E-GEOD-6203
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA100693
PROVIDER: E-GEOD-6203 | ExpressionAtlas | 2015-06-01
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:We have used a strain of Tobacco etch potyvirus (TEV) experimentally adapted to Arabidopsis thaliana ecotype Ler-0 to infect a set of seven A. thaliana plant ecotypes(Col-0, Ei-2, Wt-1, ler-0, Oy-0, St-0). Each ecotype was inoculated with the same amount of the virus. Using commercial microarrays containing probes Arabidopsis thaliana ssp. Col-0 plant transcripts, we explored the effect of viral infection in the plant transcriptome
2012-07-04 | GSE37269 | GEO
Project description:The aim of this study was to analyze the impact of autotetraploidy on gene expression in Arabidopsis thaliana by comparing diploid versus tetraploid transcriptomes. In particular, this included the comparison of the transcriptome of different tetraploid A. thaliana ecotypes (Col-0 vs. Ler-0). The study was extended to address further aspects. One was the comparison of the transcriptomes in subsequent generations. This intended to obtain information on the genome wide stability of autotetraploid gene expression. Another line of work compared the transcriptomes of different diploid vs. tetraploid tissues. This aimed to investigate whether particular gene groups are specifically affected during the development of A. thaliana autotetraploids. Samples 1-8: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 9-12: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 13-24: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Col-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 25-32: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of diploid vs. tetraploid Ler-0 leaves (6th - 8th). The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 33-36: Arabidopsis thaliana Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Ler-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Ler-0 lines. Samples 37-40: Arabidopsis thaliana Col-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid vs. tetraploid Col-0 seedlings from the second (F2) and third (F3) generation after induction, respectively. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 lines. Samples 41-44: Arabidopsis thaliana Col-0/Ler-0 diploid transcriptome. Transcriptional profiling and comparison of diploid Col-0 vs. diploid Ler-0 seedlings. The experiment was carried out with pedigree of esrablished lines. Samples 45-48: Arabidopsis thaliana Col-0/Ler-0 tetraploid transcriptome. Transcriptional profiling and comparison of tetraploid Col-0 vs tetraploid Ler-0 seedlings. The experiment was carried out with pedigree of independently generated and assessed tetraploid Col-0 and Ler-0 lines.
2010-05-01 | GSE18482 | GEO
Project description: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. In this study, Arabidopsis ecotypes that are As-tolerant (Col-0) and -sensitive (Ws-2) were used to conduct a transcriptome analysis of the response to As (V). To begin elucidating the molecular basis of As toxicity and tolerance in Arabidopsis, seedlings of Col-0 and Ws-2 were subjected to As treatment. The root elongation rate of Col-0 was significantly higher than that of Ws-2 when exposed to As. The tolerant ecotype (Col-0) demonstrated lower accumulation of As when compared to the responses observed in the sensitive Ws-2. Subsequently, the effect of As exposure on genome-wide gene expression was examined in the two ecotypes. Comparative analysis of microarray data identified groups of genes with common and specific responses to As between Col-0 and Ws-2. The genes related to heat responses and oxidative stresses belonged to common responses, indicating conserved stress-associated changes across two ecotypes. The majority of specific responsive genes were those encoding heat shock proteins, heat shock factors, ubiquitin and transporters. The data suggested that metal transport and maintenance of protein structure may be important mechanisms for toxicity and tolerance to As. This study presents comprehensive surveys of global transcriptional regulation and identifies stress- and tolerance-associated genes in response to As.
