GEO DataSets

(Submitter supplied) Examine the abundance and length of siRNAs produced by mutant Dicer-2 in vivo and in vitro in order to understand the mechanism by which Dicer-2 produces highly precise 21 nt siRNAs.

Organism:

synthetic construct; Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21616 GPL21306

4 Samples

Download data: TXT

(Submitter supplied) Examine the abundance and length of siRNAs produced by mutant Dicer-2 in vivo and in vitro in order to understand the mechanism by which Dicer-2 produces highly precise 21 nt siRNAs.

Organism:

Drosophila melanogaster; synthetic construct

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21306 GPL21616

12 Samples

Download data: TXT

(Submitter supplied) Small interfering RNAs (siRNAs) direct RNA interference (RNAi) in eukaryotes. In flies, somatic cells produce siRNAs from exogenous double-stranded RNA as a defense against viral infection. Here, we identify 21-nt long, endogenous siRNAs (endo-siRNAs) corresponding to transposons and heterochromatic sequences in the somatic cells of Drosophila melanogaster. We also detected endo-siRNAs complementary to mRNAs: these siRNAs disproportionately mapped to the complementary regions of overlapping mRNAs predicted to form dsRNA in vivo. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL6664

14 Samples

Download data: FA

(Submitter supplied) MicroRNAs (miRNAs) are short (∼ 21-23 nt) regulatory RNAs that guide the degradation or translational repression of their RNA targets. The miRNA “seed”—nucleotides 2 through 7—establishes miRNA target specificity, because this region is the primary determinant of RNA binding by both miRNA and small interfering RNAs. Accurate processing of the miRNA 5´ end is thought to be under strong selective pressure, as a shift by just one nucleotide in the 5´ end of a miRNA would alter its seed sequence, redefining its repertoire of targets. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL6024

40 Samples

Download data: FNA, QUAL

(Submitter supplied) High-throughput sequencing-by-synthesis (Genome Analyzer, Illumina, San Diego, CA, USA) was as for pyrosequencing in Seitz et al. (Curr. Biol. 18, 147 (2008)) except that RNA Ligase 2 [Rnl2(1-249)K227Q] (Addgene, Cambridge, MA, USA) was used for 3´ ligation. Linkers and primers for sequencing-by-synthesis were: 5´ adaptor, 5´-rGrUrU rCrArG rArGrU rUrCrU rArCrA rGrUrC rCrGrA rCrGrA rUrC-3´ (Dharmacon, Lafayette, CO, USA); 3´ preadenylated linkers, 5´-rAppdCdT dGdTdA dGdGdC dAdCdC dAdTdC dAdAdT ddC-3´. more...

Organism:

Drosophila melanogaster

1 Series

14 Samples

Download data

(Submitter supplied) While mammalian somatic cells are incapable of mounting an effective RNA interference (RNAi) response to viral infections, plants and invertebrates are able to generate high levels of functional short interfering RNAs (siRNAs) of viral origin that can effectively control many infections. In Drosophila, the RNAi response is mediated by the Dicer 2 enzyme (dDcr2) acting in concert with two co-factors called Loqs-PD and R2D2. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

12 Samples

Download data: BED

(Submitter supplied) We sequenced small RNA from total RNA samples in two siRNA-pathway mutants in fly ovaries. This submission comes from a modENCODE project. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

2 Samples

Download data

(Submitter supplied) modENCODE_submission_2834 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

1 Sample

Download data: SAM

(Submitter supplied) modENCODE_submission_2833 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

1 Sample

Download data: SAM

(Submitter supplied) modENCODE_submission_2749 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

1 Sample

Download data: SAM

(Submitter supplied) modENCODE_submission_2748 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

1 Sample

Download data: SAM

(Submitter supplied) modENCODE_submission_2746 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

1 Sample

Download data: SAM

(Submitter supplied) modENCODE_submission_2744 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

1 Sample

Download data: SAM

(Submitter supplied) We used SOLiD technology to deep sequence libraries prepared from 18-35 nt PAGE purfied small RNAs derived from female Drosophila. The objective of our study was to compare the impact of R2D2 or loquacious mutantions on different small RNA populations in the fruit fly.

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9521

3 Samples

Download data: TXT

(Submitter supplied) High-throughput sequencing of Drosophila melanogaster small RNAs. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH Keywords: High-throughput solexa sequencing

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

4 Samples

Download data

(Submitter supplied) In Drosophila, siRNAs are classified as endo- or exo-siRNAs based on their origin. Both are processed from double-stranded RNA precursors by Dcr-2, then loaded into the Argonaute protein Ago2. While exo-siRNAs serve to defend the cell against viruses, endo-siRNAs restrict the spread of selfish DNA in somatic cells, analogous to piRNAs in the germ line. Endo- and exo-siRNAs display a differential requirement for double-stranded RNA binding domain proteins (dsRBPs): R2D2 is needed to load exo-siRNAs into Ago2 while the PD isoform of Loquacious (Loqs-PD) stimulates Dcr-2 during the nucleolytic processing of hairpin-derived endo-siRNAs. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

4 Samples

Download data: FA, MAP, TXT

(Submitter supplied) Years after the discovery that Dicer is a key enzyme in gene-silencing, the role of its helicase domain remains enigmatic. Here we show that this domain is critical for accumulation of certain endogenous small interfering RNAs (endo-siRNAs) in C. elegans. The domain is required for the production of the direct products of Dicer, or primary endo-siRNAs, and consequently, affects levels of downstream intermediates, the secondary endo-siRNAs. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9269

3 Samples

Download data: TXT

(Submitter supplied) Mammals have one Dicer gene required for biogenesis of small RNAs in microRNA (miRNA) and RNA interference (RNAi) pathways. Yet, endogenous RNAi is highly active in oocytes but not in somatic cells. Here, we provide a mechanistical explanation for high RNAi activity in mouse oocytes. The main Dicer isoform in oocytes is transcribed from an intronic MT-C retrotransposon, which functions as a promoter of an oocyte-specific Dicer isoform (denoted DicerO). more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL14602

19 Samples

Download data: BED

(Submitter supplied) Drosophila Dicer-1 produces microRNAs (miRNAs) from pre-miRNA, whereas Dicer-2 generates small interfering RNAs (siRNAs) from long dsRNA. loquacious (loqs) encodes three Dicer partner proteins, Loqs-PA, Loqs-PB, and, Loqs-PD, generated by alternative splicing. To understand the function of each Loqs isoform, we constructed loqs isoform-specific rescue flies. Loqs-PD promotes siRNA production in vivo by Dicer-2. more...

Organism:

Drosophila melanogaster; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9061 GPL9250

24 Samples

Download data: TXT

(Submitter supplied) We report the cloning and sequencing of both endogenous small RNAs and virus-derived siRNAs produced by the antiviral RNAi pathway in Drosophila. We find that a diverse panel of viruses are targeted by the RNAi pathway in Drosophila to produce abundant virus-derived siRNAs, and these siRNAs map to various locations within the viral genomes. Knockdown of various RNAi and miRNA pathway components alters the levels of these viral small RNAs.

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

25 Samples

Download data: TXT