Eucalyptus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA298355 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2602746.fastq.gz | Fastqsanger.gz | |||
| SRR2602747.fastq.gz | Fastqsanger.gz | |||
| SRR2602748.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
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: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
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 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:We present a label free proteome dataset of the vascular sap proteome of three commercially important Eucalyptus species (Eucalyptus camaldulensis, Eucalyptus grandis and Eucalyptus urophylla). Protein extraction from the vascular system was carried out using a pressure bomb, in solution digested and peptides were analyzed using a Q-Exactive instrument. Protein identification was carried out using stringent database searches and only in silico predicted extracellular proteins were considered as part of the sap proteome. The results here described can be used as a reference for the proteome sap analysis of Eucalyptus plants grown under different conditions.
2025-05-30 | PXD037915 | Pride
Project description:Eucalyptus grandis x Eucalyptus urophylla
| PRJNA80497 | ENA
Project description:Eucalyptus urophylla x Eucalyptus grandis transcriptome project
| PRJNA48577 | ENA
Project description:Eucalyptus urophylla vs Eucalyptus grandis Transcriptome or Gene expression
| PRJNA257368 | ENA
Project description:The intense human activities can cause irreversible environmental problems. Eucalyptus is a forest species widely used in planted forests, with a great capacity to assist in the mitigation of CO2 emissions and accumulation due to its C3 metabolism and high retention of carbon molecules in its biomass. The objective of this study was to investigate the differences in the sap proteome of two Eucalyptus species grown in an atmosphere enriched with CO2. For this purpose, young Eucalyptus grandis and Eucalyptus urophylla plants were grown in growth chambers 20 days under controlled atmospheric CO2 rates. The vascular proteome revealed 146 extracellular proteins, and their relative abundance was associated with the enriched atmosphere treatments. The analysis of protein function and abundance revealed that E. grandis proteins are mainly involved in organic substance metabolism and proteolysis, while less abundant proteins are related to cellular defense responses. Similar results were obtained for E. urophylla, with the most abundant proteins performing metabolic functions, while the least abundant protein was related to oxidative stress. These results may contribute to a better understanding of the mechanisms involved in the response of eucalyptus species to increased CO2 and provide useful information for the management and cultivation of these species in high levels of carbon dioxide environments.
2025-05-30 | PXD050082 | Pride
Project description:Eucalyptus urophylla x Eucalyptus grandis Transcriptome or Gene expression
| PRJNA262843 | ENA