL18245
32 Samples
Download data
Series
Accession:
GSE89890
ID:
200089890
20.

ADARs regulate small RNAs mapped to edited sequences

(Submitter supplied) Cellular RNAs containing double-stranded RNA (dsRNA) structures are subject to A-to-I RNA editing by the adenosine deaminases that act on RNA (ADARs). While A-to-I editing can alter mRNA coding potential, most editing is observed in non-coding sequences, the function of which remains poorly characterized. To correlate small RNA population with expression patterns of ADARs and hyperedited RNAs (editing-enriched regions: EERs) defined and characterized in a separate RNAseq analysis, we re-analyzed existing smallRNAseq datasets of a wildtype strain and a strain lacking ADARs (adr-1;adr-2). more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing; Third-party reanalysis
Download data: TXT, XLS
Series
Accession:
GSE89765
ID:
200089765
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