GEO DataSets

(Submitter supplied) Numerous gene expression datasets from diverse tissue samples from the plant variety Arabidopsis thaliana have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of all of the publicly available Arabidopsis datasets to identify Boolean logical relationships between genes. more...

Organism:

Arabidopsis thaliana; Arabidopsis halleri; Arabidopsis; Brassica napus; Arabidopsis lyrata subsp. petraea

Type:

Expression profiling by array; Third-party reanalysis

Download data: TXT

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

Organism:

Arabidopsis thaliana; Arabidopsis lyrata

Type:

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

Platforms:

GPL13222 GPL19447 GPL17639

60 Samples

Download data: TXT

(Submitter supplied) Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24 nt small RNAs are reduced in TEs and enriched in genes compared to the embryo. more...

Organism:

Arabidopsis lyrata; Arabidopsis thaliana

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19447 GPL13222

49 Samples

Download data: BED, FA, TXT

(Submitter supplied) Gene copy number variation (CNV) is a form of genetic polymorphism that contributes significantly to genome size and function but remains poorly characterized due to technological limitations. Inter-specific comparisons of CNVs in recently diverged plant species are crucial to uncover selection patterns underlying adaptation of a species to stressful environments. Especially given that gene amplifications have long been implicated in emergence of species-specific traits, we conducted a genome-wide survey to identify species-specific gene copy number expansions and deletions in the model extremophile species - Arabidopsis halleri that has diverged in evolutionarily recent time from Arabidopsis thaliana. more...

Organism:

Arabidopsis lyrata; Arabidopsis halleri; Arabidopsis thaliana

Type:

Genome variation profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) Using A. lyratamicroarray platform the transcriptomic response of shoot tissues was characterized at two different time points- 3h and 27h after 250mM and 500mM of NaCl treatments.

Organism:

Arabidopsis lyrata; Arabidopsis lyrata subsp. lyrata

Type:

Expression profiling by array

Platform:

GPL21706

18 Samples

Download data: TXT

(Submitter supplied) By using A. lyrata microarray platform, the transcriptomic response of shoot tissues was characterized at 4h and 8h post exposure to UV-B radiation at wavelength of 300 nm..

Organism:

Arabidopsis lyrata; Arabidopsis lyrata subsp. lyrata

Type:

Expression profiling by array

Platform:

GPL21706

12 Samples

Download data: TXT

(Submitter supplied) Using A. lyrata microarray platform the transcriptomic response of shoot tissues was characterized at two different time points- 8d and 11d after withdrawal of regular water application..

Organism:

Arabidopsis lyrata; Arabidopsis lyrata subsp. lyrata

Type:

Expression profiling by array

Platform:

GPL21706

12 Samples

Download data: TXT

(Submitter supplied) Using A. lyrata microarray platform the root and flower bud specific gene expression was characterized.

Organism:

Arabidopsis lyrata; Arabidopsis lyrata subsp. lyrata

Type:

Expression profiling by array

Platform:

GPL21706

8 Samples

Download data: TXT

(Submitter supplied) In plants, imprinted gene expression occurs in endosperm seed tissue and can be associated with differential DNA methylation between maternal and paternal alleles. Imprinting is theorized to have been selected for because of conflict between parental genomes in offspring, but most studies of imprinting have been conducted in Arabidopsis thaliana, an inbred primarily self-fertilizing species that should have limited parental conflict. more...

Organism:

Arabidopsis lyrata

Type:

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

Platform:

GPL19447

38 Samples

Download data: FA, GTF, TXT

(Submitter supplied) In plants, CG DNA methylation is prevalent in the transcribed regions of constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum, has lost gbM from its genome, the first known instance for a flowering plant. Of all known DNA methyltransferases, only CHROMOMETHYLTRANSFERASE 3 (CMT3) is missing from E. more...

Organism:

Brassica oleracea; Eutrema salsugineum; Brassica rapa; Arabidopsis lyrata; Arabidopsis thaliana; Capsella rubella

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

10 related Platforms

44 Samples

Download data: BED, TSV

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

Organism:

Arabidopsis lyrata subsp. lyrata; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20226 GPL17639

19 Samples

Download data

(Submitter supplied) Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. more...

Organism:

Arabidopsis thaliana; Arabidopsis lyrata

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19447 GPL20223

3 Samples

Download data: CSV

(Submitter supplied) Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. more...

Organism:

Arabidopsis lyrata; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13222 GPL19447

9 Samples

Download data: CSV

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

Organism:

Arabidopsis lyrata; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13222 GPL20223 GPL19447

12 Samples

Download data: CSV

(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. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. more...

Organism:

Arabidopsis lyrata subsp. lyrata; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20226 GPL17639

7 Samples

Download data: GFF, XLSX

(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 thaliana; Arabidopsis lyrata subsp. lyrata

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20226 GPL17639

12 Samples

Download data: GFF, XLSX

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

Organism:

Arabidopsis thaliana; Arabis alpina; Arabidopsis lyrata

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL11221 GPL16940 GPL18238

30 Samples

Download data

(Submitter supplied) Chromatin, DNA and RNA were extracted from young A. alpina Pajares primary stem leaves. Chromatin and DNA methylation immunoprecipitation experiments were performed using commercially available antibodies and analyzed by Illumina sequencing (ChIP-seq and MeDIP-seq). Transcriptome data were generated by RNA-seq.

Organism:

Arabidopsis lyrata

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL16940

12 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Self-pollen rejection in the Brassicaceae is determined by the diploid genotype of the pollen-producing plant, and it has long been known that the alleles show a dominance hierarchy. How this hierarchy is controlled and evolves has been a classical puzzle since the pre-molecular days of genetics. Here, we uncover the system of at least 17 small RNA (sRNA) producing loci and their multiple target sites that collectively control the dominance hierarchy among alleles of a self-incompatible Arabidopsis species. more...

Organism:

Arabidopsis halleri; Arabidopsis lyrata

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18640 GPL18638 GPL18639

12 Samples

Download data: FA, TXT

(Submitter supplied) we demonstrate that 3' end tag profiling vi deep sequencing is a powerful approach to mesure allele-specific expression genome-wide.

Organism:

Arabidopsis thaliana; Arabidopsis lyrata; Arabidopsis thaliana x Arabidopsis lyrata

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platforms:

GPL13338 GPL13337 GPL10142

3 Samples

Download data: FA, TXT