Arabidopsis thaliana
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-13930E-GEOD-13929E-GEOD-13927
PROVIDER: PRJNA114605 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This study describes physiological changes, morphological adaptations and the regulation of pathogen defense responses in Arabidopsis crown galls. Crown gall development was induced on intact plants under most natural conditions with Agrobacterium tumefaciens. Differential gene expression and the metabolite pattern was determined by comparing crown galls with mock-inoculated inflorescence stalk segments of the same age.
2009-11-19 | GSE13927 | GEO
Project description:The intention of these gene expression analysis was to study host responses to an infection with Agrobacterium tumefaciens at different stages of crown gall development. Therefore the transcriptome of infected inflorescence stalk tissue and mature crown galls of Arabidopsis thaliana (WS-2) was determined of three different time points. These were compared with the transcriptome of mock-infected inflorescence stalk tissue (reference) of the same age. The following time points were analyzed: (i) three hours post inoculation, before the T-DNA is integrated into the host genome (ii) six days after inoculation when the T-DNA is present in the nucleus and the oncogenes are expressed in the host cell, and (iii) 35 days after inoculation when a mature tumors has developed. For the three-hour- (3hpi) and six-day- time point (6dpi) plants were infected with the virulent strain C58, harboring a T-DNA, or with strain GV3101, containing a disarmed Ti-plasmid. This allows discrimination between signals which derive from the bacterial pathogen and the T-DNA encoded oncogenes. This SuperSeries is composed of the following subset Series:; GSE13929: Arabidopsis thaliana three hours after infection with Agrobacterium tumefaciens; GSE13930: Arabidopsis thaliana six days after infection with Agrobacterium tumefaciens; GSE13927: Transcriptome of mature A. thaliana crown galls. Experiment Overall Design: Refer to individual Series
2009-12-02 | E-GEOD-14106 | biostudies-arrayexpress
Project description:This study describes physiological changes, morphological adaptations and the regulation of pathogen defense responses in Arabidopsis crown galls. Crown gall development was induced on intact plants under most natural conditions with Agrobacterium tumefaciens. Differential gene expression and the metabolite pattern was determined by comparing crown galls with mock-inoculated inflorescence stalk segments of the same age. Experiment Overall Design: The bases of Arabidopsis thaliana (WS-2) inflorescence stalks were wounded and immediately inoculated with Agrobacterium tumefaciens, strain C58, or mock-inoculated. Plants were cultivated for another 35 days under short day conditions (8 h illumination, 16 h darkness). Gene expression values of four independent experiments of treated material (C58 35dpi 1 to 4) were compared with four non-treated samples of the same age (reference 35dpi 1 to 4). Differential gene expression was analyzed by applying the LIMMA package (Linear Models for Microarray Data; Smyth, G.K. (2004) Applic. Genet. Mol. Biol. 3, Article 3; http://www.bepress.com/sagmb/vol3/iss1/art3/).
2009-12-02 | E-GEOD-13927 | biostudies-arrayexpress
Project description:Genome-wide analysis of the cytosine methylation profile in Arabidopsis thaliana crown galls
| PRJNA162677 | ENA
Project description:The intention of these gene expression analysis was to study host responses to an infection with Agrobacterium tumefaciens at different stages of crown gall development. Therefore the transcriptome of infected inflorescence stalk tissue and mature crown galls of Arabidopsis thaliana (WS-2) was determined of three different time points. These were compared with the transcriptome of mock-infected inflorescence stalk tissue (reference) of the same age. The following time points were analyzed: (i) three hours post inoculation, before the T-DNA is integrated into the host genome (ii) six days after inoculation when the T-DNA is present in the nucleus and the oncogenes are expressed in the host cell, and (iii) 35 days after inoculation when a mature tumors has developed. For the three-hour- (3hpi) and six-day- time point (6dpi) plants were infected with the virulent strain C58, harboring a T-DNA, or with strain GV3101, containing a disarmed Ti-plasmid. This allows discrimination between signals which derive from the bacterial pathogen and the T-DNA encoded oncogenes. This SuperSeries is composed of the SubSeries listed below.
2009-11-19 | GSE14106 | GEO
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:Integration of the bacterial T-DNA into the plant genome by virulent agrobacteria causes crown gall development on many plant species. Plant tumor development shares fundamental similarities with mammalian cancer progression despite obvious differences in initiation of tumor development. For neoplastic growth in mammals, DNA methylation changes are known to be essential. The role of epigenetic modifications for plant tumor development is addressed here. Genome-wide comparison of methylation profiles of Arabidopsis crown galls and tumor-free tissue revealed 2,876 annotated genes that were affected by differential methylation. Thereof, 1,822 genes were hit by hypermethylated regions and 1,100 genes overlapped with hypomethylated regions (sum of hyper-and hypomethylated genes is higher than the number of affected genes because one gene may contain several differentially methylated regions [DMRs]). DMRs found to be methylated only in tumor-free tissue covered 275 kb of the genome, whereas those methylated only in crown galls total to 560 kb. Contrary to the globally hypermethylated tumor genome, promoter regions of protein coding genes appeared to be rather hypomethylated. In contrast, mammalian cancer cells are associated with global hypomethylation and local hypermethylation of gene promoters. In summary, while aberrant DNA methylation in mammals increases malignacy of the cancer phenotype, our results indicate that methylation events in the plant genome rather confine tumor growth. All 15,431 mCIP-enriched regions reported in the paper are contained in the supplementary BED files. mCIP of gDNA from crown galls vs. mCIP of gDNA from inflorescence stalks (3 biol. replicates each)
2013-02-18 | E-GEOD-37680 | biostudies-arrayexpress
Project description:Integration of the bacterial T-DNA into the plant genome by virulent agrobacteria causes crown gall development on many plant species. Plant tumor development shares fundamental similarities with mammalian cancer progression despite obvious differences in initiation of tumor development. For neoplastic growth in mammals, DNA methylation changes are known to be essential. The role of epigenetic modifications for plant tumor development is addressed here. Genome-wide comparison of methylation profiles of Arabidopsis crown galls and tumor-free tissue revealed 2,876 annotated genes that were affected by differential methylation. Thereof, 1,822 genes were hit by hypermethylated regions and 1,100 genes overlapped with hypomethylated regions (sum of hyper-and hypomethylated genes is higher than the number of affected genes because one gene may contain several differentially methylated regions [DMRs]). DMRs found to be methylated only in tumor-free tissue covered 275 kb of the genome, whereas those methylated only in crown galls total to 560 kb. Contrary to the globally hypermethylated tumor genome, promoter regions of protein coding genes appeared to be rather hypomethylated. In contrast, mammalian cancer cells are associated with global hypomethylation and local hypermethylation of gene promoters. In summary, while aberrant DNA methylation in mammals increases malignacy of the cancer phenotype, our results indicate that methylation events in the plant genome rather confine tumor growth. All 15,431 mCIP-enriched regions reported in the paper are contained in the supplementary BED files.
2013-02-18 | GSE37680 | 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:The goal of this study is to compare the transcriptome profilling (RNA-seq) of galls (G) formed in Arabidopsis roots infected by Meloidogyne javanica at 3 days post infection compared to uninfected root segments (RC).
2022-07-31 | GSE155171 | GEO