E-GEOD-38344
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-38344 | ExpressionAtlas | 2019-01-08
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-38344-analysis-methods.tsv | Tabular | |||
| E-GEOD-38344-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-38344-coexpressions.tsv.gz | Tabular | |||
| E-GEOD-38344-configuration.xml | Xml | |||
| E-GEOD-38344-factors.xml | Xml |
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Project description:This reports the transcript profiling of the aleurone and starchy endosperm layers of wheat seed over 3 time points critical in the development of the aleurone layer. Wheat is a critical food source globally. The aleurone layer develops from the starchy endosperm and is a concentrated source of vitamins and minerals, essential for the germination of the plant embryo. However the molecular mechanisms behind the development of this layer remain poorly understood. Here we present the first direct systematic comparison of the transcriptomes of the aleurone and starchy endosperm tissues of the wheat seed (Triticum aestivum) at time points critical to the development of the aleurone layer of 6, 9 and 14 days post anthesis. Gene expression patterns reflect the changing role of these tissues in seed development. Illumina sequencing gave 25 to 55 million sequence reads per tissue, of the trimmed reads, 70 – 81% mapped to reference expressed sequence transcripts. To quantify transcript abundance, RNA-Seq normalisation was performed to generate RPKM values, these were used in comparative analyses between the tissues at each time point using Kals Z-test. Sequences with significantly different RPKM values were categorised on the basis of tissue and time point expression and functionally annotated using standardised gene ontology vocabularies, revealing two very distinct tissues. In conclusion we show the relationships between and the fundamental biological reprogramming of the two major biologically and economically significant tissues of the wheat seed over time. Understanding these changes in gene expression profiles is essential to mining the potential these tissues hold for human nutrition and contributing to foundational and systems biology of this important crop. Examines the transcript profile of aleurone and starchy endoperm tissues at 6,9 and 14DPA. A minimum of 5 individual seeds from 3 separate spikes from three individual plants were pooled for each tissue preparation.
2012-08-15 | E-GEOD-38344 | biostudies-arrayexpress
Project description:This reports the transcript profiling of the aleurone and starchy endosperm layers of wheat seed over 3 time points critical in the development of the aleurone layer. Wheat is a critical food source globally. The aleurone layer develops from the starchy endosperm and is a concentrated source of vitamins and minerals, essential for the germination of the plant embryo. However the molecular mechanisms behind the development of this layer remain poorly understood. Here we present the first direct systematic comparison of the transcriptomes of the aleurone and starchy endosperm tissues of the wheat seed (Triticum aestivum) at time points critical to the development of the aleurone layer of 6, 9 and 14 days post anthesis. Gene expression patterns reflect the changing role of these tissues in seed development. Illumina sequencing gave 25 to 55 million sequence reads per tissue, of the trimmed reads, 70 – 81% mapped to reference expressed sequence transcripts. To quantify transcript abundance, RNA-Seq normalisation was performed to generate RPKM values, these were used in comparative analyses between the tissues at each time point using Kals Z-test. Sequences with significantly different RPKM values were categorised on the basis of tissue and time point expression and functionally annotated using standardised gene ontology vocabularies, revealing two very distinct tissues. In conclusion we show the relationships between and the fundamental biological reprogramming of the two major biologically and economically significant tissues of the wheat seed over time. Understanding these changes in gene expression profiles is essential to mining the potential these tissues hold for human nutrition and contributing to foundational and systems biology of this important crop.
2012-08-15 | GSE38344 | GEO
Project description:Grain development is a key life cycle stage of many plants. The development of seeds is the basis of agriculture and the primary source of calories consumed by humans. Here, we employ laser micro dissection (LMD) combined with shotgun proteomics to generate a cell-type proteome atlas of developing wheat endosperm at the early and late grain filling stages. We identified 1803 proteins from four different cell layers (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE), and endosperm transfer cells (ETCs)) of developing endosperm at 15 Days after anthesis (DAA) and 26 DAA. Sixty-seven differentially expressed proteins in the aleurone, 31 in the sub-aleurone, 27 in the starchy endosperm, and 50 in the endosperm transfer cells were detected between these two-time points. The results revealed highly distinguishable proteome dynamics in the different cell layers of endosperm over the time course. We observed high general metabolic activity of the grain with regard to carbohydrate metabolism, defence against oxidative stress, and signalling in the different cell layers during the grain filling process. Cell-specific identification of SUT and GLUT transporters suggest a grain filling model via nucellar projections and endosperm transfer cells (ETCs) initiating starch biosynthesis in the starchy endosperm (SE). The identification and regulation dynamics of proteins in the different cell layers demonstrate a functional switch of the proteome from the early to the late grain filling stage. Based on these data, we proposed a model for sugar loading and starch biosynthesis in wheat developing endosperm, including an abundance switch of cell-type-specific key proteins.
