Endothelium-Transcriptome analysis of the tannin-producing cells in Arabidopsis
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE8063 | GEO | 2007/06/20
SECONDARY ACCESSION(S): PRJNA100897
REPOSITORIES: GEO
Similar Datasets
Project description:Arabidopsis seeds expressing the castor fatty acid hydroxylase accumulate hydroxylated fatty acids up to 17% of total fatty acids in seed triacylglycerols, however total seed oil is also reduced up to 50%. Investigations into the cause of the reduced oil phenotype through in vivo [14C]acteate and [3H]2O metabolic labeling of developing seeds surprisingly revealed that the rate of de novo fatty acid synthesis within the transgenic seeds was approximately half that of control seeds. Addition of castor phospholipid:diacylglycerol acyltransferase (PDAT) increased hydroxylated fatty acid content of the seed oil, increased the rate of fatty acid synthesis, and mostly restored seed oil levels. RNAseq analysis indicated no changes in expression of fatty acid synthesis genes in hydroxylase-expressing plants.
2014-01-10 | GSE53952 | GEO
Project description:Arabidopsis seeds expressing the castor fatty acid hydroxylase accumulate hydroxylated fatty acids up to 17% of total fatty acids in seed triacylglycerols, however total seed oil is also reduced up to 50%. Investigations into the cause of the reduced oil phenotype through in vivo [14C]acteate and [3H]2O metabolic labeling of developing seeds surprisingly revealed that the rate of de novo fatty acid synthesis within the transgenic seeds was approximately half that of control seeds. Addition of castor phospholipid:diacylglycerol acyltransferase (PDAT) increased hydroxylated fatty acid content of the seed oil, increased the rate of fatty acid synthesis, and mostly restored seed oil levels. RNAseq analysis indicated no changes in expression of fatty acid synthesis genes in hydroxylase-expressing plants. Transcript profiles of Arabidopsis developing seeds of three lines, at three stages of development were generated by deep sequencing, in triplicate, using Illumina.
2014-01-10 | E-GEOD-53952 | biostudies-arrayexpress
Project description:Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops yield visually homogenous seeds. Using automated phenotype analysis, we observed that in Arabidopsis small seeds tend to have higher primary and secondary dormancy levels when compared to large ones. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds had higher expression of translation-related genes implicated in germination competence. In contrast, small seeds showed elevated expression of many positive regulators of dormancy, including a key regulator of this process – the DOG1 gene. Differences in DOG1 expression were associated with differential production of its alternative cleavage and polyadenylation isoforms where in small seeds proximal poly(A) site is selected resulting in a short mRNA isoform. Furthermore, single-seed RNA-seq analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single seed level, the expression of genes affected by seed size was correlated with the expression of genes positioning seeds on the path towards germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species producing highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.
2023-10-16 | GSE203310 | 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
Project description:To establish the basis for understanding molecular mechanism of seed germination response to temperature, we analyzed transcriptomes in freshly harvested dormant and dry stored after-ripened seeds. The after-ripened seeds started to show visible germination from 36h after the start of imbibition, and almost all the seeds germinated after 3 days. The freshly harvested seeds stayed dormant by imbibition at 26°C, and germination of the after-ripened seeds was almost completely inhibited at 34°C. Total RNA was prepared from 0 (dry), 6 and 24h imbibed seeds to find regulatory genes of seed dormancy and germination.
2023-10-20 | GSE229182 | GEO
Project description:ra12-02_aba-seed - ra12-02_aba-seed - Identification of ABA signaling factors and targets in Arabidopsis developing seeds by comparing ABA deficient and wild type genotypes - Transcriptome comparison of developing seeds harvested at 10 DAP from two ABA-deficient mutants (nced2 nced5 nced9 and nced2 nced5 nced6 nced9) and wild type (Columbia-0)
2019-01-25 | GSE125573 | GEO
Project description:We collected linear-cotyledon stage seed compartments from 5 to 7 micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments from seeds containing linear-coyledon-stage embryos. For the purposes of this study we captured 7 compartments: embyro proper, cellularized endosperm, chalazal endosperm, chalazal seed coat, general seed coat, whole seeds and micropylar endosperm.
