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:

Drosophila melanogaster; synthetic construct

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21306 GPL21616

12 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:

synthetic construct; Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21616 GPL21306

4 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) 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) 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

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(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

(Submitter supplied) Background: RNA silencing pathways play critical roles in gene regulation, virus infection, and transposon control. RNA interference (RNAi) is mediated by small interfering RNAs (siRNAs), which are liberated from double stranded (ds) RNA precursors by Dicer and direct the RNA-induced silencing complex (RISC) to target transcripts. Recent efforts have uncovered important principles governing small RNA (smRNA) sorting into RISC, yet mechanisms defining substrate selection by Dicer proteins remain uncharacterized. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

24 Samples

Download data: FASTA, TXT

(Submitter supplied) A hallmark of RNA silencing is a class of ~22 nt RNAs which are processed from dsRNA precursor by Dicer. Accurate processing by Dicer is critical for the functionality of microRNAs (miRNAs). According to the current model, Dicer measures the length by anchoring the 3' overhang of the dsRNA terminus. Here we find that human Dicer binds to the 5' end of RNA and utilizes the 5' end as an additional reference point for cleavage site selection (5' counting rule). more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9250

5 Samples

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

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

20 Samples

Download data: TSV

(Submitter supplied) Dicer plays a key role in small RNA biogenesis by processing double-stranded RNAs (dsRNAs). Human DICER (hDICER) is specialized in processing of small hairpins such as pre-microRNAs (pre-miRNAs) with a limited activity towards long dsRNAs, unlike its homologs in lower eukaryotes and plants which cleave long dsRNAs. While the mechanism of long dsRNA cleavage has been well documented, our understanding of pre-miRNA processing is limited due to lack of the structure of hDICER in a catalytic state. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

30 Samples

Download data: TSV

(Submitter supplied) RNA silencing relies on specific and efficient processing of dsRNA by DICER which produces microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, our current knowledge of DICER’s specificity is restricted to the secondary structures of its substrates: a dsRNA than 22 bp with a 2-nt 3′ overhang. We recently found evidence pointing to additional sequence-dependent determinant(s) beyond these features. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TSV

(Submitter supplied) RNA silencing relies on specific and efficient processing of dsRNA by DICER which produces microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, our current knowledge of DICER’s specificity is restricted to the secondary structures of its substrates: a dsRNA than 22 bp with a 2-nt 3′ overhang. We recently found evidence pointing to additional sequence-dependent determinant(s) beyond these features. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: TSV

(Submitter supplied) Cis-natural antisense transcripts (cis-NATs) have been speculated to be substrates for endogenous RNA interference (RNAi), but little experimental evidence for such a pathway in animals has been reported. Analysis of massive Drosophila melanogaster small RNA data sets now reveals that endogenous small interfering RNAs (siRNAs) are produced via bidirectional transcription. >100 cis-NATs with overlapping 3' exons generate 21-nt, Dicer-2 (Dcr-2)­dependent, 3'-end modified siRNAs. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

2 Samples

Download data: CEL, CHP

(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) High throughput seqeuncing of small RNAs (PAGE isolated from total RNA or Argonaute immunoprecipitates) from Drosophila melanogaster using the Illumina platform. Adapter ligation requires 5' monophosphate and 3' OH. Full analysis of all libraries in this set is published (Czech B. et al. 2008), leading to the description of endogenous siRNAs in flies. Keywords: Solexa sequences

Organism:

Drosophila melanogaster; Flock House virus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9058 GPL9402

9 Samples

Download data: TXT

(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) RNA silencing is a conserved mechanism in which small RNAs trigger various forms of sequence specific gene silencing by guiding Argonaute complexes to target RNAs via base-pairing. RNA silencing is thought to have evolved as a form of nucleic-acid-based immunity to inactivate viruses and transposable elements (TEs). Although the activity of TEs in animals has been thought to be largely restricted to the germline, recent studies have shown that they may also actively transpose in somatic cells, creating somatic mosaicism in animals3. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL6452

1 Sample

Download data: TXT