GEO DataSets

(Submitter supplied) Pack-TYPE transposons are a unique class of potentially mobile non-autonomous elements that can capture, merge and relocate fragments of chromosomal DNA. It has been postulated that their activity accelerates the evolution of host genes. However, this important presumption is based only on the sequences of currently inactive Pack-TYPE transposons and the acquisition of chromosomal DNA has not been recorded in real time. more...

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL19580

70 Samples

Download data: TXT

(Submitter supplied) Epigenomic mapping of DNA methylation polymorphisms segregating within an epigenetic Recombinant Inbred Line population resultant from crossing the wild-type Col-0 and DNA maintenance methyltransferase mutant, met1-3, parental lines. Each line within the epiRIL population was self-fertilized for 7 generations, 10 individual F7 plants were then bulk harvested to create the F8 generation. Here, data files for three DNA methylation profiled epiRIL lines (epi01, epi12, epi28) are deposited. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by genome tiling array

Platform:

GPL10977

5 Samples

Download data: BAR, CEL, TXT

(Submitter supplied) The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wt Col ecotype of Arabidopsis thaliana. In plants mutant for the SWI/SNF2 histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Activated TEs go through additional non-canonical forms of RdDM. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13222 GPL11221

19 Samples

Download data: TXT

(Submitter supplied) The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wild-type reference strains of Arabidopsis thaliana. In plants mutant for the SWI/SNF histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Transcriptionally activated TEs go through additional non-canonical forms of RdDM that are dependent on RNA Polymerase II expression. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19580

21 Samples

Download data: TSV, TXT

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data

(Submitter supplied) Purpose: The goal of this study is to compare the whole genome bisulfite sequencing of inflorescences infected with tobacco ratle virus (TRV) to mock inoculated inflorescences (negative controls), in Arabidopsis plants Methods: Inflorescences of systemically TRV infected or mock-inoculated plants were collected from more than 40 independent Arabidopsis plants, at 14 days post-inoculation (dpi). TRV and mock mRNA profiles were generated by deep sequencing by Illumina HiSeq 2000. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: TXT, XLS, XLSX

(Submitter supplied) Purpose: The goal of this study is to compare the transcriptome profilling (RNA-seq) of inflorescences infected with tobacco ratle virus (TRV) to mock inoculated inflorescences (negative controls), in Arabidopsis plants Methods: Inflorescences of systemically TRV infected or mock-inoculated plants were collected from more than 40 independent Arabidopsis plants, at 14 days post-inoculation (dpi). TRV and mock mRNA profiles were generated by deep sequencing by Illumina HiSeq 2000. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

2 Samples

Download data: TXT

(Submitter supplied) We conducted whole-genome bisulfite sequencing (WGBS) of Arabidopsis thaliana mutation accumulation (MA) lines under different temperature treatments over sucessive generations, and then we identified the global methylation in each MA line. Our result showed taht DNA methylation was observed more frequently at DNA mutation sites, indicating its contribution to the mutation process at elevated temperatures.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17639

15 Samples

Download data: TXT

(Submitter supplied) We sequenced mRNA from leaves of Arabidopsis under the control (CK), warming (W) and heat (H) treatments using the Illumina HiSeq4000 platform to generate the transcriptome dynamics that may serve as a gene expression profile blueprint for different response patterns under prolonged warming versus rapid-onset heat stress in Arabidopsis.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

9 Samples

Download data: TXT

(Submitter supplied) 9,216 single-spotted cDNA clones from embryo, seed coat, flower and whole pod libraries Keywords = soybean

Organism:

Glycine max

5 Series

131 Samples

Download data

(Submitter supplied) Ecotype-specific differences in genome methylation were assayed in Arabidopsis Col and Ler variations using genomic tiling microarrays. Comparative genome hybridization was also performed so that the contribution of ecotype-specific amplifications and deletions could be estimated and integrated into the analysis of differential DNA methylation. Keywords: methylation analysis and comparative genome hybridization

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Methylation profiling by array

Platform:

GPL5116

3 Samples

Download data

(Submitter supplied) Background: The majority of plant transposable elements (TEs) are found in a silenced state that is epigenetically propagated by the maintenance of symmetrical DNA methylation. TE methylation is established and reinforced by a mechanism of RNA-dependent DNA methylation, which is dependent on transcription of the PolIV RNA polymerase. Recently, a pathway has been described that initiates de novo DNA methylation dependent on components of the RNAi post-transcriptional silencing pathway, independent of PolIV. more...

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11221

4 Samples

Download data: TXT

(Submitter supplied) The CMT2 and RNA-directed DNA methylation (RdDM) pathways have been proposed to separately maintain CHH methylation in specific regions of the Arabidopsis thaliana genome. Here, we show that dysfunction of the chromatin remodeller DDM1 causes hundreds of genomic regions to switch from CMT2-dependency to RdDM-dependency in DNA methylation. These converted loci are enriched at the edge regions of long transposable elements (TEs). 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; Genome variation profiling by high throughput sequencing

Platforms:

GPL23157 GPL17639

42 Samples

Download data: BW, TDF, TSV, WIG

(Submitter supplied) Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation, and is implicated in the pathology of cancer and ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels of eccDNA containing the copper resistance gene CUP1. Transcription of CUP1 causes CUP1 eccDNA accumulation, which occurs in the absence of phenotypic selection. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

30 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana; Arabidopsis lyrata

Type:

Expression profiling by genome tiling array; Expression profiling by high throughput sequencing

Platforms:

GPL11022 GPL10977

7 Samples

Download data: BED, CEL

(Submitter supplied) A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL10977

3 Samples

Download data: CEL, TXT

(Submitter supplied) Transposable elements (TEs) are often the primary determinant of genome size differences among eukaryotes. In plants, the proliferation of TEs is countered through epigenetic silencing mechanisms that prevent transposition. Recent studies using the model plant Arabidopsis thaliana have revealed that methylated TE insertions are often associated with reduced expression of nearby genes, and these insertions may be subject to purifying selection due to their effect on nearby genes. more...

Organism:

Arabidopsis lyrata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11022

4 Samples

Download data: BED

(Submitter supplied) Here we present the first whole-genome assemblies of Arabidopsis thaliana strains since the release of the 125 Mb reference genome sequence a decade ago. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone.

Organism:

Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9302

8 Samples

Download data: FASTQ, TXT

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

83 Samples

Download data: BEDGRAPH, TXT, WIG