GEO DataSets

(Submitter supplied) We compared the expression between inter-specific hybrids (A. thaliana-A. lyrata, A. thaliana-A. halleri) and mid parent values of their parental lines.

Organism:

Arabidopsis thaliana; Arabidopsis lyrata subsp. lyrata; Arabidopsis thaliana x Arabidopsis lyrata; Arabidopsis thaliana x Arabidopsis halleri subsp. gemmifera; Arabidopsis halleri subsp. gemmifera

Type:

Expression profiling by array

Platform:

GPL198

10 Samples

Download data: CEL, CHP

(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) High throughput Illumina sequencing of poly-A selected RNA from Arabidopsis Col and Ler reciprocal F1 hybrid embryo and endosperm tissue isolated at 6-7 days after pollination to identify imprinted genes.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

4 Samples

Download data: SAM

(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) We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1).

Organism:

Arabidopsis thaliana; Arabidopsis lyrata; Arabidopsis thaliana x Arabidopsis lyrata

Type:

Expression profiling by SNP array; Genome variation profiling by SNP array

Platform:

GPL13483

24 Samples

Download data: CEL

(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) a2e_heterosis - h3k4me2_col_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in Col

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10772

8 Samples

Download data: GPR

(Submitter supplied) a2e_heterosis - h3k4me2_colxc24_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in ColxC24 hybrids

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10772

8 Samples

Download data: GPR

(Submitter supplied) a2e_heterosis - h3k27me3_col(c24) - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in Col

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10920 GPL10919

8 Samples

Download data: PAIR

(Submitter supplied) a2e_heterosis - h3k27me3_c24 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in C24

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10919 GPL10920

7 Samples

Download data: PAIR

(Submitter supplied) a2e_heterosis - h3k27me3_colxc24 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in ColxC24 hybrids

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10920 GPL10919

8 Samples

Download data: PAIR

(Submitter supplied) a2e_heterosis - h3k4me2_col(cvi) - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in Col-0

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10919 GPL10920

8 Samples

Download data: PAIR

(Submitter supplied) a2e_heterosis - h3k4me2_cvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in Cvi

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10920 GPL10919

8 Samples

Download data: PAIR

(Submitter supplied) a2e_heterosis - h3k4me2_colxcvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K4me2 profiling in ColxCvi hybrids

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10919 GPL10920

8 Samples

Download data: PAIR

(Submitter supplied) a2e_heterosis - h3k27me3_col(cvi) - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in Col

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10920 GPL10919

7 Samples

Download data: PAIR

(Submitter supplied) a2e_heterosis - h3k27me3_cvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in Cvi seedlings

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10919 GPL10920

8 Samples

Download data: PAIR

(Submitter supplied) a2e_heterosis - h3k27me3_colxcvi - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - H3K27me3 profiling in ColxCvi hybrids

Organism:

Arabidopsis thaliana

Type:

Genome variation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10919 GPL10920

8 Samples

Download data: PAIR