2024-12-11 | PXD035848 | Pride
Project description:Transcriptional profiling of developing rice endosperm at seven days after flowering comparing aleurone layers with central starchy endosperm. Cereal productivity is dependent on the accumulation of storage compounds in the endosperm, a nutritive tissue that is composed of aleurone cells in the outermost regions and starchy endosperm in the inner region. The transcriptional analyses provides clues to the molecular basis for different metabolic pathways in response to the spatial and nutritional differences between rice aleurone cells and starchy endosperm.
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Project description:Transcriptional profiling of developing rice endosperm at seven days after flowering comparing aleurone layers with central starchy endosperm. Cereal productivity is dependent on the accumulation of storage compounds in the endosperm, a nutritive tissue that is composed of aleurone cells in the outermost regions and starchy endosperm in the inner region. The transcriptional analyses provides clues to the molecular basis for different metabolic pathways in response to the spatial and nutritional differences between rice aleurone cells and starchy endosperm. Two-condition experiment, Aleurone layers vs. central starchy endosperm. 3 biological replicates with color swap for each biological replicate
2012-11-27 | E-GEOD-42489 | biostudies-arrayexpress
Project description:The high molecular weight (HMW) subunits of wheat glutenin are synthesised only in the starchy endosperm tissue of the developing wheat grain. The transcriptomes of the lines L88-18 and L88-31 (Lawrence, G.J., Macritchie, F. & Wrigley, C.W. Dough and baking quality of wheat lines in glutenin subunits controlled by Glu-A1, Glu-B1 and Glu-D1 loci. J. Cereal. Sci. 7,109-112 (1988)) coming from the same cross were compared. Transcriptomes analysis was performed in endosperm tissue (14 and 28 days post anthesis-dpa) and in leaf tissue (8 days post germination dpg). Each of the transcriptome comparisons was performed using three biological replicates (i.e. per line/tissue /developmental stage selected). Hybridisations were performed in reverse dye labelling.
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Project description:Inner pericarp, outer pericarp and endosperm layers from developing grain of bread wheat cv. Holdfast at 12 days post-anthesis.
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Project description:Tissue layers from developing wheat grain at 12 days post-anthesis
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Project description:The high molecular weight (HMW) subunits of wheat glutenin are synthesised only in the starchy endosperm tissue of the developing wheat grain. We studied the effect of introducing transgenes on the global gene expression profiles of selected transgenic wheat lines, particularly during wheat seed development. For these particular set of experiments a direct comparison between the hexaploid bread transgenic line B102,1-1 (Rooke, L., Steele, S.H., Barcelo, P.,Shewry, P.R. & Lazzeri,P. Transgene inheritance, segregation and expression in bread wheat. Euphytica 129, 301-309 (2003)) and it background, non transformed L88-31 wheat line (Lawrence,G.J., Macritchie, F. & Wrigley, C.W. Dough and baking quality of wheat lines in glutenin subunits controlled by Glu-A1, Glu-B1 and Glu-D1 loci. J. Cereal. Sci. 7,109-112 (1988)) was performed. Transcriptome comparison analysis was performed in endosperm tissue (14 and 28 days post anthesis-dpa) and in leaf tissue (8 days post germination ?dpg). The transcriptome comparisons analysis was performed using three biological replicates (i.e. per line/tissue /developmental stage selected). Hybridisations were performed in reverse dye labelling.
2005-10-05 | E-MEXP-306 | biostudies-arrayexpress
Project description:The high molecular weight (HMW) subunits of wheat glutenin are synthesised only in the starchy endosperm tissue of the developing wheat grain. We compared the expressed genomes of the transgenic wheat line B102,1-1 (Rooke et al. Transgene inheritance, segregation and expression in bread wheat. Euphytica 129, 301-309 (2003)). Both lines were shown to express the HMW-GS Ax1 gene (Halford, N.G. et al. Analysis of HMW glutenin subunits encoded bychromosome 1A of bread wheat (Triticum aestivum L.) indicates quantitative effects on grain quality. Theor Appl Genet 83, 373-378 (1992).) to the expressed genome of conventionally bred wheat line L88-18 (Lawrence et al. Dough and baking quality of wheat lines in glutenin subunits controlled by Glu-A1, Glu-B1 and Glu-D1 loci. J. Cereal. Sci. 7,109-112 (1988)) which results in the same effects on traits. Transcriptomes comparison analysis was performed in endosperm tissue (14 and 28 days post anthesis-dpa) and in leaf tissue (8 days post germination dpg), respectively. Each of the transcriptome comparisons was performed using three biological replicates (i.e. per line/tissue /developmental stage selected). Hybridisations were performed in reverse dye labelling.Exceptionally, biological replica 2 was only performed for B102,1-1 (green)/L88-18 (red) labelling and not swap
2005-10-05 | E-MEXP-309 | biostudies-arrayexpress