GEO DataSets

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL19580

14 Samples

Download data: TXT

(Submitter supplied) The Arabidopsis thaliana multi-subunit RNA Polymerase IV largest subunit DeCL domain was functionally assessed with an NRPD1 DeCL domain deletion construct.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19580

8 Samples

Download data: TXT

(Submitter supplied) The Arabidopsis thaliana multi-subunit RNA Polymerase IV largest subunit DeCL domain was functionally assessed with an NRPD1 DeCL domain deletion construct.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19580

6 Samples

Download data: TXT

(Submitter supplied) DNA methylation is an epigenetic modification that plays critical roles in gene silencing, development, and the maintenance of genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and is targeted by 24 nt small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM)1. This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis and Pol-V, which functions in the downstream DNA methyltransferase targeting phase of the RdDM pathway to generate scaffold transcripts that recruit downstream RdDM factors1,2. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL13222

28 Samples

Download data: WIG

(Submitter supplied) DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase Pol IV transcribes target sequences to initiate 24-nt siRNA production and action. The Arabidopsis DTF1/SHH1 has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL11221 GPL13222

8 Samples

Download data: WIG

(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) 24 nucleotide siRNAs are central players in RNA-directed DNA methylation (RdDM), a process that establishes DNA methylation at transposable elements to ensure genome stability. The plant-specific RNA polymerase IV (Pol IV) is required for siRNA biogenesis and is thought to transcribe RdDM loci to produce primary transcripts that serve as precursors to siRNAs. Yet, no such transcripts have ever been reported. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL13222

36 Samples

Download data: WIG

(Submitter supplied) Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of dcl2/3/4/nrpd1 and nrpd1 mutants

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: BEDGRAPH

(Submitter supplied) Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of dcl2/3/4, dcl1/2/3/4 and WT

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13222

3 Samples

Download data: BEDGRAPH

(Submitter supplied) Using MethylC-Seq to provide single-base resolution of DNA methylation status in Col-0 and some RdDM mutants

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

23 Samples

Download data: WIG

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21785

56 Samples

Download data: BW

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17639 GPL13222

39 Samples

Download data: BW

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

40 Samples

Download data: TXT

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL21785 GPL13222

45 Samples

Download data: BW

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL13222 GPL17639

66 Samples

Download data: TXT

(Submitter supplied) The RNA-directed DNA methylation (RdDM) pathway in plants controls gene expression via cytosine DNA methylation. The ability to manipulate RdDM would shed light on the mechanisms and applications of DNA methylation to control gene expression. Here, we identified diverse RdDM proteins that are capable of targeting methylation and silencing in Arabidopsis when tethered to an artificial zinc finger (ZF-RdDM). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21785 GPL13222 GPL17639

246 Samples

Download data: BW, TXT

(Submitter supplied) To investigate the effect of AGO4 upon small RNA accumulation in Arabidopsis, we analyzed small RNA accumulation in ago4, ago4/ago6/ago9 triple mutant, stable transgenic lines expressing wild-type AGO4 and slicing-defective AGO4 in ago4 and ago4/ago6/ago9 background.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

21 Samples

Download data: TXT

(Submitter supplied) Small RNA sequences from Arabidopsis thaliana Col-0 inflorescence tissues of three biological replicates. The data were analyzed to identify non-templated nucleotides in Arabidopsis small RNAs.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17639

3 Samples

Download data: TXT

(Submitter supplied) In plants, the biogenesis of 24 nt and 23 nt small interfering RNAs (siRNAs) requires NUCLEAR RNA POLYMERASE IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3). We show that single-stranded M13 bacteriophage DNA can be used as a template for siRNA synthesis in vitro. Deep sequencing of RNAs produced from the in vitro reactions of Pol IV, RDR2 and DCL3 shows that Pol IV transcribes the DNA into first-strand RNAs which RDR2 then uses as templates to synthesize complementary second strands. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL19424

4 Samples

Download data: TXT