Ontology highlight
ABSTRACT:
PROVIDER: PRJNA503133 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8141400.fastq.gz | Fastqsanger.gz | |||
| SRR8141401.fastq.gz | Fastqsanger.gz | |||
| SRR8141402.fastq.gz | Fastqsanger.gz | |||
| SRR8141403.fastq.gz | Fastqsanger.gz | |||
| SRR8141404.fastq.gz | Fastqsanger.gz |
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Project description:Eucalyptus grandis e Eucalyptus globulus are among the most widely cultivated trees, differing in lignin composition and plantation areas. As temperature is a key modulator in plant metabolism, a large-scale proteome analysis was carried out to investigate changes induced in plantlets grown at different temperatures.
2017-09-25 | PXD005743 | Pride
Project description:Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. It is essential to maximize the effectiveness of these plantations by increasing their productivity, the quality and value of their products. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven individual E. grandis trees. A 1532-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP fragments and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) and could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated. A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes.
2009-10-01 | GSE14707 | GEO
Project description:The daily cycle of night and day affects the behaviour and physiology of almost all living things. At the molecular level, many genes show daily changes in expression levels. To determine whether changes in transcript abundance occur in wood forming tissues of Eucalyptus trees we used a cDNA microarray to examine gene expression levels at roughly four hour intervals throughout the day. Experiments were performed using RNA extracted from two biological replicates - GU (Eucalyptus grandis x E. urophylla) and GC (Eucalyptus grandis x camaldulensis) trees. A loop design was used, linking six time points. A dye swap was incorporated to eliminate dye bias.
2010-06-25 | E-GEOD-11731 | biostudies-arrayexpress
Project description:Eucalyptus rust is caused by the biotrophic fungus, Austropuccinia psidii, which affects commercial plantations of Eucalyptus, a major raw material for the pulp and paper industry in Brazil. Aiming to uncover the molecular mechanisms involved in rust resistance and susceptibility in Eucalyptus grandis, we used epifluorescence microscopy to follow the fungus development inside the leaves of two contrasting half-sibling genotypes (rust-resistance and rust-susceptible), to determine the time-course for comparative metabolomic and proteomic analyses in plantlets artificially inoculated with rust. Within 24 hours of complete fungal invasion, a total of 709 plant metabolites showed that the rust-resistant genotype suppressed many metabolites 6 hours after inoculation (hai), with responses being progressively induced after 12 hai. In contrast, the rust-susceptible genotype displayed an alternated metabolite response to infection, which culminated in a strong suppression at 24 hai. Multivariate analyses of genotypes and time points were used to select 16 differential metabolites chemically classified as flavonoids, benzenoids and other compounds. Applying the Weighted Gene Co-Expression Network Analysis (WGCNA), rust-resistant and rust-susceptible genotypes had, respectively, 871 and 852 proteins grouped into 14 and 13 modules, of which 10 and 7 protein modules were significantly correlated to the selected metabolites. Functional analyses revealed roles for oxidative-dependent responses leading to temporal activity of metabolites and proteins after 12 hai in rust-resistance, while the initial over-accumulation of metabolites and correlated proteins caused a lack of progressive response after 12 hai in rust-susceptible genotype. This study provides a brief understand on the temporal divergences of resistant and susceptible molecular responses of E. grandis plants to rust.
2021-09-09 | PXD021280 | Pride
Project description:Illumina HiSeq technology was used to generate mRNA profiles from in vitro Eucalyptus grandis roots interacting with two different Pisolithus microcarpus strains (SI-9 and SI-12) and under two different CO2 concentrations (400 and 650 ppm) . Control roots or ectomycorrhizal root tips were harvested after 1 month and used for RNA extraction. Paired-end (2X150bp) reads were generated and aligned to Eucalyptus grandis transcripts (http://www.phytozome.net/; primarytranscripts only) using CLC Genomics Workbench 6.
2014-10-10 | GSE62227 | GEO
Project description:Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. It is essential to maximize the effectiveness of these plantations by increasing their productivity, the quality and value of their products. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven individual E. grandis trees. A 1532-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP fragments and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) and could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated. A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes. Transcriptional profiling and genotyping of seven E. grandis trees , namely (741-H (high lignin), 108-L (low lignin), 243-L (low lignin), 1/23/4-HS (high splitting), 1/71/6-HS (high splitting), 1/91/7-LS (low splitting) and 1/92/7-LS (low splitting), were performed with an in-house spotted cDNA microarray. All trees were characterized for their splitting qualities and lignin content and only the trees best corresponding to the selected traits were used for further analysis (Verryn and Turner 2000). RNA was isolated and cDNA synthesis was performed. A reference design microarray experiment was conducted and tree 1/23/4-HS served as a reference. Samples were fluorescently labelled with Cy5 or Cy3 dye and co-hybridized overnight. Two biological and one technical replicate (using independent labelling reactions) was performed, each replication consisting of a reverse labelling experiment.
