GEO DataSets

(Submitter supplied) To understand an effect of an ONSEN insertion for a gene network, a genome wide gene expression on the ONSEN inserted lines was analyzed by a microarray. The microarray analysis identified 6,520 and 7,262 significant different expressed genes (3/2 fold or 2/3 fold, FDR < 0.05) in 13-7 and 19-4 respectively under ABA stress.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL20796

24 Samples

Download data: TXT

(Submitter supplied) Identification of the newly insertied site of heat-activaed ONSEN transposon on Arabidopsis thaliana

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL14599

6 Samples

Download data: TXT, XLS

(Submitter supplied) Plants adapt to abiotic and biotic stresses by activating abscisic acid-mediated (ABA) abiotic stress-responsive and salicylic acid-(SA) or jasmonic acid-mediated (JA) biotic stress-responsive pathways, respectively. Although the abiotic stress-responsive pathway interacts antagonistically with the biotic stress-responsive pathways, the mechanisms that regulate these pathways remain largely unknown. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL7299

8 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana; Oryza sativa Japonica Group; Zea mays subsp. mays

Type:

Expression profiling by array

Platforms:

GPL18525 GPL18523 GPL17639

8 Samples

Download data: GTF

(Submitter supplied) Long intergenic noncoding RNAs (lincRNAs) are widespread in cellular organisms, however, the origins and functions of many lincRNAs remain to be explored. Transposable elements (TEs) are widely distributed in many eukaryotic genomes, and often account for large fractions of plant and animal genomes. By using strand-specific RNA sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified TE-associated lincRNAs (TE-lincRNAs). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

4 Samples

Download data: TXT

(Submitter supplied) Long intergenic noncoding RNAs (lincRNAs) are widespread in cellular organisms, however, the origins and functions of many lincRNAs remain to be explored. Transposable elements (TEs) are widely distributed in many eukaryotic genomes, and often account for large fractions of plant and animal genomes. By using strand-specific RNA sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified TE-associated lincRNAs (TE-lincRNAs). more...

Organism:

Zea mays subsp. mays; Arabidopsis thaliana; Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18525 GPL17639 GPL18523

4 Samples

Download data: GTF

(Submitter supplied) ATH1 GeneChip was used for gene expression analysis of wild-type plants and dor mutant under drought treatment (both the wild-type and dor plants were grown under normal watering conditions for 24 days and then stressed by completely depriving of irrigation for 10 days). Two biological repeat experiments were conducted and the raw data was analyzed applying Affymetrix GCOS software. Keywords: both the wild-type and dor plants were grown under normal watering conditions for 24 days and then stressed for 10 days

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

8 Samples

Download data: CEL

(Submitter supplied) Allantoin is a metabolic intermediate of purine catabolism that often accumulates in stressed plants. Recently, using Arabidopsis knockout mutants (aln) of ALLANTOINASE, we showed that this purine metabolite activates ABA production, thereby stimulating stress-related gene expression and enhancing seedling tolerance to abiotic stress. A detailed re-examination of the microarray data of an aln mutant (aln-1) not only confirmed increased expression of ABA-inducible genes, but also revealed altered expression of genes involved in jasmonic acid (JA) responses, likely under the control of MYC2, a master switch in the JA signaling pathway. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

4 Samples

Download data: CEL, TXT

(Submitter supplied) Purine catabolism is regarded as a housekeeping function that remobilizes nitrogen for plant growth and development. However, emerging evidence suggests that certain purine metabolites might contribute to stress protection of plants. Here, we show that in Arabidopsis, the intermediary metabolite allantoin plays a role in abiotic stress tolerance via activation of abscisic acid (ABA) metabolism. The aln loss-of-function of ALN, encoding allantoinase, results in increased allantoin accumulation, genome-wide up-regulation of stress-related genes, and enhanced tolerance to drought-shock and osmotic stress in aln mutant seedlings. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

4 Samples

Download data: CEL

(Submitter supplied) The main objective of this analysis was to investigate the methylome changes in Arabidopsis plants treated with drugs affecting DNA methylation.

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: TXT

(Submitter supplied) We report the application of a high-throughput sequencing approach that is specifically designed to analyze the active mobilome of eukaryotes after simultaneous inhibition of RNA polymerase II and/or DNA methylation in O. sativa japonica. We found that the simultaneous inhibition of Pol II and DNA-methylation activated the evolutionary young Houba-Retrotransposon in O. sativa suggesting a crucial role of Pol II in regulating retrotransposition in plants.

Organism:

Oryza sativa Japonica Group

Type:

Other

Platform:

GPL22703

4 Samples

Download data: BIGWIG

(Submitter supplied) Heat stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, which however is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. Loss of H1 caused activation of pericentromeric GYPSY elements upon heat treatment, despite that these elements remained highly methylated. more...

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL17639

25 Samples

Download data: TXT

(Submitter supplied) Improving plant stress response holds great agricultural potential. One promising, yet speculative, possibility is the formation of plant stress memory facilitating enhanced responses to recurring stress. One possibility is the involvement of environmentally-induced variation in reversible chromatin marks, such as DNA methylation, leading to the altered regulation of underlying genetic elements that promote enhanced stress tolerance. more...

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17639

29 Samples

Download data: BED, COV

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

Organism:

Arabidopsis thaliana; Arabidopsis lyrata subsp. lyrata

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20226 GPL17639

19 Samples

Download data

(Submitter supplied) Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. To identify heat stress induced genes, we performed RNA-sequencing of rosette leaves from mock-treated, heat-stressed and heat-stressed-recoved plants of both species.

Organism:

Arabidopsis lyrata subsp. lyrata; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20226 GPL17639

12 Samples

Download data: GFF, XLSX