Ontology highlight
ABSTRACT:
PROVIDER: PRJNA389482 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5649982_1.fastq.gz | Fastqsanger.gz | |||
| SRR5649982_2.fastq.gz | Fastqsanger.gz | |||
| SRR5649983_1.fastq.gz | Fastqsanger.gz | |||
| SRR5649983_2.fastq.gz | Fastqsanger.gz | |||
| SRR5649984_1.fastq.gz | Fastqsanger.gz |
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Project description:Bermudagrass is an important warm-season turfgrass species with both erect growing shoots and prostrate growing stolons, however, the mechanism how bermudagrass shoots and stolons form and maintain their unique geotropic growth modes are still unclear. In this study, we compared the proteome of the internode section of shoots and stolons at the same developmental stage in bermudagrass cultivar Yangjiang. The results indicated that 376 protein species were differentially accumulated in the two types of stems.
2019-09-12 | PXD012336 | Pride
Project description:As an important perennial warm-season turfgrass species, bermudagrass (Cynodon dactylon L.) form underground-growing rhizomes and aboveground-growing stolons simultaneously, making it a fast propagating clonal plant with strong regeneration ability. However, the intrinsic difference between the two types of specialized stems are still uncharacterized, especially at the molecular level. In the current study, we compared the internode proteomes of rhizomes and stolons at the same developmental stage in the bermudagrass cultivar Yangjiang using isobaric tags for relative and absolute quantitation (iTRAQ). The results indicated that 228 protein species were differentially accumulated in the two specialized stems. These DAPs comprise complex protein networks to finely regulate diverse cellular activities in the two types of specialized stems. Notably, photosynthesis and flavonoid biosynthesis were significantly regulated in stolons, whereas sucrose and starch metabolism were significantly regulated in rhizomes.
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Project description:Transcriptome Analysis of LincRNA TUNA Knockdown in Mouse Embryonic Stem Cells
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Project description:Stem internodes of grasses function in mechanical support, transport, and, in some species are a major sink organ for carbon in the form of cell wall polymers. To establish the rice elongating internode as a model for secondary cell wall development, we conducted cell wall composition, proteomic and metabolomic analyses of the second rice internode at booting stage. We measured major secondary cell wall components along eight segments of an elongating internode. Cellulose, lignin, and xylose increase as a percentage of cell wall material from the younger to the older internode segments, indicating active cell wall synthesis. With the whole elongating internode, we measured peptides via liquid-chromatography mass spectrometry (LC-MS) following trypsin digestion of size fractionated proteins. This identified a total of 3249 protein groups with at least two unique peptides, including many glycosyltransferases, acyltransferases, glycohyrolases, cell wall-localized proteins, and protein kinases that have or may have functions in cell wall biosynthesis or remodeling. In addition, GO over-representation analysis and KO pathway analysis indicate many proteins involved in biosynthetic processes, especially the synthesis of secondary metabolites such as phenylpropanoids, flavonoids, and tepenoids. Therefore, we also used LC-MS to measure methanol-extracted secondary metabolites from the whole internode at the elongation stage and three post-elongation stages, and from leaf and root at the second post-elongation stage. The results indicate secondary metabolites in stems are distinct from those of roots and leaves, and show different profiles during stem development. This study fills a void of knowledge of proteomics and metabolomics data for grass stems, especially of rice, and provides baseline knowledge for more detailed studies of cell wall synthesis and other biological processes during internode development. This and future work is aimed at optimizing stem development and cell wall composition of grasses to improve agronomic properties and biofuel production.
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Project description:We report the application of laser capture microdissection (LCM) for high resolution transcriptome profiling of the second internode of the Arabidopsis thaliana inflorescence stem. In this series, we used LCM to determine and compare the transcriptome profiles of the phloem cap, the pith, and the remaining vascular bundle area.
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Project description:Background. Carbon allocation between vegetative and reproductive tissues impacts cereal grain production. Despite their great agricultural importance, sink-source relationships have not been fully characterized at early reproductive stages in maize. Here we quantify the accumulation of non-structural carbohydrates and patterns of gene expression in the top internode of the stem and the female inflorescence of maize at the onset of grain filling (reproductive stage R1). Methods. Top internode stem and female inflorescence tissues of the Puma maize inbred line were collected at reproductive stage R1 (without pollination). The accumulation of non-structural carbohydrates was quantified by spectrophotometry. Global gene expression was evaluated in both tissues by RNA sequencing. Results. At reproductive stage R1, the maize female inflorescence accumulates non-structural carbohydrates, notably starch, at higher levels than the top internode of the stem. Gene expression analysis identified 491 genes to be differentially expressed between the female inflorescence and the stem top internode. Gene ontology classification of differentially expressed genes showed enrichment for sucrose synthesis, the light-dependent reactions of photosynthesis, and transmembrane transporters. Our results suggest that sugar transporters play a key role in sugar partitioning in the maize stem and reveal previously uncharacterized differences between the female inflorescence and the top internode of the stem at early reproductive stages.
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Project description:We report the deep sequencing of small RNA populations derived from apex, internode 3, internode 6, internode 16, leaf +3, calli and suspesion cells from sugarcane cultivar Q117
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