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Expression and methylation data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE119363 | GEO | 2020/07/28

REPOSITORIES: GEO

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Expression data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

Project description:The COP9 signalosome (CSN) is a highly conserved complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. Mutations in each of the CSN subunits exhibits diverse pleiotropic phenotypes We used microarrays to compare gene expression of two CSN mutants with their corresponding wild types: a non-lethal csn5a-1 mutant, vs. columbia ecotype, and a lethal, csn8 mutant, vs. Wassilewskija ecotype

2020-07-28 | GSE108376 | GEO

Genome-wide bisulfite sequencing of methylation from seedings of of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

Project description:The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 Signalosome exhibit a number of diverse pleiotropic phenotypes. Total or partial loss of COP9 Signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. Results: We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function mutants of the COP9 Signalosome. Our results indicate that the COP9 Signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. In addition, our analyses suggest that COP9 Signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes. These results suggest that the COP9 Signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 Signalosome conservation among eukaryotes may also suggest that COP9 Signalosome regulates methylation not only in plants but also in other eukaryotes, including humans. We report the application of Bisulfite-sequencing to compare methylation of two CSN mutants with their corresponding wild types: a non-lethal csn5a-1 mutant, vs. columbia ecotype, and a lethal, csn8 mutant, vs. Wassilewskija ecotype

2020-07-28 | GSE119259 | GEO

Expression and methylation data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes.

Project description:Expression and methylation data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes.

| PRJNA488899 | ENA

Expression data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

Project description:Expression data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

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Arabidopsis thaliana seedlings: Wild type vs. zrf1 mutants

Project description:Transcriptional profiling of 6-day-old seedlings of Arabidopsis wild type control and zrf1 mutants is performed using Agilent's Whole Arabidopsis Gene Expression Microarray (4x44K).

2016-12-31 | GSE76244 | GEO

Cell Wall Polysaccharide-Mediated Cadmium Tolerance Between Two Arabidopsis thaliana Ecotypes.

Project description: Not available

| S-EPMC7239314 | biostudies-literature

Genome-wide bisulfite sequencing of methylation from seedings of of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

Project description:Genome-wide bisulfite sequencing of methylation from seedings of of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

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Arabidopsis thaliana ecotypes Rodasen-47 (Sweden) and Castelnuovo-12 (Italy) grown in high light and/or cold

Project description:Illumina HiSeq RNAseq data from the youngest fully developed leaf collected from two ecotypes of Arabidopsis thaliana, Rodasen-47 (Sweden) and Castelnuovo-12 (Italy), adapted to contrasting local climates, grown at different temperatures and/or light levels. Plants were all vegatively growing in one gallon pots to prevent root bounding. Plants were sampled at the 40th day of growth.

2020-07-14 | GSE154349 | GEO

Arabidopsis thaliana seedlings: Wild type vs. sdg8, hub2 and sdg8hub2 mutants

Project description:Transcriptional profiling of 6-day-old seedlings of Arabidopsis wild type control and mutants is performed using Affymetrix IVT Arabidopsis ATH1 Genome Array.

2019-01-21 | GSE109424 | GEO

Histone methylation in wild type and ddm1 Arabidopsis thaliana seedlings

Project description:Histone 3 lysine 4 and histone 3 lysine 9 methylation in wild type and ddm1 Arabidopsis thaliana seedlings. The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thanliana genotype. Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype. This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization. The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3. In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively. This SuperSeries is composed of the SubSeries listed below.

2004-06-12 | GSE1356 | GEO

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