Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA102273 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:CG Methylation of Col, Van and reciprocal hybrids using HpaII and MspI digestion followed by bioprime random labeling, and hybridization to AtTILE1 forward array. Study on constitutive and ploymorphic CG methylation between arabidopsis thaliana accessions Col-0 and Van-0. Study on the inheritance of CG methylation in reciprocal hybrids. Keywords: genomic hybridization
2008-04-11 | GSE8890 | GEO
Project description:Gene expression of Col, Van and reciprocal hybrids
| PRJNA102275 | ENA
Project description:Genomic hybridization of Col, Van and reciprocal hybrids
| PRJNA110645 | ENA
Project description:Gene expression of Col, Van and reciprocal hybrids using double-stranded cDNA followed by bioprime random labeling, and hybridization to AtTILE1 forward array. Study on gene expression polymorphism between arabidopsis thaliana accessions Col-0 and Van-0. Study on the inheritance of gene expression in reciprocal hybrids. Keywords: cDNA hybridization
2008-04-11 | GSE8891 | GEO
Project description:Genomic DNA of Col, Van and reciprocal hybrids, bioprime random labeling, and hybridization to AtTILE1 forward array. Study on genetic ploymorphic between arabidopsis thaliana accessions Col-0 and Van-0, and set the scale of F1 hybrid intensity for SFPs.
2008-11-18 | GSE13620 | GEO
Project description:Col-0 and Van-0 total RNA were mixed at 1:1. Total RNA also extracted from F1 hybrid samples from Col x Van and Van x Col. PolyA RNA were purified and double-strand cDNA were synthesized, followed by bioprime random labeling. A total of 16ug labelled products were hybridized to AtSNPtile1. cis regulatory effect was identified as allele specific expression in F1 hybrids. Composite trans regulatory effect was detected as deviation between parental expression and F1 hybrids expression.
2009-08-15 | GSE16506 | GEO
Project description:Arabidopsis thaliana mid torpedo embryo transcriptome of reciprocal Col-0/C24 triploid hybrids
| PRJNA358016 | ENA
Project description:Col-0 and Van-0 total RNA were mixed at 1:1. Total RNA also extracted from F1 hybrid samples from Col x Van and Van x Col. PolyA RNA were purified and double-strand cDNA were synthesized, followed by bioprime random labeling. A total of 16ug labelled products were hybridized to AtSNPtile1. cis regulatory effect was identified as allele specific expression in F1 hybrids. Composite trans regulatory effect was detected as deviation between parental expression and F1 hybrids expression. Each sample type has four replicates. Single chanel. Three sample types (Col and Van RNA 1:1 mixture, Col x Van F1 hybrids, Van x Col F1 hybrids). Total 12 samples.
2010-05-06 | E-GEOD-16506 | biostudies-arrayexpress
Project description:Despite of the paramount importance of heterosis in agriculture, the molecular mechanisms underlying heterosis remain elusive. Recent studies in Arabidopsis suggested possible involvement of DNA methylation in heterosis. We tested this hypothesis genetically by crossing homozygous mutants in DNA methylation-related genes in the Columbia (Col) ecotype with homozygous mutants in the same DNA methylation-related genes in the C24 ecotype. When genes in the RNA-directed DNA methylation (RdDM) pathway were mutated, the resultant F1 hybrids did not show appreciable loss of best parent heterosis (BPH) performances in early seedling growth. In contrast, mutations in the putative chromatin remodeling protein DECREASE OF DNA METHYLATION 1 (DDM1) caused ddm1-Col like growth pattern of ddm1-F1 hybrids, a mid-parent heterosis (MPH) performance. To understand the underlying molecular mechanisms, we compared the transcriptomes of the parental plants and reciprocal F1 hybrids in the wild type and ddm1 mutant backgrounds, and identified 183 non-additively expressed (NAE) genes, which were functionally enriched in defense response, a group of genes negatively associated with plant size. Interestingly, for the expression levels of the NAE genes, WT-F1 hybrids were enriched in the Golden Ration between mid-parent values (MPVs) and Col parents in WT, but ddm1-F1 hybrids were comparable to ddm1-Col parent in ddm1 mutant, which explained the MPH performance of ddm1-F1 hybrids. DNA methylation analyses revealed only one third of the NAE genes with highly methylated promoters whose expression is negatively associated with DNA methylation of promoters, strongly suggesting that DDM1 regulates heterosis by multiple epigenetic modifications.
2016-11-07 | GSE74551 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE34655: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq GSE34656: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - small RNA-seq GSE34657: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq Refer to individual Series
2011-12-22 | E-GEOD-34658 | biostudies-arrayexpress