GEO DataSets

(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

(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; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19757 GPL32326

57 Samples

Download data: TXT

(Submitter supplied) RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, majority of RNAi components are located in phase-separated perinuclear germ granules, including P granule, Mutator foci, Z granule, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19757

36 Samples

Download data: TXT

(Submitter supplied) RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, majority of RNAi components are located in phase-separated perinuclear germ granules, including P granule, Mutator foci, Z granule, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32326

9 Samples

Download data: TXT

(Submitter supplied) RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, majority of RNAi components are located in phase-separated perinuclear germ granules, including P granule, Mutator foci, Z granule, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32326

12 Samples

Download data: TXT

(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

(Submitter supplied) To explore the roles of piRNAs and WAGO-class 22G-RNAs in regulating gene expression and transposon silencing in Caenorhabditis elegans, we used RNA-seq to assess changes in small RNA and mRNA levels in prg-1 and mut-16 mutants, which disable the piRNA and WAGO-class 22G-RNA pathways respectively. We identified numerous roles for piRNAs and WAGO-class 22G-RNAs in regulating germline genes, including transposons, histones, and spermatogenic and oogenic transcripts.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19757

39 Samples

Download data: XLSX

(Submitter supplied) Proteins containing LOTUS and Tudor domains have critical roles in the germline, including in small RNA biology. LOTR-1 is the only protein expressed in the germline of C. elegans which has LOTUS and Tudor domains. Here, to understand the influence of LOTR-1 in small RNA biology, we sequenced small RNAs of wild-type and lotr-1 mutant animals. This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19757 GPL18245

12 Samples

Download data: BW, TSV

(Submitter supplied) Proteins containing LOTUS and Tudor domains have critical roles in the germline, including in small RNA biology. LOTR-1 is the only protein expressed in the germline of C. elegans which has LOTUS and Tudor domains. Here, to understand the influence of LOTR-1 in small RNA biology, we sequenced small RNAs of wild-type and lotr-1 mutant animals.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19757

6 Samples

Download data: BW, TSV

(Submitter supplied) Proteins containing LOTUS and Tudor domains have critical roles in the germline, including in small RNA biology. LOTR-1 is the only protein expressed in the germline of C. elegans which has LOTUS and Tudor domains. Here, to understand the influence of LOTR-1 in small RNA biology, we sequenced small RNAs of wild-type and lotr-1 mutant animals.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18245

6 Samples

Download data: BW, TSV

(Submitter supplied) Argonaute-associated siRNAs and Piwi-associated piRNAs have overlapping roles in silencing mobile genetic elements in animals. In C. elegans, mutator-class (mut) genes mediate siRNA-guided repression of transposons as well as exogenous RNA-directed gene silencing (RNAi), but their roles in endogenous RNA silencing pathways are not well understood. To characterize the endogenous small RNAs dependent on mutator-class genes, small RNA populations from a null allele of mut-16, as well as a regulatory mut-16(mg461) allele that disables only somatic RNAi, were subjected to deep sequencing.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9269

5 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9269 GPL200

16 Samples

Download data: BED, CEL

(Submitter supplied) piRNAs are required to maintain germline integrity and fertility but their mechanism of action is poorly understood. Here we demonstrate that C. elegans piRNAs silence transcripts in trans through imperfectly complementary sites. We find that target silencing is independent of Piwi endonuclease activity or “slicing”. Instead, we show that piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

9 Samples

Download data: CEL

(Submitter supplied) piRNAs are required to maintain germline integrity and fertility but their mechanism of action is poorly understood. Here we demonstrate that C. elegans piRNAs silence transcripts in trans through imperfectly complementary sites. We find that target silencing is independent of Piwi endonuclease activity or “slicing”. Instead, we show that piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9269

7 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18245

36 Samples

Download data

(Submitter supplied) sRNAseq was conducted on the hrde-1; meg-3 meg-4 triple mutant, revealing that the hrde-1 mutation suppresses the rde-11 and sid-1 sRNA upregulation phenotype of meg-3 meg-4 mutants .    

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18245

6 Samples

Download data: TXT

(Submitter supplied) sRNAseq was conducted on four independently generated meg-3 meg-4 lines, and upregulation of sRNAs targeting several RNAi genes was found. mRNAseq found that the transcript levels for several of these genes was also down. meg-3 meg-4 mutants also showed a similar pattern of sRNA misregulation as the rde-11 mutant.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL18245

18 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18245

12 Samples

Download data: TXT

(Submitter supplied) Eukaryotic genomes harbor invading transposable elements silenced by PIWI-interacting RNAs (piRNAs) to maintain genome integrity in animal germ cells. However, whether piRNAs also regulate endogenous gene expression programs remains unclear. Here, we show that C. elegans piRNAs trigger the transcriptional silencing of hundreds of spermatogenic genes during spermatogenesis, promoting sperm differentiation and function. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19757

40 Samples

Download data: BW

(Submitter supplied) Eukaryotic genomes harbor invading transposable elements silenced by PIWI-interacting RNAs (piRNAs) to maintain genome integrity in animal germ cells. However, whether piRNAs also regulate endogenous gene expression programs remains unclear. Here, we show that C. elegans piRNAs trigger the transcriptional silencing of hundreds of spermatogenic genes during spermatogenesis, promoting sperm differentiation and function. more...

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL19757

24 Samples

Download data: BW