GEO DataSets

(Submitter supplied) The Arabidopsis genome contains a highly complex and abundant population of small RNAs, and many of the endogenous siRNAs are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. By analyzing an rdr2 loss-of-function mutant using two different parallel sequencing technologies, MPSS and 454, we characterized the complement of miRNAs expressed in Arabidopsis inflorescence to considerable depth. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Expression profiling by MPSS

Platforms:

GPL2675 GPL4011

6 Samples

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(Submitter supplied) Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9361

3 Samples

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(Submitter supplied) Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of the Arabidopsis RDR2 gene. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL7071

2 Samples

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(Submitter supplied) Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9141

2 Samples

Download data: TXT

(Submitter supplied) To identify novel miRNA and NAT-siRNAs that are associated with abiotic stresses in Arabidopsis, we generated small RNA sequences from adult Arabidopsis plants under control and under dought, salt, and cold stress treatments. Over 23 million reads were generated.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9062

4 Samples

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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL9062 GPL13222 GPL198

26 Samples

Download data: CEL, TXT

(Submitter supplied) Utilizing whole-genome sRNA-seq to analyze transposon derived siRNAs in DNA methylation mutants, and RNAi mutants, compared to wildtype.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

9 Samples

Download data: TXT

(Submitter supplied) Utilizing whole-genome BIS-seq to analyze transposon methylation in DNA methylation mutants, and RNAi mutants, compared to wildtype.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9062

5 Samples

Download data: TXT

(Submitter supplied) Utilizing whole-genome Parallele Analysis of RNA Ends (PARE)-seq to analyze the degradome to assess miRNA-binding of transposons in DNA methylation mutants, and RNAi mutants, compared to wildtype.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) Utilizing Affymetrix ATH1 microarrays to analyze transposon expression in DNA methylation mutants, and RNAi mutants, compared to wildtype.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

8 Samples

Download data: CEL

(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) We used a two-component transgene system to study the RNA-dependent DNA methylation (RdDM) and transcriptional gene silencing (TGS) in Arabidopsis. By profiling the small RNA population in  mutants defected in RdDM or RNA polymerase II-transcribed trigger for generating silencing siRNA, we investigated how repetitive loci such as tandem repeats were regulated transcriptionally through the action of RNA polymerase IV.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

6 Samples

Download data: TXT

(Submitter supplied) In plants, RNA polymerase II (Pol II) transcription of inverted DNA repeats produces hairpin RNAs that are processed by several DICER-LIKE enzymes into siRNAs that are 21-24-nt in length. When targeted to transcriptional regulatory regions, the 24-nt size class can induce RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS). In a forward genetic screen to identify mutants defective in RdDM of a target enhancer leading to TGS of a downstream GFP reporter gene in Arabidopsis thaliana, we recovered a structurally mutated silencer locus, named SΔ35S, in which the 35S promoter driving transcription of an inverted repeat of target enhancer sequences had been specifically deleted. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

1 Sample

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) 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