2009-10-01 | E-GEOD-14707 | biostudies-arrayexpress
Project description:The study was conducted to identify differentially expressed polyethylene glycol (PEG) induced water stress responsive genes in E. grandis. Forty day old rooted cutting of E. grandis was subjected to -0.225 MPa PEG treatment and total RNA was isolated from leaves of water treated control and PEG treated samples after three hours of treatment. The differential expression of water stress responsive genes was analyzed using microarray technique. Agilent two-color experiment, Organism: Eucalyptus,Custom Agilent Eucalyptus 8x60k Microarray Gene expression (AMADID: 59849 ) designed by Genotypic Technology Pvt.Ltd.
2016-07-03 | E-GEOD-73106 | biostudies-arrayexpress
Project description:In order to pinpoint the most differentially expressed genes between Eucalyptus grandis leaf blades and vascular (xylem) tissues as well as between E. grandis and Eucalyptus globulus xylem tissues, a total number of nine 50mer-oligoprobes covering the length of each one of 21,432 unique sequences derived from the Genolyptus EST dataset were synthesized “on-chip” in duplicate, randomly distributed in two blocks of each slide. Probes were also synthesized from ten cDNA sequences encoding known human proteins as negative controls, totaling 21,442 sequences. Leaves and xylem samples were taken from two E. grandis clonal trees, i.e., both derived from the same matrix tree and harboring the same genotype. Two additional xylem samples were collected from two other E. grandis clonal trees of a different genotype, as well as from two E. globulus clonal trees. Therefore, ten cDNA samples and ten identical chips were produced at Roche NimbleGen for the microarray assays, with a total number of 385,956 features per slide. Besides the discovery of differentially expressed genes between leaf and xylem, we wanted to test the validity of the assumed “technical” and “biological duplicates” since all trees were field-grown and four years-old in age. A ten chip study using total RNA recovered from mature leaf and vascular (xylem) tissues of Eucalyptus grandis and xylem from Eucalyptus globulus trees. Two clonal trees of E. grandis (E.grandis_Clone A_Ramet 1 and E.grandis_Clone A_Ramet 2), derived from a single matrix tree and therefore genomically identical, were the source of two samples of leaf RNA and two samples of xylem RNA, individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Two other clonal trees of E. grandis (E.grandis_Clone B_Ramet 1 and E.grandis_Clone B_Ramet 2), derived from a different matrix tree, were the source of two additional samples of xylem RNA individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Likewise, two pairs of clonal trees of E. globulus (E.globulus_Clone A_Ramet 1 and E.globulus_Clone A_Ramet 2/ E.globulus_Clone B_Ramet 1 and E.globulus_Clone B_Ramet 2), derived from two distinct matrix trees, were the source of four additional samples of xylem RNA, individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Each chip measures the expression level of 21,432 genes from Eucalyptus sp. and ten human genes (negative controls) with nine 50-mer probe pairs (PM/MM) per gene in two separate blocks per chip (technical duplicate), totalizing 18 hybridization signal values per gene per chip.
2011-12-31 | E-GEOD-31696 | biostudies-arrayexpress
Project description:Background: The change from juvenile to mature phase in woody plants is often accompanied by a gradual loss of rooting ability, as well as by reduced microRNA (miR) 156 and increased miR172 expression. Results: We characterized the population of miRNAs of Eucalyptus grandis and compared by Northern blot the gradual reduction in miR156 and increase in miR172 expression during development to the loss of rooting ability. Forty known and eight novel miRNAs were discovered and their predicted targets are listed. The expression pattern of nine miRNAs was determined during adventitious root formation in juvenile and mature cuttings. While the expression levels of miR156 and miR172 were inverse in juvenile and mature tissues, no mutual relationship was found between high miR156 expression and rooting ability, or high miR172 expression and loss of rooting ability. This is shown both in E. grandis and also in E. brachyphylla, in which explants that underwent rejuvenation in tissue culture conditions were also examined. Conclusions: It is suggested that in these Eucalyptus species, there is no correlation between the switch of miR156 with miR172 expression in the stems and the loss of rooting ability. Examination of microRNA in seedlings of Eucalyptus grandis
2014-10-01 | E-GEOD-58367 | biostudies-arrayexpress
Project description:In order to pinpoint the most differentially expressed genes between Eucalyptus grandis leaf blades and vascular (xylem) tissues as well as between E. grandis and Eucalyptus globulus xylem tissues, a total number of nine 50mer-oligoprobes covering the length of each one of 21,432 unique sequences derived from the Genolyptus EST dataset were synthesized “on-chip” in duplicate, randomly distributed in two blocks of each slide. Probes were also synthesized from ten cDNA sequences encoding known human proteins as negative controls, totaling 21,442 sequences. Leaves and xylem samples were taken from two E. grandis clonal trees, i.e., both derived from the same matrix tree and harboring the same genotype. Two additional xylem samples were collected from two other E. grandis clonal trees of a different genotype, as well as from two E. globulus clonal trees. Therefore, ten cDNA samples and ten identical chips were produced at Roche NimbleGen for the microarray assays, with a total number of 385,956 features per slide. Besides the discovery of differentially expressed genes between leaf and xylem, we wanted to test the validity of the assumed “technical” and “biological duplicates” since all trees were field-grown and four years-old in age.
2011-12-31 | GSE31696 | GEO