GEO DataSets

(Submitter supplied) Dicer enzymes function at the core of RNA silencing to defend against exogenous RNA, or as an endogenous mechanism of gene regulation. Plant DICER-LIKE4 (DCL4) performs dual functions, acting in antiviral defense, as well as in development via the biogenesis of tasiR-ARFs. These small RNAs play an essential role in the grasses and act to spatially define the expression domain of AUXIN RESPONSE FACTOR3 (ARF3) transcription factors. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15463

12 Samples

Download data: TXT

(Submitter supplied) Maize LEAFBLADELESS1 (LBL1) and Arabidopsis SUPPRESSOR OF GENE SILENCING3 (SGS3) play orthologous roles in the biogenesis of 21 nucleotide trans-acting short-interfering RNAs (tasiRNAs). The phenotypes conditioned by mutation of lbl1 and SGS3 are, however, strikingly different, suggesting that the activities of these small RNA biogenesis components, or the tasiRNAs and their targets might not be entirely conserved. more...

Organism:

Zea mays

Type:

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

Platforms:

GPL13977 GPL15463

10 Samples

Download data: TXT, XLS

(Submitter supplied) In this study, we analyzed function of the rice RDR701 and various DCLs proteins in small RNA processing. small RNA deep sequencing analyses revealed that RDR701 and OsDCL4 is involved in tasiRNAs and 21- and 24-nt phasiRNAs biogenesis. Further analyses indicate RDR701 coupling with OsDCL4 and OsDCL3b are required for the biogenesis of 21- and 24-nt phasiRNAs, respectively. The triggering miRNAs for intial both size phasiRNAs,are also shown RDR701- and OsDCL4-dependent, suggesting two sequential round activity of RDR701 in associated with different DCLs are essential for rice phasiRNAs biogenesis.

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9147

4 Samples

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(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) 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) Paired-end Illumina RNA sequencing of Arabidopsis thaliana Col-0 siliques.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Parallel RNA silencing pathways regulate gene expression in plants, either by transcriptional gene silencing via RNA-dependent DNA methylation (RdDM), or by post-transcriptional silencing targeting mRNAs. Both pathways rely on distinct Dicer-like proteins to cleave double-stranded RNA into small-interfering RNAs. Experiments to determine the subcellular localization of Dicer-like proteins in Arabidopsis revealed that DCL4 is predominantly expressed as a transcriptional start site isoform that encodes a cytoplasmic protein. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

4 Samples

Download data: TXT

(Submitter supplied) Paired-end Illumina RNA sequencing of Arabidopsis thaliana Col-0 inflorescences

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: BEDGRAPH

(Submitter supplied) To investigate the effects of dcl3,dcl4,mDCL,rdr2,rdr6,nrpd1b, and nrpd1c mutations upon small RNAs in Physcomitrella patens , small RNA-seq was performed.

Organism:

Physcomitrium patens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17793

30 Samples

Download data: TXT

(Submitter supplied) Small RNA-seq from 10 day-old wild-type Physcomitrella patens was performed using 5 biological replicates. Replicates were grown in three batches at different times. Batch 1 had one replicate from strain "old WT", Batch 2 had two replicates from strain "old WT", and batch 3 had two replicates from strain "2009 WT". Old WT and 2009 WT were collected from Gransden wood, England; "old" has been in lab cultivation for at least 10 years, while "2009" was more recently collected from the wild (in 2009.)

Organism:

Physcomitrium patens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16754

10 Samples

Download data: TXT

(Submitter supplied) gen107_ptgs - gene profiling in silencing suppressor plants or in mirna mutants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - HcPro, P15, P19, CHS-RNAi (control), were grown on MS solid medium, and tissues were harvested at different developmental stages. dcl1-9, hen1-1 and La-er (control) were grown on MS solid medium, and tissues harvested at different developmental stages. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL10892

40 Samples

Download data: GPR

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

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array; Expression profiling by genome tiling array

Platforms:

GPL10892 GPL6403 GPL10772

144 Samples

Download data: GPR

(Submitter supplied) gen107_ptgs - gene profiling in silencing suppressor plants or in mirna mutants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - HcPro, P15, P19, CHS-RNAi (control), were grown on MS solid medium, and tissues were harvested at different developmental stages. dcl1-9, hen1-1 and La-er (control) were grown on MS solid medium, and tissues harvested at different developmental stages. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array; Expression profiling by genome tiling array

Platforms:

GPL6403 GPL10892

120 Samples

Download data: GPR

(Submitter supplied) gen107_ptgs - chip in silencing suppressor plants or in mirna plants - What are the genes that are differentially regulated in various tissues derived from silencing suppressor plants or miRNA mutants? - How are the histone modifications and the chromatin structure in miRNA mutants or in silencing suppressor plants?

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10772

24 Samples

Download data: GPR

(Submitter supplied) DICER-like proteins produce small RNAs that silence genes involved in development and defenses against viruses and pathogens. Which DCLs participate in plant-herbivore interactions remains unstudied. We identified four distinct DCL genes and stably silenced their expression by RNAi in Nicotiana attenuata, a model system for the study of plant-herbivore interactions. Silencing DCL1 expression was lethal to the plants. more...

Organism:

Nicotiana attenuata

Type:

Expression profiling by array

Platform:

GPL13527

9 Samples

Download data: TXT

(Submitter supplied) Rosette leaves (5-8) and inflorescence stages (1-12) from dcl1-7, rdr6-15, and dcl4-2 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 trans-acting siRNAs). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS1466

Platform:

GPL198

27 Samples

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Analysis of rosette leaf and inflorescence tissues from the DICER-LIKE (DCL) 4 mutant dcl4-2. DCL genes have specialized functions in small RNA biogenesis for RNA interference-related processes. Results provide insight into the role of DCL4 in the trans-acting siRNA pathway.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, transformed count, 6 genotype/variation, 2 tissue sets

Platform:

GPL198

Series:

GSE3011

27 Samples

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(Submitter supplied) To study the function of Physcomitrella DCL4, a knockout plant line was created. Small RNAs from ~10-day old protonemata were obtained and sequenced using a SOLiD 2 instrument.

Organism:

Physcomitrium patens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9393

2 Samples

Download data: FA

(Submitter supplied) MicroRNAs (miRNAs) are emerging as essential, albeit poorly characterized, regulators of biological processes. The miRNA in gymnosperms is under-identified, which limits the progress of miRNA in gymnoperms. Using the high-throughput sequencing, a total of 87 conserved miRNAs were identified from Larix leptolepis. Eighteen novel miRNAs were discovered in our library, most of which were Larix-specific miRNAs.

Organism:

Larix kaempferi

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13980

1 Sample

Download data: TXT

(Submitter supplied) Endogenous 24nt short interfering RNAs (siRNAs) derived mostly from intergenic and repetitive genomic regions constitute a major class of endogenous small RNAs in Arabidopsis thaliana. Accumulation of A. thaliana 24nt siRNAs requires the Dicer family member DCL3, and clear homologs of DCL3 exist in both flowering and non-flowering plants. However, the absence of a conspicuous 24nt peak in the total RNA populations of several non-flowering plants has raised the question of whether this class of siRNAs might, in contrast to the ancient 21nt microRNAs (miRNAs) and 21-22nt trans-acting siRNAs (tasiRNAs), be an angiosperm-specific innovation. more...

Organism:

Physcomitrium patens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9391

6 Samples

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