Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA108021 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We used microarrays to detail Arabidopsis gene expression in response to paraquat, a herbicide that acts as a terminal oxidant of photosystem I that in the light leads to the enhanced generation of superoxide and hydrogen peroxide inside plastids. Within a few hours after paraquat treatment changes in nuclear gene expression occur. Distinct sets of genes were activated that were different from those induced by another reactive oxygen species, singlet oxygen. Experiment Overall Design: Arabidopsis thaliana rosette leaves were harvested 1, 2, and 4 h after spraying either with a solution of 20 microM paraquat (methyl viologen, Sigma) in 0.1% Tween or with Tween alone for RNA extraction and hybridization on Affymetrix ATH1 microarrays. Plants were grown on soil for 3 weeks under continuous light at 90 mmol. m-2 . s-1. For each sample, the rosette leaves of five to six 3-week-old plants (before they start bolting) were collected for RNA extraction. Total RNAs from two separate biological experiments were pooled for the preparation of cDNA and the subsequent synthesis of biotin-labeled complementary RNA as recommended by Affymetrix.
2008-04-08 | E-GEOD-10464 | biostudies-arrayexpress
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:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. To identify heat stress induced genes, we performed RNA-sequencing of rosette leaves from mock-treated, heat-stressed and heat-stressed-recoved plants of both species.
2015-08-01 | GSE69077 | GEO
Project description:Expression data from Arabidopsis thaliana (Ler) rosette leaves after the release of singlet oxygen inside plastids
| PRJNA107263 | ENA
Project description:We sequenced the total RNA from a tissues mixed sample (inflorescences, rosette leaves, cauline leaves and stems) of Arabidopsis thaliana. After total RNA extraction, the same amount of tissue RNA were mixed. Ribosomal RNAs were deleted from the mixed tissue total RNAs using RiboMinus™ Plant Kit repeated three times. We also sequenced 9 poly(A)- RNAs from seedlings treated with different stress conditions at different times. The poly(A)- RNAs were collected by removing poly(A)+ RNAs four times . Then rRNAs were removed from poly(A)- RNAs three times.
2014-09-18 | GSE49325 | GEO
Project description:Diurnal gene expression in Arabidopsis thaliana Col-0 rosette leaves
| PRJNA93443 | ENA
Project description:To explore the overall long noncoding RNA (lncRNA) involved in growth and development of Arabidopsis thaliana across the lifespan, we deeply sequenced samples of whole plants from different developmental stages (4 rosette leaves>1mm, 14 rosette leaves>1mm, rosette growth complete, first flower buds visible, flourishing florescence, first silique shattered, senescence) using strand-specific RNA sequencing (ssRNA-seq) menthod. We obtained 28.8 Gb raw data and identified 156 novel lncRNAs (unreported in all public plant lncRNA databases) . We also categorized the novel lncRNAs as intergenic, intronic, antisense, overlapped with perhaps pseudogenes and mRNA based on their location on the Arabidopsis genome. Furthermore, lncRNAs targeted protein-coding genes were predicted and functional annotated. In addition, we constructed a network of interactions between ncRNAs (miRNAs, lncRNA) and mRNAs. Our results suggest that the identified novel lncRNAs are important in modulating development process of Arabidopsis, and provide a rich resource for further research on the function of these novel lncRNAs.
2017-07-22 | GSE98141 | GEO
Project description:Arabidopsis thaliana and Arabidopsis lyrata are two closely related Brassicaceae species, which are used as models for plant comparative biology. They differ by lifestyle, predominant mating strategy, ecological niches and genome organization. To identify heat stress induced genes, we performed RNA-sequencing of rosette leaves from mock-treated, heat-stressed and heat-stressed-recoved plants of both species. Analysis of genetic element transcriptional changes in response to 6 hours of 37°C heat stress and 48 hours of recovery in Arabidopsis thaliana Col-0 and Arabidopsis lyrata MN47.
2015-08-01 | E-GEOD-69077 | biostudies-arrayexpress
Project description:Although evidence accumulates on the role of plant peptides in the response to external conditions, the number of peptide-encoding genes in the genome is still underestimated. In order to identify novel oxidative stress-induced peptides in Arabidopsis thaliana a tiling array analysis (GeneChipM-BM-. Arabidopsis Tiling 1.0R Arrays ) was performed on mRNA extracted from leaves treated with paraquat (PQ), an reactive oxygen species inducer and water (control), resulting in the identification of 92,844 and 86,272 transcriptionally active regions (TARs), respectively. Normalized log signals were obtained using the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. ON and OFF probes were selected using a treshold, based on positive controls. Next, groups of 4-13 successive ON probes were combined into short TARs and a selection was made of TARs having an average signal intensity at least 2.6-fold higher after PQ treatment compared to the control treatment, resulting in 176 TARS induced by PQ. paraquat treated A. thaliana leaves (2 replicates) vs control (water) treated A. thaliana leaves (2 replicates), (4 samples in total)
2013-08-31 | E-GEOD-49001 | biostudies-arrayexpress
Project description:To exlore more circRNAs involved in Arabidopsis thaliana, we deeply sequenced 14 samples including whole plants from four developmental stages (rosette leaves > 1 mm in length; rosette growth complete; 50% of flowers to be produced have opened; first silique shattered), aerial part of plants from four stress treatments (control, drought, salinity and heat), five organs (roots, stems, leaves, flowers and siliques) and a mixed sample from whole plants across the lifespan (cotyledons emergence, rosette leaves﹥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and paired-end (PE) sequenced by Illumina HiSeq 2500 (read length, PE125, the mixed sample) and Illumina Hiseq X Ten (read length, PE150, 13 independent samples) platforms. We obtained 181.97 Gb raw data (151.37 Gb from 13 samples and 30.6 Gb from a mixed sample) and identified 5861 circRNAs with expression quantity. We annotated the parent genes of these circRNAs and predicted their target sites of microRNAs.
2016-09-01 | GSE77672 | GEO