2008-08-12 | GSE12403 | GEO
Project description:We collected pre-globular stage seed compartments from 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of seeds containing pre-globular-stage embryos was identified as those seeds containing embryo propers made up of between 2 and 8 cells. For the purposes of this study we captured 6 compartments: embyro proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and general seed coat. Serial sections of entire seeds were also captured for comparison. Keywords: cell type comparison
2008-08-12 | GSE12402 | GEO
Project description:Mannitol is a sugar alcohol that serves as a compatible solute contributing to exceptional salt tolerance in several plant species. Arabidopsis plants transformed with the mannose-6-phosphate reductase (M6PR) gene from celery were dramatically more salt tolerant. Following treatment with 100mM NaCl, transgenic plants, relative to wild type (WT), were more successful in bolting, flowering, and production of viable seed, were less chlorotic/necrotic, and with less inhibition of growth (leaf number, rosette diameter, plant height, stalk number, and dry weight). When irrigated with 200 mM NaCl, both transformants and WT plants died without producing seeds, but M6PR transformants bolted and showed significantly less chlorosis and necrosis and had higher survival rates and dry weights than those of WT. Under normal growth conditions there were no negative effects of the M6PR transgene on overall growth (leaf number, rosette diameter, plant height, stalk number, and dry weight), or time to bolting/flowering or seed production compared to wild type (WT). Despite the lack of effects on phenotype in the absence of salt stress, genome wide expression analyses indicated that expression levels of more than 2000 genes were altered by presence of the M6PR transgene: however, there were many fewer differences observed between the M6PR and non-transgenic plants in the presence of salt stress (459), suggesting that M6PR pre-conditioned the plants for exposure to salinity. Gene categories most affected in the M6PR transgenic plants were involved in DNA binding, signal transduction, metabolism/energy, cell structure, membrane transport, defense response, and transcription. Notably, a large number of known stress genes were induced, including those related to cell walls, biotic stress, and ABA- and ethylene-responses. Our work and that in other labs has suggested that mannitol acts as an osmoprotectant, but mannitol levels are invariably quite low, and perhaps inadequate to explain its effects as an osmoprotectant. The gene expression data here indicate that stress tolerance of mannitol-producing Arabidopsis is also due, at least in part, to enhanced expression of a number of stress inducible genes related to both biotic and abiotic stress tolerance. Both M6PR transgenic and Col WT plants were grown in the growth chamber in the absence and presence of salt stress. Plants from 20 days after sowing (6 days after salt treatment) were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and salt treatment combination.
2010-03-07 | E-GEOD-18217 | biostudies-arrayexpress
Project description:As part of an investigation into mechanisms of HDG silencing in Arabidopsis, we have produced transgenic plants containing extra copies of the chalcone synthase (CHS) gene. The CHS gene mediates an early step in the biosynthesis of the purple pigment anthocyanin. The insertion of extra copies of CHS in Arabidopsis caused the gene to be silenced in some plants. Seeds harvested from these CHS-silenced plants were mutated by treatment with ems. The progeny of these seeds were screened for "revertants" in which the effects of CHS silencing was alleviated and plants were able to produce anthocyanin. These revertants were found to contain a single recessive mutation; the trait has been termed hog1 (for homology dependant gene silencing 1). Our previous experiment used the Affymetrix 8200 chip to make comparisons between gene expression in the two genetic variants: the CHS-silenced type (ECG) and the anthocyanin-producing revertants (15B). Results showed that there were over 100 genes with at least a 10-fold increase or decrease in expression. However, the variation between 2 reps of each genetic variant was high. We would now like to carry out a modified version of this experiment using the 25K Affymetrix chip. It is intended to increase the number of reps to 4, and take samples at an earlier stage than previously in order to decrease the effect of developmental spread. To reduce the effects of interplant variability, samples will be generated from total plant tissue from a pool of 10 plants at GS 1.04. RNA will be purified using RNeasy kits from Qiagen.
2022-11-21 | E-NASC-36 | biostudies-arrayexpress