Arabidopsis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA669593 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR12880900_1.fastq.gz | Fastqsanger.gz | |||
| SRR12880900_2.fastq.gz | Fastqsanger.gz | |||
| SRR12880901_1.fastq.gz | Fastqsanger.gz | |||
| SRR12880901_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE24494: cgh_colvsc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE24831: cgh_colvsc24_wg-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE24835: cgh_colvscvi_wg-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25049: h3k4me2_c24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25050: h3k27me3_colxcvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25051: h3k27me3_cvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25052: h3k27me3_col(cvi)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25053: h3k4me2_colxcvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25054: h3k4me2_cvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25056: h3k4me2_col(cvi)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25057: h3k27me3_colxc24-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25058: h3k27me3_c24-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25059: h3k27me3_col(c24)-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25060: h3k4me2_colxc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions GSE25061: h3k4me2_col_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions Refer to individual Series
2011-05-17 | E-GEOD-24836 | biostudies-arrayexpress
Project description:Reduced DNA methylation in Arabidopsis allopolyploids induces genome-specific changes in gene expression
| PRJNA103309 | ENA
Project description:Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant species A. thaliana and A. arenosa. Here we report that reduced DNA methylation in met1-RNAi A. suecica lines altered the expression of ~200 genes encoding transposons, centromeric and heterochromatic RNAs, and predicted proteins. Reduced DNA methylation occurred frequently in promoter regions of the upregulated genes but not of the repressed genes and led to increased mobility of En/Spm-like transposons in met1-RNAi A. suecica lines. Compared to A. arenosa centromeres, A. thaliana centromeres were hypermethylated, which correlates with higher levels of small RNA accumulation in A. thaliana centromeres than that in A. arenosa centromeres. Derepression of the genes examined was primarily derived from A. thaliana subgenome, and A. arenosa genes are less affected by methylation defects. Moreover, non-CG (CC) methylation in the promoter region of A. thaliana At2g23810 was maintained in resynthesized allotetraploids, and the methylation spread within the promoter region in natural A. suecica, leading to silencing of At2g23810, which was demethylated and reactivated in met1-RNAi A. suecica lines. We suggest that a subset of A. thaliana and A. arenosa genes are differentially methylated in natural allopolyploids, and some A. thaliana genes including centromeres are subjected to transcriptional repression and genome-specific RNA-mediated DNA methylation in Arabidopsis allopolyploids. Keywords: gene expression in reduced DNA methylation lines in Arabidopsis allotetraploids
2008-03-30 | GSE9512 | GEO
Project description:The study uncovers epigenomic changes associated with dexamethasone response heterogeneity in myeloma cells, revealing rewired promoter-enhancer interactions and DNA loop stabilization
| EGAS00001007411 | EGA
Project description:Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
| PRJNA99003 | ENA
Project description:Genome-wide analysis of gene expression has documented differential gene expression between closely related species in plants or animals and nonadditive gene expression in hybrids and allopolyploids compared to the parents. In Arabidopsis, 15-43% of genes are expressed differently between the related species, A. thaliana and A. arenosa, and the majority of them are nonadditvely expressed (differently from mid-parent value) in allotetraploids relative to the parents. The gene expression variation is associated with transcriptional and posttranscriptional mechanisms. Although transcriptional regulation by epigenetic mechanisms plays a role in nonadditive gene expression, the effects of posttranscriptional regulation on nonadditive gene expression is largely unknown. Here we reported a comprehensive genome-wide analysis of mRNA decay in Arabidopsis allotetraploids using oligo gene microarrays. Among ~26,000 annotated genes on the arrays, over 1% of genes showed a rapid decay rate with an estimated half-life of less than 60 min, and these genes are known as genes with unstable transcripts (GUTs). Interestingly, 30% of GUTs matched the nonadditively expressed genes, and their expression levels were significantly negatively correlated. These nonadditively expressed GUTs are highly enriched with a 2-8-fold increase compared to the proportion of all genes in the Gene Ontology (GO) classifications in response to stress, abiotic and biotic stimulus, signal transduction, and transcription. The data are consistent with the enrichment of nonadditvely-expressed genes in those categories in allopolyploids of Arabidopsis, wheat and cotton. Interestingly, the GUTs include some key transcription factors including circadian clock regulators, suggesting a mechanism for rapid response to light signalling and clock regulation in allotetraploids. These data collectively suggest an important role of mRNA stability in nonadditive expression of homoeologous genes in allopolyploids.
2011-09-16 | GSE26065 | GEO
Project description:Arabidopsis msh1 mutants display developmental reprogramming (dr) phenotypes, include reduction in growth, enhanced branching, and delayed maturation and flowering time. MSH1-epi lines were derived by crossing msh1 lines with Col-0 wild type, followed by selection for homozygous MSH1/MSH1 F2 plants and serial self-pollination. MSH1-epiF3 plants displayed phenotypic variation in plant growth, showing enhanced growth, larger rosette diameter, thicker floral stems and earlier flowering time. We carried bisulfite sequencing and uncover the methylome changes accompany the heritable MSH1-epi phenotypes that condition dramatic variation in plant growth.
2013-12-01 | GSE43993 | GEO
Project description:Plant BBR/BPC transcription factors contain the conserved Basic-Pentacystein (BPC) DNA-binding domain. Arabidopsis group II BBR/BPC proteins interact with PRC1 component LHP1 in vivo. Microarray experiments with Arabidopsis bpc4 bpc6, lhp1-4 and lhp1-4 bpc4 bpc6 suggest an importance of this interaction in the concerted repression of homeotic genes. In this study, we used the ATH1 GeneChip microarray to investigate transcript abundance in different Arabidopsis thaliana genotypes.
2015-04-30 | GSE68437 | GEO
Project description:cgh_colvsc24_chr4-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
| PRJNA133523 | ENA
Project description:h3k4me2_colxcvi-Analysis of epigenomic changes in hybrids Arabidopsis thaliana Col-0, C24 and Cvi accessions
| PRJNA134559 | ENA