GEO DataSets

(Submitter supplied) In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character—as is found in small interfering RNAs (siRNAs)—directs duplexes into Ago2, whereas central mismatches, like those found in miRNA/miRNA* duplexes, direct duplexes into Ago1. Central to this sorting decision is the affinity of the small RNA duplex for the Dcr-2/R2D2 heterodimer, which loads small RNAs into Ago2. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL9058

11 Samples

Download data: TAR, TXT

(Submitter supplied) In flies, microRNAs (miRNAs) are synthesized as a short imperfect duplex, where the miRNA is paired to another small RNA, dubbed the "miRNA*". Usually, miRNA*s are degraded in the last steps of miRNA maturation, but we found evidence that some of them can be loaded on the Ago2 protein.

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9058

7 Samples

Download data

(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) High-throughput sequencing of Drosophila melanogaster small RNAs from S2 cells. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH 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

1 Sample

Download data

(Submitter supplied) Drosophila Argonaute-1 and Argonaute-2 differ in function and small RNA content. AGO2 binds to siRNAs, whereas AGO1 is almost exclusively occupied by microRNAs. microRNA duplexes are intrinsically asymmetric, with one strand, the miR strand, preferentially entering AGO1 to recognize and regulate the expression of target mRNAs. The other strand, miR*, has been viewed as a by-product of microRNA biogenesis. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

5 Samples

Download data: CSV

(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) Ago1-IP small RNA sequencing from S2R+ cells, with dsRNA knockdown of Dicer1 (and GFP control)

Organism:

Drosophila melanogaster

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13304

2 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19132

48 Samples

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(Submitter supplied) To examine the effect of loss of dFOXO on the small RNA landscape of aging animals, we sequenced total small RNA collected from whole wildtype (wDah) and dFOXO-null (dfoxoΔ94) flies at young (5-6 days) and old (31 days) age.

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19132

16 Samples

Download data: TXT

(Submitter supplied) To examine the effect of loss of dFOXO on Ago1 and Ago2 RISC loading in aging animals, we sequenced RNA immunoprecipitated from Ago1 and Ago2 RISC collected from whole wildtype (wDah) and dFOXO-null (dfoxoΔ94) flies at young (5 days) and old (35 days) age. dFOXO is a transcription factor that regulates Ago1 and Ago2 as well as lifespan.

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL19132

32 Samples

Download data: TXT

(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) Target-directed degradation (TDD) of microRNAs (miRNAs) plays an important role in shaping miRNA abundances across bilateria. Some endogenous small interfering RNAs (siRNAs) of Drosophila cells have target sites resembling those that trigger miRNA TDD, raising the question as to whether they too might undergo such regulation. Here, we find that at least seven of these siRNAs are indeed sensitive to TDD when loaded into AGO1, the Argonaute paralog that preferentially associates with miRNAs. more...

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL17275

36 Samples

Download data: CSV, 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) 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