GEO DataSets

(Submitter supplied) Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant species A. thaliana and A. arenosa. Here we report that reduced DNA methylation in met1-RNAi A. more...

Organism:

Arabidopsis thaliana; Arabidopsis suecica

Type:

Expression profiling by array

Platform:

GPL5680

1 Sample

Download data: GPR

(Submitter supplied) MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced in diverse species and control gene expression and epigenetic regulation. Although physiological and developmental roles of miRNAs and siRNAs have been extensively studied in plants and animals, expression diversity and evolution of miRNAs and siRNAs in closely related species are poorly understood. Here we report comprehensive analyses of miRNA expression and siRNA distribution in two closely related species (Arabidopsis thaliana and A. more...

Organism:

Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis suecica; Arabidopsis arenosa x Arabidopsis thaliana

Type:

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

5 related Platforms

58 Samples

Download data: FNA, QUAL, TXT

(Submitter supplied) This oligonucleotide array is produced from the Operon Version 1.0 Array-Ready Oligo set (AROS). The 70-mer oligo was designed from the 3'-end of 26,090 annotated genes. Every 70-mer oligo is spotted once on each slide.

Organism:

Arabidopsis thaliana

1 Series

1 Sample

Download data

(Submitter supplied) This oligonucleotide array is produced from the Operon Version 1.0 Array-Ready Oligo set (AROS). The 70-mer oligo was designed from the 3'-end of 26,090 annotated genes. Every 70-mer oligo is spotted once on each slide.

Organism:

Arabidopsis thaliana

1 Series

1 Sample

Download data

(Submitter supplied) 11199 probes were detected to be differentially expressed between leaves of Arabidopsis thaliana and Arabidopsis arenosa Protocol: This oligonucleotide array is produced from the Operon Version 1.0 Array-Ready Oligo set (AROS). The 70-mer oligo was designed from the 3'-end of 26,090 annotated genes. Every 70-mer oligo is spotted once on each slide.

Organism:

Arabidopsis thaliana

1 Series

1 Sample

Download data

(Submitter supplied) In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

3 Samples

Download data: TXT

(Submitter supplied) Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: WIG

(Submitter supplied) Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7143

6 Samples

Download data: PAIR

(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 high throughput sequencing

Platforms:

GPL7143 GPL13222

8 Samples

Download data: PAIR, WIG

(Submitter supplied) The 70-mer oligo was designed from the 3'-end of 26,090 annotated genes. Every 70-mer oligo is spotted once on each slide. Protocol: This oligonucleotide array is produced from the Operon Version 1.0 Array-Ready Oligo set (AROS). The 70-mer oligo was designed from the 3'-end of 26,090 annotated genes. Every 70-mer oligo is spotted once on each slide.

Organism:

Arabidopsis thaliana

3 Series

18 Samples

Download data

(Submitter supplied) Functional genomic states are maintained by reinforcing chromatin interactions that exclude the components of other states. Plant heterochromatin features methylation of histone H3 at lysine 9 (H3K9me) and extensive DNA methylation. However, DNA methylation is also catalyzed by a mostly euchromatic small RNA-directed pathway (RdDM) thought to seek H3K9me. How RdDM is excluded from H3K9me-rich heterochromatin is unclear. 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

Platforms:

GPL21785 GPL19580

62 Samples

Download data: BW, GFF

(Submitter supplied) Transcriptional profiling of Arabidopsis comparing wild type with vim1,2,3 triple mutant to investigate epigenetic function of VIM family genes

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

4 Samples

Download data: TXT

(Submitter supplied) DNA methylation is essential for silencing transposable elements and some genes in higher eukaryotes, implying that this modification must be tightly controlled. However, accidental changes in DNA methylation can be transmitted through mitosis, as in cancer, or meiosis, leading to epiallelic variation. Here, we demonstrate the existence of an efficient and faithful mechanism that protects against transgenerational loss of DNA methylation in the plant Arabidopsis. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9386

2 Samples

Download data

(Submitter supplied) RNA-directed DNA methylation (RdDM) in Arabidopsis thaliana depends on the synthesis of non-coding RNAs by nuclear RNA polymerase E (NRPE or Pol V) 1-3, but the mechanism by which Pol V is targeted is unknown. Here we show that genome-wide Pol V association with chromatin redundantly requires the SU(VAR)3-9 homologs, SUVH2 and SUVH9. These proteins resemble histone methyltransferases, however a crystal structure reveals that SUVH9 lacks a peptide-substrate binding cleft and lacks a properly formed S-Adenosyl methionine (SAM) binding pocket necessary for normal catalysis, consistent with a lack of methyltransferase activity for these proteins. 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

18 Samples

Download data: WIG

(Submitter supplied) We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis axe1-5 and met1-3 mutants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platforms:

GPL10977 GPL10978

24 Samples

Download data: CEL, TXT

(Submitter supplied) Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. more...

Organism:

Arabidopsis suecica; Arabidopsis arenosa x Arabidopsis thaliana; Arabidopsis thaliana; Arabidopsis arenosa

Type:

Expression profiling by high throughput sequencing

4 related Platforms

5 Samples

Download data: TXT

(Submitter supplied) Cytosine DNA methylation is important for transposon silencing and epigenetic regulation of endogenous genes. Using a single-chip tiling microarray with 35 bp resolution, we carried out the first unbiased mapping of DNA methylation in the entire genome of the flowering plant Arabidopsis thaliana.Pericentromeric heterochromatin, repetitive sequences and regions producing small interfering RNAs were heavily methylated. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by genome tiling array

Platform:

GPL1979

24 Samples

Download data: CEL

(Submitter supplied) Cytosine DNA methylation is important for transposon silencing and epigenetic regulation of endogenous genes. Using a single-chip tiling microarray with 35 bp resolution, we carried out the first unbiased mapping of DNA methylation in the entire genome of the flowering plant Arabidopsis thaliana.Pericentromeric heterochromatin, repetitive sequences and regions producing small interfering RNAs were heavily methylated. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array; Methylation profiling by array

Platforms:

GPL1979 GPL1980

18 Samples

Download data: CEL

(Submitter supplied) Heterochromatin is an inert region in the genome and composed of mainly remnants of transposons and repetitive elements. In Arabidopsis, the major heterchromatin regions are present at around centromeres (pericentromeric regions) and at a region on the short arm of chromosome 4 (heterochromatin knob). Histones and DNAs in heterochromatin have characteristic features with abundant H3H9me2 and cytosine methylation, respectively. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platforms:

GPL10977 GPL10978

12 Samples

Download data: CEL, TXT

(Submitter supplied) Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known.  Here we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of siRNA-targeted sequences.  Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences.  Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements.  Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9302

4 Samples

Download data: GFF, TXT