GEO DataSets

(Submitter supplied) Genomic DNA of COl-0 and Van-0 were labeled using Bioprime randon labeling kit. Labelled products were hybridized to AtSNPtile1 at a total amount of 6ug, 9ug, 12ug, 15ug, and 18ug. This experiment is to test whether the overall target amount affect the log allele intensity ratio.

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL8655

10 Samples

Download data: CEL

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

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL8655

43 Samples

Download data: CEL

(Submitter supplied) Col-0 and Van-0 total RNA were mixed at 1:1. Total RNA also extracted from F1 hybrid samples from Col x Van and Van x Col. PolyA RNA were purified and double-strand cDNA were synthesized, followed by bioprime random labeling. A total of 16ug labelled products were hybridized to AtSNPtile1. cis regulatory effect was identified as allele specific expression in F1 hybrids. Composite trans regulatory effect was detected as deviation between parental expression and F1 hybrids expression.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array; Expression profiling by SNP array

Platform:

GPL8655

12 Samples

Download data: CEL

(Submitter supplied) Genomic DNA of Col-0 and Van-0 were mixed at 1:1 and labeled using Bioprime randon labeling kit. A total of 16ug labelled products were hybridized to AtSNPtile1. Used as the reference of equal allele expression.

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL8655

4 Samples

Download data: CEL

(Submitter supplied) Genomic DNA of Col-0, Van-0 and their mixture at different proportion were labeled using Bioprime randon labeling kit. A total of 16ug labelled products were hybridized to AtSNPtile1. This experiment is to test whether the log allele intensity ratio efficiently detects the allelic variation within targets.

Organism:

Arabidopsis thaliana

Type:

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

Platform:

GPL8655

17 Samples

Download data: CEL

(Submitter supplied) Gene expression of Col, Van and reciprocal hybrids using double-stranded cDNA followed by bioprime random labeling, and hybridization to AtTILE1 forward array. Study on gene expression polymorphism between arabidopsis thaliana accessions Col-0 and Van-0. Study on the inheritance of gene expression in reciprocal hybrids. Keywords: cDNA hybridization

Organism:

Arabidopsis thaliana

Type:

Expression profiling by genome tiling array

Platform:

GPL1979

16 Samples

Download data: CEL

(Submitter supplied) CG Methylation of Col, Van and reciprocal hybrids using HpaII and MspI digestion followed by bioprime random labeling, and hybridization to AtTILE1 forward array. Study on constitutive and ploymorphic CG methylation between arabidopsis thaliana accessions Col-0 and Van-0. Study on the inheritance of CG methylation in reciprocal hybrids. Keywords: genomic hybridization

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by genome tiling array

Platform:

GPL1979

32 Samples

Download data: CEL

(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 x Arabidopsis lyrata; Arabidopsis thaliana; Arabidopsis lyrata

Type:

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

Platform:

GPL13483

24 Samples

Download data: CEL

(Submitter supplied) eQTL mapping in a F1 diversity panel generated from 111 A.thaliana natural accessions

Organism:

Arabidopsis thaliana

Type:

Expression profiling by SNP array; Expression profiling by genome tiling array

Platform:

GPL10855

57 Samples

Download data: CEL

(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) 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) 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) We estimate Allele-specific expression in F1 hybrids between Col-0 and Cvi-0 accessions grown under well watered and drought stress conditions. We found that ~90% of the genes showed similar ASE under both stresses. Trans-effects were less robust across environments, however its effect was milder compared to cis-variation.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

11 Samples

Download data: TXT

(Submitter supplied) Affymetrix expression analysis was used to validate the role of NPR1 in SA mediated transcription.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

8 Samples

Download data: CEL, CHP

(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