GEO DataSets

(Submitter supplied) We anlalyzed gene expession using an Arabidopsis 26K 70mer spotted microarray Differential expression was tested using two ANOVA models: 1) a per-gene variance ANOVA, and 2) a common variance ANOVA

Organism:

Arabidopsis thaliana; Brassica napus; Brassica sp.; Brassica oleracea; Brassica rapa

Type:

Expression profiling by array

Platform:

GPL7536

7 Samples

Download data: GPR

(Submitter supplied) Analysis of the different gene expression profiles of natural and resynthesized Brassica polyploids with Illumina deep sequencing technology could help to improve our knowledge of polyploid genome evolution. We obtained approximately 6 million sequence tags per sample,and 6018254, 5930726, 6022170, 5950123, 5991210, 5798939, 5823113, 5772449,5858527 and 5657697 clean tags were obtained in libraries of B. more...

Organism:

Brassica rapa; Brassica juncea; Brassica napus; Brassica nigra; Brassica oleracea; Brassica carinata

Type:

Expression profiling by high throughput sequencing

6 related Platforms

10 Samples

Download data: TXT

(Submitter supplied) Transcription profiling of Brassica rapa, Brassica oleracea and Brassica napus I and II The nuclear genomes of the resynthesised B. napus lines should be identical but, as one (B. napus I) involved a cross of B. oleracea onto B. rapa, and the other (B. napus II) involved a cross of B rapa onto B. oleracea, they differ in cytoplasm, and hence contain different chloroplast and mitochondrial genomes.

Organism:

Brassica rapa; Brassica napus; Brassica; Brassica oleracea

Type:

Expression profiling by array

Platform:

GPL8513

16 Samples

Download data: TXT

(Submitter supplied) Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both natural and resynthesized lines of polyploid Brassica napus, along with the progenitors B. more...

Organism:

Brassica napus; Brassica oleracea; Brassica rapa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28300 GPL32188 GPL29911

24 Samples

Download data: TXT

(Submitter supplied) 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

1 Series

1 Sample

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(Submitter supplied) 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

1 Series

1 Sample

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(Submitter supplied) 11199 probes were detected to be differentially expressed between leaves of Arabidopsis thaliana and Arabidopsis arenosa 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

1 Series

1 Sample

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(Submitter supplied) Genome-wide analysis of gene expression has documented differential gene expression between closely related species in plants or animals and nonadditive gene expression in hybrids and allopolyploids compared to the parents. In Arabidopsis, 15-43% of genes are expressed differently between the related species, A. thaliana and A. arenosa, and the majority of them are nonadditvely expressed (differently from mid-parent value) in allotetraploids relative to the parents. more...

Organism:

Arabidopsis thaliana; Arabidopsis

Type:

Expression profiling by array

Platform:

GPL11298

8 Samples

Download data: GPR

(Submitter supplied) The effect of the number of pods on the main inflorescence (NPMIs) on seed yield in Brassica napus plants grown at high density is a topic of great economic and scientific interest. We sought to identify patterns of gene expression that are associated with inflorescence and PMI differentiation and development in Brassica napus.

Organism:

Brassica rapa; Brassica napus; Brassica oleracea

Type:

Expression profiling by array

Platform:

GPL18717

12 Samples

Download data: TXT

(Submitter supplied) Serial Analysis of Gene Expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in a non-model organism was demonstrated for the highly complex, neither fully sequenced nor annotated genome of B. napus by applying a tag-to-gene matching strategy based on Brassica ESTs and the annotated proteome of the closely related model crucifer A. more...

Organism:

Brassica napus

Type:

Expression profiling by SAGE

Platform:

GPL8033

2 Samples

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(Submitter supplied) Arabidopsis is a suitable system for testing the hypothesis that duplicate genes accelerate evolution of expression diversity among species diverged from shared whole genome duplications (WGDs) and recurrent events of WGD. In Arabidopsis, at least 9 species split after WGD of the common ancestor and new allotetraploids were formed in nature and can be resynthesized between closely related species. Using genomic and gene expression microarrays, we detected WGD duplicate and single-copy genes preserved in A.thaliana and A.arenosa in addition to change of gene expression levels among those species. more...

Organism:

Arabidopsis suecica; Arabidopsis thaliana; Arabidopsis arenosa

Type:

Expression profiling by array

Platform:

GPL7498

1 Sample

Download data: GPR

(Submitter supplied) Polyploidy or whole genome duplication (WGD) provides raw genetic materials for sequence and expression evolution of duplicate genes. However, the mode and tempo of expression divergence between WGD duplicate genes in closely relates species and recurrent allopolyploids are poorly understood. Arabidopsis is a suitable system for testing the hypothesis that duplicate genes increase expression diversity and regulatory networks. more...

Organism:

Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis suecica

Type:

Expression profiling by array; Genome variation profiling by array

5 related Platforms

5 Samples

Download data: GPR, TAR

(Submitter supplied) MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced in diverse species and control gene expression and epigenetic regulation. Although physiological and developmental roles of miRNAs and siRNAs have been extensively studied in plants and animals, expression diversity and evolution of miRNAs and siRNAs in closely related species are poorly understood. Here we report comprehensive analyses of miRNA expression and siRNA distribution in two closely related species (Arabidopsis thaliana and A. more...

Organism:

Arabidopsis arenosa x Arabidopsis thaliana; Arabidopsis thaliana; Arabidopsis arenosa; Arabidopsis suecica

Type:

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

5 related Platforms

58 Samples

Download data: FNA, QUAL, TXT

(Submitter supplied) We have set up an Arabidopsis gain-of-function mutant pool overexpressing rapeseed full-length cDNAs under the control of chemically inducible promoter. This data comes from one mutant line

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: DIFF

(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) We explored the transcriptomic changes of synthetic Brassica allohexaploid by comparing to its parents using a high-throughput RNA-Seq method. A total of 35644409 sequence reads were generated, and 32642 genes were aligned from the data. There were 29260, 29060 and 29697 genes identified in Brassica rapa, Brassica carinata, and Brassica allohexaploid, respectively. We screened differentially expressed genes (DEGs) by a standard of two-fold or greater change in expression and false discovery rate (FDR) no more than 0.001. more...

Organism:

Brassica rapa; Brassica carinata; Brassica carinata x Brassica rapa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17053 GPL16443 GPL16440

3 Samples

Download data: TXT

(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 thaliana; Arabidopsis arenosa; Arabidopsis suecica; Arabidopsis arenosa x Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

4 related Platforms

5 Samples

Download data: TXT