2011-11-26 | GSE31977 | GEO
Project description:Gene expression Arabidopsis 24h cold-treated, 4c, seedlings to identify a *gold-standard* set of cold-responsive transcripts. Most of the CBF overexpression lines are in WS, therefore, it is necessary to identify a consistent set of transcripts that are detectible as cold-induced on the ATH1 platform for both WS and Columbia, so that appropriate comparisons can be made to determine the effects of low temperature in CBF overexpressing or loss of function plants in a WS background and an attempt can be made to compare the results of altered CBF function to published microarray studies. We aimed to identify a set of *gold-standard* cold responsive transcripts that were induced in multiple different experiments performed by different researchers and were detectible in both the WS and Col-0 ecotypes. This series contributes the 24h cold-treated WS ecotypes, along with additional Col-0 cold-treated and control samples for normalization purposes. Keywords: Expression profiling by array
2014-12-31 | GSE64575 | GEO
Project description: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. In this study, Arabidopsis ecotypes that are As-tolerant (Col-0) and -sensitive (Ws-2) were used to conduct a transcriptome analysis of the response to As (V). To begin elucidating the molecular basis of As toxicity and tolerance in Arabidopsis, seedlings of Col-0 and Ws-2 were subjected to As treatment. The root elongation rate of Col-0 was significantly higher than that of Ws-2 when exposed to As. The tolerant ecotype (Col-0) demonstrated lower accumulation of As when compared to the responses observed in the sensitive Ws-2. Subsequently, the effect of As exposure on genome-wide gene expression was examined in the two ecotypes. Comparative analysis of microarray data identified groups of genes with common and specific responses to As between Col-0 and Ws-2. The genes related to heat responses and oxidative stresses belonged to common responses, indicating conserved stress-associated changes across two ecotypes. The majority of specific responsive genes were those encoding heat shock proteins, heat shock factors, ubiquitin and transporters. The data suggested that metal transport and maintenance of protein structure may be important mechanisms for toxicity and tolerance to As. This study presents comprehensive surveys of global transcriptional regulation and identifies stress- and tolerance-associated genes in response to As. Comparison of Arabidopsis ecotype Col-0 and Ws-2 in response to As with the Affymetrix GeneChip were performed by the Affymetrix Gene Expression Service Lab (http://ipmb.sinica.edu.tw/affy/), supported by Academia Sinica, Taiwan
2011-11-26 | E-GEOD-31977 | biostudies-arrayexpress
Project description:Transcript profiling analysis of Hydraulic conductivity of Root 1 (HCR1) mutant compared to wild type (Col-0) using ARABIDOPSIS GENE1.1ST ARRAY STRIP (901793, Affymetrix, Santa Clara, USA).
2017-02-19 | GSE78087 | GEO
Project description:Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the grf1/grf2/grf3 triple mutant and transgenic plants overexpressing miR396-resistant variants of GRF1 (P35S:rGRF1) or GRF3 (P35S:rGRF3) with those of the corresponding wild-type (Col-0 or WS). Wild-type (Arabidopsis thaliana ecotypes Col-0 and Ws), the triple mutant grf1/grf2/grf3, and transgenic plants overexpressing rGRF1 or rGRF3 were grown in vertical culture dishes on modified KnopM-bM-^@M-^Ys medium for 2 weeks and then root tissues were collected for RNA extraction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tarek Hewezi. The equivalent experiment is AT109 at PLEXdb.] genotype: Arabidopsis thaliana ecotypes Col-0(3-replications); genotype: Arabidopsis thaliana ecotypes WS(3-replications); genotype: Triple mutant grf1/grf2/grf3(3-replications); genotype: P35S:rGRF1 overexpression(3-replications); genotype: P35S:rGRF3 overexpression(3-replications)
2012-03-13 | E-GEOD-31593 | biostudies-arrayexpress
Project description:Transcription profiling of Arabidopsis thaliana root tip region comparing argonaute1-101 (SALK_035319), scr-3 and wild-type Col-0.
2009-12-31 | GSE16460 | GEO
Project description:Transcriptional profiling of Arabidopsis comparing 1μM 3OC6-HSL-treated Arabidopsis wild-type Col-0 with control untreated Col-0. A transcriptomic analysis for Arabidopsis responses to bacterial quorum sensing molecule N-3oxo-hexanoyl-homoserine lactone (3OC6-HSL).
2016-09-21 | GSE78079 | GEO
Project description:We have used a strain of Tobacco etch potyvirus (TEV) experimentally adapted to Arabidopsis thaliana ecotype Ler-0 to infect a set of seven A. thaliana plant ecotypes(Col-0, Ei-2, Wt-1, ler-0, Oy-0, St-0). Each ecotype was inoculated with the same amount of the virus. Using commercial microarrays containing probes Arabidopsis thaliana ssp. Col-0 plant transcripts, we explored the effect of viral infection in the plant transcriptome This microarray can be useful to study gene activity of Arabidopsis thaliana associated with response to virus infection. For ecotypes ST-0, Wt-1, Ler-0, Di-2 there are five biological replicates and for ecotype Oy-0 there are three. As control we used four technical replicates of each ecotype, but five for Ler-0. Rows and columns are numbered as scanned by a GenePix Scanner (barcode on the bottom, DNA on the front surface).
2012-07-03 | E-GEOD-37269 | biostudies-arrayexpress