GEO DataSets

(Submitter supplied) We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. more...

Organism:

Arabidopsis thaliana x Arabidopsis halleri; Arabidopsis thaliana x Arabidopsis lyrata

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21749 GPL21748

18 Samples

Download data: 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) 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) Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL16226

207 Samples

Download data: XYS

(Submitter supplied) To understand the gene network that controls plant tolerance to cold stress, we carried out a near full genome transcript expression profiling in Arabidopsis using Affymetrix GeneChips that contain approximately 24,000 genes. For microarray analysis, Arabidopsis seedlings were cold treated at 0 C for 0 h, 3 h, 6 h, and 24 h. A total of 939 genes were statistically determined to be cold-regulated with 655 being up-regulated and 284 down-regulated. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Dataset:

GDS1502

Platform:

GPL198

16 Samples

Download data: CEL, EXP

Analysis of inducer of CBF expression 1 (ICE1) mutant seedlings exposed to 0 C for up to 24 hours. Transcription factor ICE1 is required for chilling/freezing tolerance. Results identify a major role for ICE1 in controlling the expression of many cold-responsive genes during cold stress.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array, count, 2 genotype/variation, 2 protocol, 4 time sets

Platform:

GPL198

Series:

GSE3326

16 Samples

Download data: CEL, EXP

(Submitter supplied) au06-03_tsn_fj - tsn_fj - Root transcriptome of the tsn1 tsn2 double mutant - Comparison of a tsn1 tsn2 double mutant line (A10.9.3- or A13.3.11-) and an isogenic line complemented by TSN2 (A10.9.5) or TSN1 (A13.3.2) Keywords: gene knock in (transgenic),gene knock out

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL6403

12 Samples

Download data: GPR

(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) Transcriptional profiling of arsenic-induced toxicity and tolerance in Arabidopsis plants of different ecotypes Arsenic (As) is a toxic metalloid found ubiquitously in the environment and has widely been known as an acute poison and carcinogen. As toxicity is a major factor leading to root growth inhibition in plants. However, the molecular mechanisms of plants in response to As has not been extensively characterized. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

15 Samples

Download data: CEL

(Submitter supplied) Five members of the Arabidopsis thaliana NF-YA gene family are strongly induced by several stress conditions via transcriptional and miR169-related posttranscriptional mechanisms. These transcription factors participate in gene regulation via two different mechanisms, one depending on binding to the CCAAT-box in the promoter of regulated genes and the other, independent of the CCAAT-box, in which NF-YA prevents the interaction of the NF-YB/YC heterodimer with transcription factors.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL7725

24 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of rossette leaves comparing wild type (Col-0) and the mutant (hsi2-5) under no drought or simulated drought stress.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

10 Samples

Download data: TXT

(Submitter supplied) We sequenced mRNA of WT, p35S:AtBBD1 (OX) and atbbd1 (KO) plants. Plants were grown in soil for three weeks at 23 ℃ with 60% relative humidity. mRNA was isolated 6 hours after threating with 20% PEG.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

4 Samples

Download data: XLSX

(Submitter supplied) Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4°C). Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by SAGE

Platform:

GPL25

5 Samples

Download data

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

Organism:

Homo sapiens; Pan troglodytes

Type:

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

Platform:

GPL27803

33 Samples

Download data

(Submitter supplied) Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27803

25 Samples

Download data: TXT

(Submitter supplied) Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27803

8 Samples

Download data: TXT