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Links from GEO DataSets

Items: 20

1.

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
2.

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
3.

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
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 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
6.

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
7.

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
8.

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
9.

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
10.

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
11.

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
12.

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
13.

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
14.

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
15.

dsRNAs expressed in C. elegans development

(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. Using a dsRNA immunoprecipitation and high-thoughput sequencing (dsRIP-Seq) approach, we identify 1523 expressed A-to-I edited regions and characterize their expression during Caenorhabditis elegans development. more...
Organism:
Caenorhabditis elegans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13657
8 Samples
Download data: BED, BW, TXT
Series
Accession:
GSE79375
ID:
200079375
16.

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
17.

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
18.

The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications.

(Submitter supplied) To characterize the role of the ERI-6/7 helicase in endogenous small RNA pathways in C. elegans, small RNA populations from null alleles of eri-6 and eri-7, and from mutants of known endogenous RNAi pathway factors, eri-1 and ergo-1, were determined by deep sequencing, and compared to wild type.
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL9269
7 Samples
Download data
Series
Accession:
GSE32366
ID:
200032366
19.

RNA interference and retinoblastoma related genes are required for repression of endogenous siRNA targets in C. elegans

(Submitter supplied) Expession data from L1-L2 stage nematodes (C. elegans), wild type and four mutants (alg-1, zfp-1, rde-4, lin-35). In C. elegans, a vast number of endogenous short RNAs corresponding to thousands of genes have been discovered recently. This finding suggests that these short interfering RNAs may contribute to regulation of many developmental and other signaling pathways in addition to silencing viruses and transposons. more...
Organism:
Caenorhabditis elegans
Type:
Expression profiling by array
Platform:
GPL200
15 Samples
Download data: CEL
Series
Accession:
GSE13258
ID:
200013258
20.

Analysis of transgene siRNAs and ARL-8-dependent siRNAs in Caenorhabditis elegans

(Submitter supplied) We analyzed the C. elegans small RNA response to high copy transgene sequences expressed in the soma in a wild type and an eri-6/7 mutant background. We also analyzed small RNA defects in the arl-8(tm2472) mutant. Transgene siRNAs are 22 nt long, mostly antisense, and correspond to the promoter, coding regions, the 3'UTR and plamsid sequences present on the transgene. Transgene siRNAs are decreased in the eri-6/7 mutant. more...
Organism:
Caenorhabditis elegans
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13657
6 Samples
Download data: TXT
Series
Accession:
GSE52785
ID:
200052785
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