Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA97083 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression Level Polymorphism Project (ELP) - Est
| PRJNA97081 | ENA
Project description:Expression Level Polymorphism Project (ELP) - Kin-0
| PRJNA97087 | ENA
Project description:Expression Level Polymorphism Project (ELP) - Col-0
| PRJNA97077 | ENA
Project description:Expression Level Polymorphism Project (ELP) - Van-0
| PRJNA97085 | ENA
Project description:Expression Level Polymorphism Project (ELP) - Mt-0
| PRJNA97089 | ENA
Project description:Expression Level Polymorphism Project (ELP) - Cvi-1
| PRJNA97079 | ENA
Project description:Expression level polymorphisms (ELPs) often result in cis-acting expression quantitative trait loci (cis-eQTL), which are important QTL and association mapping tools and account significantly for phenotypic variability. Generally, it is assumed that such stably heritable ELP represent regulatory element polymorphisms in the respective genes. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here we analyzed heritability of ELP observed between Arabidopsis thaliana accessions Eil-0 and Lc-0 by comparing genotyped recombinant inbred lines (RIL) to their parents in microarray analyses. Keywords: expression level polymorphism, Arabidopsis thaliana accessions, recombinant inbred lines
2008-11-18 | GSE13628 | GEO
Project description:Expression level polymorphisms (ELPs) often result in cis-acting expression quantitative trait loci (cis-eQTL), which are important QTL and association mapping tools and account significantly for phenotypic variability. Generally, it is assumed that such stably heritable ELP represent regulatory element polymorphisms in the respective genes. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here we analyzed heritability of ELP observed between Arabidopsis thaliana accessions Eil-0 and Lc-0 by comparing genotyped recombinant inbred lines (RIL) to their parents in microarray analyses. Keywords: expression level polymorphism, Arabidopsis thaliana accessions, recombinant inbred lines In order to analyze expression level polymorphisms between the accessions Eil-0 and Lc-0, three independently grown seedling pools were analyzed by two color co-hybridization of the labeled cDNAs in dyeswap experiments, giving a total of six slides. For the analysis of gene expression in seedlings of 7 different RILs, each RIL sample was co-hybridized with each parent (Eil-0 and Lc-0) in a dyeswap, resulting in two slides per parent vs. RIL comparison. The total number of slides in this study was 34.
2010-05-16 | E-GEOD-13628 | biostudies-arrayexpress
Project description:Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects. In these studies we sought to examine differential gene expression in response to cold for two widely used Arabidopsis thaliana ecotypes, C24 and Columbia (Col).
2012-12-01 | GSE37130 | GEO
Project description:These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 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. Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India). 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. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content.
2010-02-17 | GSE20340 | GEO