Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA116653 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in aba2-1, cyp707a1-1a2-1a3-1 triple mutants seeds, embryo and endosperm tissues
2010-04-16 | GSE15700 | GEO
Project description:Untargeted metabolomic analyses were carried out on seed coat/endosperm and seed embryo (dry seeds) of Arabidopsis thaliana Columbia-0 genotype. Three biological replicates were analyzed for each sample.
| MSV000095844 | MassIVE
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in aba2-1, cyp707a1-1a2-1a3-1 triple mutants seeds, embryo and endosperm tissues Freshly harvested seeds were imbibed in 8.5 cm Petri dishes containing two filter papers (approximately 7 cm diameter) and 2 mL of water and harvested. Dissection of embryo and endosperm from 24-h-imbibed seeds was carried out under a stereoscopic microscope. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.
2010-04-15 | E-GEOD-15700 | biostudies-arrayexpress
Project description:This series analyses germinating Arabidopsis seeds with both temporal and spatial detail, revealing two transcriptional phases that are separated with respect to testa rupture. Performed as part of the ERA-NET Plant Genomics grant vSEED. Arabidopsis seeds were dissected into four tissues at nine time-points during seed germination. The tissues were the combined micropylar and chalazal endosperm (MCE), the remaining endosperm (PE), the radicle and embryonic axis (RAD) and the cotyledons (COT). At testa and endosperm rupture the seeds were sampled in separate pre- and post-ruptured populations.
2013-07-16 | E-GEOD-41212 | biostudies-arrayexpress
Project description:Untargeted metabolomic analyses were carried out on seed coat/endosperm and seed embryo (dry seeds) of Arabidopsis thaliana Columbia-0 genotype. Three biological replicates were analyzed for each sample.
| MSV000095844 | GNPS
Project description:In Arabidopsis mature seeds, the onset of the embryo-to-seedling transition is nonautonomously controlled, being blocked by endospermic abscisic acid (ABA) release under unfavorable conditions. Mature embryos lack an impermeable cuticle, unlike seedlings, consistent with their endospermic ABA uptake capability. Seedling cuticle formation occurs after germination rather than during embryogenesis. Mature endosperm removal prevents seedling cuticle formation and seed reconstitution by endosperm grafting onto embryos shows that the endosperm promotes seedling cuticle development. Grafting different endosperm and embryo mutant combinations, together with biochemical, microscopy and mass spectrometry approaches, reveals that endospermic release of Tyrosyl Sulfate Transferase (TPST)-sulfated CIF2 and PSY1 peptides promotes seedling cuticle development. Endosperm-deprived embryos produced nonviable seedlings bearing numerous developmental defects, in a manner unrelated to embryo nourishment, all restored by exogenously provided endosperm. Hence, seedling establishment is nonautonomous, requiring the mature endosperm.
2021-11-10 | PXD028576 | Pride
Project description:Seeds are the basis of agriculture, yet their full transcriptional complexity has remained unknown. Here, we employ single-nucleus RNA-sequencing to characterize developing Arabidopsis thaliana seeds, with a focus on endosperm. Endosperm, the site of gene imprinting in plants, mediates the relationship between the maternal parent and embryo. We identify new cell types in the chalazal endosperm region, which interfaces with maternal tissue for nutrient unloading. We further demonstrate that the extent of parental bias of maternally expressed imprinted genes varies with cell cycle phase, and that imprinting of paternally expressed imprinted genes is strongest in chalazal endosperm. These data indicate imprinting in endosperm is heterogeneous and suggest that parental conflict, which is proposed to drive the evolution of imprinting, is fiercest at the boundary between filial and maternal tissues.
2021-04-06 | GSE157145 | GEO
Project description:H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction. H2A.X is encoded by two genes in Arabidopsis genome, HTA3 and HTA5. We generated h2a.x double mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However, h2a.x mutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under the H2A.X promoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation in h2a.x developing seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide in h2a.x mutant seeds. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling. h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA. Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Alternatively, H2A.X may be involved in recruiting methyltransferases to those sites. Overall, our data show that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.
2023-08-07 | GSE233920 | GEO
Project description:Arabidopsis seed germination is coordinated with the strong induction of metabolic pathways required for the mobilisation and utilization of seed storage reserves. These are essential to support the seedling before the establishment of photoauxotrophic growth. The activity of genes encoding enzymes required for lipid mobilisation is regulated largely at the level of transcription, but our knowledge of how this regulation occurs is extremely limited. After germination the rate of lipid reserve mobilisation is determined by the carbohydrate status of the seedling and by the osmotic potential of the growth substrate. The plant response to both of these requires the action of the hormone abscisic acid (ABA). We have shown that this regulation is tissue specific (Penfield et al., 2004 Plant Cell 16, 2705-2718), and that although lipid breakdown in the embryo is inhibited by ABA, lipid breakdown in the endosperm tissues is not. Furthermore, in many species the action of the endosperm is central to the processes controlling seed germination, yet very little is known about gene expression in this tissue, or of the function of the endosperm in mature Arabidopsis seeds. Mature Arabidopsis seeds can be dissected into embryo and endosperm/seed coat fractions, with the latter fraction containing RNA only from the endosperm as the seed coat cells undergo programmed cell death during the latter stages of seed development. In this experiment we divide seeds into embryo and endosperm tissues and transcript profile both shortly after germination, or when germination and lipid reserve mobilisation are inhibited by ABA or by the gibberellin biosynthesis inhibitor paclobutrazol. In this way we can discover the endosperm transcriptome and uncover candidate regulators of lipid mobilisation by searching for genes showing differential expression between embryo and endosperm before and after ABA treatment. Experimenter name = Steven Penfield Experimenter phone = 01904 328759 Experimenter fax = 01904 328762 Experimenter department = Department of Biology Experimenter institute = Centre for Novel Agricultural Products Experimenter address = University of York Experimenter address = PO BOX 373 Experimenter address = York Experimenter zip/postal_code = YO10 5YW Experimenter country = UK Keywords: organism_part_comparison_design
2007-01-08 | GSE5751 | GEO
Project description:Seeds are comprised of three major parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. Each seed part undergoes distinct developmental programs during seed development. What methylation changes occur in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of two major parts of Arabidopsis mature green stage seeds, the seed coat and embryo, using Illumina sequencing.
2014-05-17 | GSE57755 | GEO