Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA290514 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:Large-scale identification of transcripts with large cross-genotype differences in abundance provides a genome-wide approach to identify natural variation in gene function. Transcript profiling was performed in 20 Arabidopsis accessions at dusk, dawn and after a 6h extension of the night. Individual genes with a high variance in transcript abundances across accessions were identified by inspection at each individual time point and by ANOVA across all three time points. Up to 40% of genes show significant changes in transcript abundance between accessions, with over-enrichment for biotic resistance, including pathogenesis resistance proteins and glucosinolate metabolism, cell wall modification, minor carbohydrate metabolism, amino acid degradation, brassinosteroid metabolism, redox and abiotic stress and underrepresentation of photosynthesis, DNA synthesis, RNA processing, regulation of transcription, protein synthesis and protein targeting. Some functional classes were enriched at all three time points. Genes related to carbon starvation-responses were enriched specifically at dawn, when their transcript abundance varied independently of carbohydrate levels, pointing to genetic variation in the sensitivity with which low carbon is sensed. Cross-accession correlation networks were generated at each time point to identify sets of genes whose transcripts show coordinated change in abundance between accessions. A cluster that was highly enriched for cold-response genes was found at dusk and after an extension of the night. Another cluster found at all three time points was highly enriched for glucosinolate biosynthesis, and correlated with glucosinolate content. We conclude that genes involved in stress and defense related processes show especially large and coordinated natural variation in transcript abundance.
2023-12-31 | GSE71188 | GEO
Project description:Arabidopsis thaliana and Eutrema salsugineum show the ability to cold acclimate. However, the degree of freezing tolerance depends in both cases on the accession. To elucidate the transcriptional basis of this differencial freezing tolerance, we performed where we grew plants under control conditions (20°C/18°C day/night) or under cold conditions (additional 4°C for 2 weeks). Rosettes were harvested from non-acclimated and cold acclimated plants for RNA isolation. Expression patterns were compared between treatments, accessions and species.
2018-01-01 | GSE100108 | GEO
Project description:Usually starch is nearly depleted at the end of the night. To induce a gradual depletion of carbon, we have analysed the global response of transcripts during an extension of the night, where carbon becomes severely limiting from about four hours onwards. Experiment Overall Design: Arabidopsis thaliana rosettes were harvested in successive timpoints in an extended night situation.
2008-04-09 | E-GEOD-10016 | biostudies-arrayexpress
Project description:We have sequenced messenger RNA isolated from seedling tissue for 19 accessions of Arabidopsis thaliana (with biological replication). The 19 accessions for which RNA-Seq reads were collected have served as the founders for the MAGIC lines, a high-resolution recombinant inbred line mapping resource. RNA sequencing data was used to examine differential gene expression among the accessions.
2011-08-29 | GSE30720 | GEO
Project description:a2e_heterosis - cgh_colvscvi_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and CVi.
2011-05-17 | GSE24835 | GEO
Project description:a2e_heterosis - cgh_colvsc24_wg - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and C24.
2011-05-17 | GSE24831 | GEO
Project description:a2e_heterosis - cgh_colvsc24_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and C24 Keywords: cgh,chip-chip
2011-05-17 | GSE24494 | GEO
Project description:These data provide a basis for the detection of sequence based polymorphisms between 10 Spring annual accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.
2012-03-12 | GSE27551 | GEO
Project description:These data provide a basis for the detection of sequence based polymorphisms between 10 Spring annual accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.
2012-03-12 | GSE27549 | GEO