Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA91041 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA methylation in wild type bolting plants, wild type seedlings, and ddm1 seedlings. The purpose of the McrBC methylation microarray assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thanliana genotype. McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb.* The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment. In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3. Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray. 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 following subset Series: GSE1329: DNA methylation in wild-type bolting Arabidopsis thaliana plants GSE1330: DNA methylation in ddm1 seedling Arabidopsis thaliana plants GSE1331: VC133+137, DNA methylation in ddm1 seedling Arabidopsis thaliana plants GSE1332: VC134+136, DNA methylation in wild-type seedling Arabidopsis thaliana plants Refer to individual Series
2010-06-09 | E-GEOD-1355 | biostudies-arrayexpress
Project description:DNA methylation in wild-type bolting Arabidopsis thaliana plants
| PRJNA91035 | ENA
Project description:DNA methylation in ddm1 seedling Arabidopsis thaliana plants
| PRJNA91037 | ENA
Project description:mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings and bolting plants. Features found to be significantly enriched for DNA methylation were determined. This SuperSeries is composed of the SubSeries listed below.
2004-06-12 | GSE1354 | GEO
Project description:mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings and bolting plants. Features found to be significantly enriched for DNA methylation were determined. This SuperSeries is composed of the following subset Series: GSE1324: EV23+24 mRNA levels in Wild-type versus ddm1/+ backcross bolting Arabidopsis thaliana plants GSE1325: EV33+34 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings GSE1326: VC109+111 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings GSE1327: EV39+40 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings GSE1328: VC110+112 mRNA levels in Wild-type versus ddm1 bolting Arabidopsis thaliana plants Refer to individual Series
2010-06-09 | E-GEOD-1354 | biostudies-arrayexpress
Project description:VC133+137, DNA methylation in ddm1 seedling Arabidopsis thaliana plants
| PRJNA91039 | ENA
Project description:Arabidopsis thaliana mutant sr45-1 has an altered flower shape. sr45 is a splicing regulator. In this study, we examined the proteins from inflorescence of sr45-1 mutant plants and wild-type. Wild type TMT labels: 126, 128, 130. sr45-1 TMT labels: 127, 129, 131.
2019-04-26 | MSV000083728 | MassIVE
Project description:How bacteria from the microbiota modulate the physiology of its host is an important question to address. Previous work revealed that the metabolic status of Arabidopsis thaliana was crucial for the specific recruitment of Streptomycetaceae into the microbiota. Here, the Arabidopsis-Actinacidiphila interaction was further depicted by inoculating axenic Arabidopsis with Actinacidiphila cocklensis DSM 42063 or Actinacidiphila bryophytorum DSM 42138(previously named Streptomyces cocklensis and Streptomyces bryophytorum). We demonstrated that these two bacteria colonize A. thaliana wild-type plants, but their colonization efficiency was reduced in a chs5 mutant with defect in isoprenoid, phenylpropanoids and lipids synthesis. We observed that those bacteria affect the growth of the chs5 mutant but not of the wild-type plants. Using a mass spectrometry-based proteomic approach, we showed a modulation of the Arabidopsis proteome and in particular its components involved in photosynthesis or phytohormone homeostasis or perception by A. cocklensis and A. bryophytorum. This study unveils specific aspects of the Actinacidiphila-Arabidopsis interaction, which implies molecular processes impaired in the chs5 mutant and otherwise at play in the wild-type. More generally, this study highlights complex and distinct molecular interactions between Arabidopsis thaliana and bacteria belonging to the Actinacidiphila genus.
2024-01-29 | PXD041221 | Pride
Project description:To comprehensively investigate the effects of glutathione on the gene expression, the microarray analysis was performed in the glutathione-fed wild-type Arabidopsis thaliana. Wild-type Arabidopsis (ecotype Columbia-0) were fed with 1 mM oxidized glutathione (GSSG) and 2 mM reduced glutathione (GSH) for comparison at equal nitrogen equivalents. To examine the effects of glutathione other than nitrogen at equal nitrogen equivalents, plants were fed with 3 mM NH4NO3. Plants grown by water were used as a control.
2023-08-01 | GSE228403 | GEO
Project description:Transcriptional profiling of Arabidopsis thaliana 12-days old seedlings comparing Col-0 wild type with transgenic plants with altered expression of dual-targetting plastid/mitochondrial organellar RNA-polymerase RPOTmp. Transgenic plants used for experiment were: overexpressor plants obtained by transformation of Col-0 WT plants with genetic constructs created in [Tarasenko et al., 2016] contained catalytic part of RPOTmp enzyme with transit peptides of RPOTm (mitochondrial) and RPOTp (plastid) by agrobacterial transformation; plants with complementation of RPOTmp functions in mitochondria or chloroplasts obtained from transformation of GABI_286E07 rpotmp knockout-mutant plants with genetic constructs created in [Tarasenko et al., 2016]. Goal was to determine the effects of RPOTmp knockout/overexpression on global Arabidopsis thaliana gene expression.
2023-12-25 | GSE251661 | GEO