GEO DataSets

(Submitter supplied) The goal of this study was to identify AGO1-dependent miRNA and tasiRNA in Arabidopsis by sequencing small RNA from wild type (Col-0) and ago1-25 plants. Keywords: Small RNA

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

6 Samples

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(Submitter supplied) In plants, tasiRNAs form a class of endogenous secondary siRNAs produced through the action of RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) upon microRNA-mediated cleavage of non-coding TAS RNAs. In Arabidopsis thaliana, TAS1, TAS2 and TAS4 tasiRNA production proceeds via a single cleavage event mediated by 22nt-long or/and asymmetric miRNAs in an ARGONAUTE-1 (AGO1)-dependent manner. By contrast, tasiRNA production from TAS3 seems to follow the so-called ‘two-hit’ process, where dual targeting of TAS3, specifically mediated by the 21nt-long, symmetric miR390, initiates AGO7-dependent tasiRNA production. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

5 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to identify small RNA-ARGONAUTE interactions in Arabidopsis. Co-immunoprecipitation assays followed by high-throughput sequencing were done to identify small RNA associated with HA-AGO2 and HA-AGO7. Keywords: small RNA - ARGONAUTE interactions

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL7029

4 Samples

Download data: TXT

(Submitter supplied) To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology. Keywords: small RNAs, high-throughput sequencing

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL4732

14 Samples

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(Submitter supplied) Identifing the miRNA-TASL-PPR-siRNA pathway in strawberry

Organism:

Fragaria vesca

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16761

1 Sample

Download data: TXT

(Submitter supplied) Small RNA from total RNA (input fraction) and immunoprecipitated HA-AGO1-complexes (IP fraction) were identified using high-throughput sequencing-by-synthesis.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

4 Samples

Download data: GFF, TXT

(Submitter supplied) Microarray expression profiles of wild-type, ago1-10, ago1-11, and dcl1-9 Arabidopsis thaliana ec. Landsberg erecta seedling at 9, 21, and 35 days after germination. Keywords: mutant response

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL71

37 Samples

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(Submitter supplied) Inflorescence stages 1 to 12 from mutants involved in Arabidopsis small RNA metabolism. Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the sample groups allow the identification of genes regulated by small RNAs (microRNAs and siRNAs). Keywords: other

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

44 Samples

Download data: CEL, CHP, RPT

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL26208 GPL23157

14 Samples

Download data: BW, TXT

(Submitter supplied) We profiled the small RNA of AGO1 NTE truncation mutant lines, and the small RNA associated with AGO1 NTE truncation mutant to study the roles of the NTE region in Arabidopsis AGO1 involved RNA-induced silencing complex (RISC) formation.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23157

8 Samples

Download data: BW

(Submitter supplied) We profiled gene expression of AGO1 NTE truncation mutant lines to study the roles of the NTE region in Arabidopsis AGO1 involved RNA-induced silencing complex (RISC) formation.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL26208 GPL23157

24 Samples

Download data: BW, TXT

(Submitter supplied) We profiled the small RNA of AGO1 NTE truncation mutant lines, and the small RNA associated with AGO1 NTE truncation mutant to study the roles of the NTE region in Arabidopsis AGO1 involved RNA-induced silencing complex (RISC) formation.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by array

Platform:

GPL23157

15 Samples

Download data: BW

(Submitter supplied) We profiled gene expression of AGO1 NTE truncation mutant lines to study the roles of the NTE region in Arabidopsis AGO1 involved RNA-induced silencing complex (RISC) formation.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: TXT

(Submitter supplied) The use of syn-tasiRNAs has been proposed as an RNA interference technique alternative to those previously described: hairpin based, virus induced gene silencing or artificial miRNAs. In this study we engineered the TAS1c locus to impair Plum pox virus (PPV) infection by replacing the five native siRNAs with two 210-bp fragments from the CP and the 3´NCR regions of the PPV genome. Deep sequencing analysis of the small RNA species produced by both constructs in planta has shown that phased processing of the syn-tasiRNAs is construct-specific. more...

Organism:

Nicotiana benthamiana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19037

2 Samples

Download data: TXT

(Submitter supplied) The osdcl4-1 mutant exhibits much severer developmental defects than dcl4 in Arabidopsis, suggesting that Os DCL4 may process broader substrates in rice. By deep sequencing of small RNAs from different tissues of wild types and osdcl4-1, we revealed that 21-nucleotide siRNAs were largely dependent on Os DCL4. Besides several tasiRNA loci reported in Arabidopsis and rice, over one thousand 21-nucleotide and several dozen 24-nucleotide phased siRNA (phasiRNA) clusters were identified in panicles but not in seedlings and grains. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9147

6 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL17639 GPL26208

30 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Plant  microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, AGO1 also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5’-3’ RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

8 Samples

Download data: TXT

(Submitter supplied) Plant  microRNAs (miRNAs) associate with ARGONAUTE1 (AGO1) to direct post-transcriptional gene silencing and regulate numerous biological processes. Although AGO1 predominantly binds miRNAs in vivo, AGO1 also associates with endogenous small interfering RNAs (siRNAs). It is unclear whether the miRNA/siRNA balance affects miRNA activities. Here we report that FIERY1 (FRY1), which is involved in 5’-3’ RNA degradation, regulates miRNA abundance and function by suppressing the biogenesis of ribosomal RNA-derived siRNAs (risiRNAs). more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

22 Samples

Download data: BEDGRAPH

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

Organism:

Arabidopsis thaliana

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17639 GPL13222

23 Samples

Download data: GFF