Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA110175 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Stable Inheritance of Spontaneous Epialleles in Arabidopsis thaliana
| PRJNA369265 | ENA
Project description:Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.
| PRJNA172021 | ENA
Project description:RNA-seq analysis of alternative splicing between two Arabidopsis accessions and its inheritance in hybrid
| PRJNA264397 | ENA
Project description:Plants grow continuously and undergo numerous changes in their vegetative morphology and physiology during their life span. The molecular basis of these changes is largely unknown. To provide a more comprehensive picture of shoot development in Arabidopsis, microarray analysis was used to profile the mRNA content of shoot apices of different ages, as well as leaf primordia and fully-expanded leaves from 6 different positions on the shoot, in early-flowering and late-flowering genotypes. This extensive dataset provides a new and unexpectedly complex picture of shoot development in Arabidopsis. At any given time, the pattern of gene expression is different in every leaf on the shoot, and reflects the activity at least 6 developmental programs. Three of these are specific to individual leaves (leaf maturation, leaf aging, leaf senescence), two occur at the level of the shoot apex (vegetative phase change, floral induction), and one involves the entire shoot (shoot aging). Our results demonstrate that vegetative development is a much more dynamic process that previously imagined, and provide new insights into the underlying mechanism of this process.
2019-11-30 | GSE122691 | GEO
Project description:This research uses consecutive generations of two independent mutation accumulation (MA) lines in model organism A. thaliana to understand transgenerational stability of epialleles via self-fertilization. With whole-genome bisulfite sequencing, regions of instability were identified and quantified. The vast majority of the methylated genome is stably inherited to offspring and the identified unstable regions do not change frequently between generations. Additionally, an epigenetic cross of two MA lines was created to understand inheritance patterns of epialleles via outcrossing in the absence of genetic variation. Whole-genome bisulfite sequencing was used to predict epigenotype of the offspring without single nucleotide polymorphisms. In regions of differential methylation between the parents, about half of regions show predictable inheritance.
2017-07-24 | GSE94298 | GEO
Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes.
2012-05-22 | GSE38109 | GEO
Project description:A major effort is underway to study the natural variation within the model plant species, Arabidopsis thaliana. Much of this effort is focused on genome resequencing, however the translation of genotype to phenotype will be largely effected through variations within the transcriptomes at the sequence and expression levels. To examine the cross-talk between natural variation in genomes and transcriptomes, we have examined the transcriptomes of three divergent A. thaliana accessions using tiling arrays. Combined with genome resequencing efforts, we were able to adjust the tiling array datasets to account for polymorphisms between the accessions and therefore gain a more accurate comparison of the transcriptomes. The corrected results for the transcriptomes allowed us to correlate higher gene polymorphism with greater variation in transcript level among the accessions. Our results demonstrate the utility of combining genomic data with tiling arrays to assay non-reference accession transcriptomes.
2012-03-12 | GSE24669 | GEO
Project description:Global transcriptome analysis in fast-growing Arabidopsis thaliana with elevated level of ATP [shoots]
| PRJNA173488 | ENA