Arabidopsis thaliana Cybrids - Whole Genome Sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB29654 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Reciprocal cybrids reveal how organellar genomes affect plant phenotypes
| PRJEB35324 | ENA
Project description:Knockout of the N-acetyltransferase AtNAA50 causes severe dwarfism the model plant Arabidopsis thaliana but does not affect the activity of the essential NatA complex.
2020-05-27 | PXD017663 | JPOST Repository
Project description:Epigenetic variation can impact gene transcription and may play roles in phenotypic diversity and adaptation. Here we report 1,107 high quality single-base resolution methylomes, and 1,210 transcriptomes from the 1001 Arabidopsis Genomes population. Analyses reveal strong effects of geographic origin on average DNA methylation levels, alterations of gene expression by epialleles and a highly complex genetic basis for DNA methylation. Physical genome maps for nine of the most diverse accessions revealed how transposable elements and other structural variations shaped the epigenome to allow rapid adaptation to environmental changes, with strong emphasis on disease resistance. Analysis of the cistromes and epicistromes in these accessions revealed a significant association between both methylation and nucleotide variation and the conservation of transcription factor binding sites. The Arabidopsis thaliana 1001 Epigenomes Project now provides a comprehensive resource to help further understand how epigenetic variation contributes to both molecular and phenotypes in natural populations of the most widely studied reference plant.
2016-07-14 | GSE80744 | GEO
Project description:Plants need to be able to respond to changes quickly due to the inability of a plant to change location. Hormones within the plant signal for these transcriptional changes that will affect the plant's ability to survive. Strigolactone is a plant hormone that was more recently discovered so has a less detailed understanding of what genes it regulates, compared to other plant hormones. First published in Brewer et al 2016, PNAS We used microarrays to determine transcriptional responses in strigolactone mutants and in wild-type plants with various physiological treatment which affect hormone levels over 24 hours.
2023-03-19 | GSE226903 | GEO
Project description:Mitochondria generate signals of adaptation that regulate nuclear genes expression via retrograde signaling. But this phenomenon is complexified when qualitatively different mitochondria and mitochondrial DNA (mtDNA) coexist within cells. Although this cellular state of heteroplasmy leads to divergent phenotypes clinically, its consequences on cellular function and the cellular transcriptome are unknown. To interrogate this phenomenon, we generated somatic cell cybrids harboring increasing levels of a common mtDNA mutation (tRNALeu(UUR) 3243A>G) and mapped the resulting cellular phenotypes and transcriptional profiles across the complete range of heteroplasmy. Small increases in mutant mtDNAs caused relatively modest defect in mitochondrial oxidative capacity, but resulted in sharp transitions in mitochondrial ultrastructure and in the nuclear and mitochondrial transcriptomes, with the critical functional threshold corresponding to the induction of epigenetic regulatory systems. Principal component analysis underscores how each heteroplasmy level occupies a different "transcriptional space", with low levels heteroplasmy (20-30%) producing a dose-response linear progression in one direction, and mutationload of 50, 60 and 90% producing changes in the opposite direction. Hence, subtle changes in mitochondrial energetics can act through the epigenome to generate the phenotypes of the common “complex” diseases. Cells were generated by transferring the wildtype (3243A) and mutant (3243G) mtDNAs from a heteroplasmic 3243A>G patient’s lymphoblastoid cell line into 143B(TK-) mtDNA-deficient (ρo) cells and selected for transmitochondrial cybrids. Subsequent mtDNA depletion, reamplification, and cloning (Wiseman and Attardi, 1978) resulted in a series of stable cybrids harboring approximately 0, 20, 30, 50, 60, 90, and 100% 3243G mutant mtDNAs. Total RNA extracted from each cell line was then extracted, depleted of rRNA, and measured in sequenced in triplicates.
2014-09-02 | E-GEOD-56158 | biostudies-arrayexpress
Project description:RNA Sequencing of transmitochondrial cybrids revealed a downregulation of oxidative phosphorylation and nicotinamide metabolism in cybrids with patient mitochondria
2022-10-19 | GSE215859 | GEO