GEO DataSets

(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 454 sequencing

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL5061

10 Samples

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(Submitter supplied) see www.454.com

Organism:

Drosophila melanogaster

1 Series

10 Samples

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(Submitter supplied) A series of transfections was performed in Drosophila S2 cells to explore: 1) the types of target sites that Drosophila microRNAs recognize, 2) the relative functional efficacy of these sites in mediating repression, and 3) the determinants that allow some sites to have greater potency than others. 3p-seq was also performed to help reannotate and quantify the landscape of 3' UTRs in Drosophila S2 cells.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

10 Samples

Download data: BED, TXT

(Submitter supplied) Characterization of miRNAs in red flour beetle Tribolium castaneum by deep sequencing of two different RNA libraries.

Organism:

Tribolium castaneum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11311

2 Samples

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(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. 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

1 Sample

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(Submitter supplied) Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 miRNAs have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, we found a novel class of miRNAs that derive from natural cis-antisense transcript pairs. This configuration generates miRNAs that can perfectly match their targets. more...

Organism:

Oryza sativa

Type:

Expression profiling by MPSS

Platforms:

GPL3777 GPL3776

5 Samples

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(Submitter supplied) microRNAs play crucial roles in the early development of an organism. However the regulation of transcription through the action of microRNAs during the initial embyonic development has not been studied. We used microarrays to detail the effect of maternal microRNA mir-34 in regulation of zygotic trancription during the initial stages of Zebrafish embryonic development from one cell stage through the maternal-zygotic transition up to 24 hours post fertilization.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

18 Samples

Download data: CEL

(Submitter supplied) MicroRNAs (miRNAs) are endogenous RNA molecules that contribute to the regulation of gene expression post-transcriptionally. Recently, patterns of sequence evolution and evolutionary emergence of miRNAs have been analyzed in detail. However, the extent to which miRNA expression levels vary within and between species, the role of stabilizing selection versus other evolutionary mechanisms in shaping the temporal dynamics of these changes, and how this variation might unveil the interplay between miRNAs and mRNAs remain poorly understood. more...

Organism:

Drosophila melanogaster; Drosophila yakuba; Drosophila simulans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11000 GPL9394 GPL9058

12 Samples

Download data: TXT, XLS

(Submitter supplied) We found two lines of evidence suggesting that miRNA abundance has been shaped by different evolutionary regimes at the two developmental stages. Attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

Organism:

Drosophila simulans; Drosophila yakuba; Drosophila melanogaster

Type:

Non-coding RNA profiling by array

Platform:

GPL18365

72 Samples

Download data: TXT

(Submitter supplied) We found two lines of evidence suggesting that miRNA abundance has been shaped by different evolutionary regimes at the two developmental stages attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL14007

24 Samples

Download data: PAIR

(Submitter supplied) miRNA sequencing of Pacific oyster Crassostrea gigas for different organs and developmental stages.

Organism:

Crassostrea gigas

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13986

21 Samples

Download data: BEDGRAPH

(Submitter supplied) Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as posttranscriptional or transcriptional regulators in plants. miRNA function is essential for normal development and therefore likely to be important in the growth of the rice grain. To investigate the likely roles of miRNAs in rice grain development we carried out deep sequencing of the small RNA populations of rice grains. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9147 GPL9388

6 Samples

Download data: FNA, QUAL, TXT

(Submitter supplied) To identify endogenous siRNAs in response to bacterial pathogen at a whole genome level, we performed small RNA profiling on Pseudomonas syringae-challenged Arabidopsis and obtained more than 24.6 million (M) reads with more than 3.8 M unique small RNAs that perfectly matched Arabidopsis genome. We found some new miRNAs and some miRNA induced by pathogen infection. We also identified more than 20K unique siRNAs from the NAT mRNAs and 22K siRNAs from the introns or intron-exon junction of the NATs.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

13 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNA) are small, endogenous RNAs that regulate the expression of mRNAs posttranscriptionally. To identify miRNAs that produce twin products, we sequenced these five small RNA libraries and collected other published datasets to represent a systematic coverage of the major tissue types (head, body and sexual organs) in D. melanogaster. To survey the repression effects of twin miRs on the their targets, we dissected testes from adult flies that lacked Dm310s due to a knock-out mutation (Tang, et al. more...

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL9061 GPL13304

9 Samples

Download data: FA, TXT, XLSX

(Submitter supplied) MicroRNAs (miRNAs) are small, endogenously expressed RNAs that regulate mRNAs post-transcriptionally. The class of miRNA genes, like other gene classes, should experience birth, death and persistence of its members. We carried out deep sequencing of miRNAs from three species of Drosophila, and obtained 107,000 sequences that map to no fewer than 300 loci that were not previously known. We observe a large class of miRNA genes that are evolutionarily young, with a rate of birth of 12 new genes per million years (Myr). more...

Organism:

Drosophila melanogaster; Drosophila simulans; Drosophila pseudoobscura

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL6197 GPL6198 GPL6196

3 Samples

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(Submitter supplied) Curration of small RNAs from four melanogaster-subgroup species (Drosophila simulans, Drosophila sechellia, Drosophila erecta, and Drosophila yakuba) for the purpose of non-coding RNA annotation and comparative genomics assessment.

Organism:

Drosophila erecta; Drosophila sechellia; Drosophila simulans; Drosophila yakuba

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNA) are small, endogenous RNAs that regulate the expression of mRNAs posttranscriptionally. Evolutionarily new miRNAs, like new protein-coding genes, are dominantly expressed in reproductive organs. To dissect the evolutionary dynamics of new miRNAs in Drosophila spp, we sequenced small RNAs from two species of Drosophila, including four samples from reproductive organs and one sample from imaginal discs / CNS. more...

Organism:

Drosophila simulans; Drosophila pseudoobscura

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13306 GPL13310

5 Samples

Download data: TXT

(Submitter supplied) We used a microarray platform to survey the daily levels of 78 D. melanogaster miRNAs in adult heads of wildtype control flies and the arrhythmic clock mutant cyc01. At least 2 miRNAs were identified that showed robust daily abundance changes in control flies but not the cyc01 mutant. Keywords: microRNA, Circadian regulation

Organism:

Homo sapiens; Mus musculus; Caenorhabditis elegans; Drosophila melanogaster; Rattus norvegicus

Type:

Non-coding RNA profiling by array

Platform:

GPL6298

48 Samples

Download data: GPR

(Submitter supplied) We report the comprehensive sequencing of small RNA libraries created from different developmental stages of the basal chordate, Ciona intestinalis. Surprisingly, half of the identified miRNA loci encode not two, but up to four distinct small RNAs. These additional RNAs, termed “moRs”, are generated from sequences adjacent to the predicted ~60-nt pre-miRNA. moRs appear to be produced by RNAse-III-like processing, are ~20-nt in length, have 5’-monophosphate and 3’-hydroxl termini, and like miRNAs, are developmentally regulated.

Organism:

Drosophila melanogaster; Ciona intestinalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9311 GPL9058

6 Samples

Download data: TXT