Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA139193 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We produced RNA-seq reads from messenger RNA isolated from aerial seedling tissue for Arabidopsis thaliana mutants in the HULK gene family. The read data were generated with biological replication (two replicates). The resulting RNA-seq data provide a resource to assess the function of HULK genes in the control of downstream gene expression in A. thaliana.
2015-01-01 | GSE54125 | GEO
Project description:Genome-wide maps of histone modifications in Arabidopsis thaliana
| PRJNA128717 | ENA
Project description:Arabidopsis thaliana (Col-4) aerial tissue collected from 14-day old plants. Grown under sterile conditions at 22 degrees Celsius and 125 uE light on 0.5xMS media.
2010-12-10 | GSE25993 | GEO
Project description:We produced RNA-seq reads from messenger RNA isolated from aerial seedling tissue for Arabidopsis thaliana mutants in the HULK gene family. The read data were generated with biological replication (two replicates). The resulting RNA-seq data provide a resource to assess the function of HULK genes in the control of downstream gene expression in A. thaliana. Examination of RNA transcript levels in HULK T-DNA mutants (and mutant combinations therein) in Arabidopsis thaliana.
2015-01-01 | E-GEOD-54125 | biostudies-arrayexpress
Project description:We produced RNA-Seq reads from messenger RNA isolated from root tissue for the 19 MAGIC founder accessions (inbred strains) of Arabidopsis thaliana (see Gan et al. 2011. Nature 477:419-23 for a description of the MAGIC genetic mapping resource). The read data was generated with biological replication (two replicates). The resulting RNA-Seq data provide a resource to assess root gene expression across different accessions of A. thaliana. Comparable RNA-Seq read data for the MAGIC founder accessions for aerial seedling tissue has previously been released under GEO series GSE30720 (Gan et al. 2011. Nature, 477:419-23).
2013-12-11 | GSE53198 | GEO
Project description:We produced RNA-Seq reads from messenger RNA isolated from aerial seedling tissue for 9 hybrids (F1s) generated by crossing in a pairwise manner 18 of the founding accessions (inbred strains) of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource for Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provides a resource to assess allele-specific gene expression between A. thaliana accessions.
2014-03-01 | GSE55482 | 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. In order to explore molecular basis of specific traits, we performed RNA-sequencing of vegetative rosettes from both species. Additionally, we sequenced apical meristems and inflorescences of A. lyrata that allow for intra-specific transcriptome comparison in several major developmental stages. Arabidopsis lyrata and Arabidopsis thaliana aerial tissues were collected from mock treated plants, total RNA isolated and poly-A RNA populations sequenced
2015-08-01 | E-GEOD-69222 | biostudies-arrayexpress
Project description:The objective of the study is to profile histone H3 lysine nine di-methylation (H3K9me2) in Arabidopsis thaliana and to correlate it with DNA methylation.
2008-09-11 | GSE12383 | GEO
Project description:Histone acetylation and methylation regulate gene expression in eukaryotes, but their effects on the transcriptome of a multicellular organism and on the transcriptomic divergence between species are still poorly understood. Here we present the first genome-wide 1-bp resolution maps of histone acetylation, histone methylation and core histone in Arabidopsis thaliana and a comprehensive analysis of these maps and gene expression data in A. thaliana, A. arenosa and allotetraploids. H3K9 acetylation (H3K9ac) and H3K4 trimethylation (H3K4me3) are correlated, and their high densities near transcriptional start sites determine constitutive expression of genes involved in translation. In contrast, broad distributions of these modifications toward coding regions determine expression variation, especially in genes involved in photosynthesis, carbohydrate metabolism, and defense responses. A dispersed distribution of H3K27me3 and depletion of H3K9ac and H3K4me3 are associated with developmentally repressed genes. Finally, genes affected by histone deacetylase mutation and species divergence tend to show high expression variation. In conclusion, changes in histone acetylation and methylation modulate developmental and environmental gene expression variation within and between species.
2011-02-02 | GSE22276 | GEO
Project description:Histone acetylation and methylation regulate gene expression in eukaryotes, but their effects on the transcriptome of a multicellular organism and on the transcriptomic divergence between species are still poorly understood. Here we present the first genome-wide 1-bp resolution maps of histone acetylation, histone methylation and core histone in Arabidopsis thaliana and a comprehensive analysis of these maps and gene expression data in A. thaliana, A. arenosa and allotetraploids. H3K9 acetylation (H3K9ac) and H3K4 trimethylation (H3K4me3) are correlated, and their high densities near transcriptional start sites determine constitutive expression of genes involved in translation. In contrast, broad distributions of these modifications toward coding regions determine expression variation, especially in genes involved in photosynthesis, carbohydrate metabolism, and defense responses. A dispersed distribution of H3K27me3 and depletion of H3K9ac and H3K4me3 are associated with developmentally repressed genes. Finally, genes affected by histone deacetylase mutation and species divergence tend to show high expression variation. In conclusion, changes in histone acetylation and methylation modulate developmental and environmental gene expression variation within and between species. ChIP-Seq: Identification of distribution of H3K9ac, H3K4me3 and H3 in Arabidopsis thaliana leaf. Expression: Gene expression in the histone deacetylase 1 mutant was generated using t-DNA insertion. mRNA expressions in leaf and flower of the AtHD1 mutant were compared with those of the wild type plants. We conducted 8 replicates of dual-channel microarrays, including 4 biological replicates and individual dye swaps.
2011-02-02 | E-GEOD-22276 | biostudies-arrayexpress