Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA97077 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression Level Polymorphism Project (ELP) - Kin-0
| PRJNA97087 | 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) - Est
| PRJNA97081 | ENA
Project description:Expression Level Polymorphism Project (ELP) - Tsu-1
| PRJNA97083 | 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: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: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