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.
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.
Project description:This SuperSeries is composed of the following subset Series: GSE24130: Gene expression in xylem tissue on an Eucalyptus pseudo-testcross population: discovery array probes GSE24195: Gene expression in xylem tissue on an Eucalyptus pseudo-testcross population: genotyping subset of discovery array probes Refer to individual Series
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.
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.
Project description:rs04-03_myb - myb - Xylogenesis is a fundamental developmental process that is specific of vascular plants. It allows the formation of xylem, also called wood in trees, a complex tridimensional tissue composed of different cell types. This process occurs through the control of fundamental cell mechanisms like cell division and differentiation, secondary cell wall synthesis, lignin deposition and programmed cell death. Xylogenesis is controlled spatially and temporally by specific genetic programs that involve hundreds of genes. For instance, lignin biosynthetic genes, CAD and CCR, are specifically expressed during xylogenesis through MYB transcription factor binding sites, a process that seems to be common to all vascular plants. We have cloned two xylem specific MYB transcription factors, EgMYB1 et EgMYB2, in Eucalyptus. Interestingly, they are able to bind MYB consensus sequences of CAD and CCR promoters in vitro and to modulate CAD and CCR expression in vivo. When overexpressed in Arabidopsis or tobacco, they affect xylem structure by changing cell wall structure and quality. To follow expression changes of Arabidopsis genes in transgenic plants overexpressing Eg MYB1 and EgMYB2 should help us to find out which genes might be target of those transcription factors. This should help us to decipher the actual role of those two MYBs in xylogenesis, two new members of a large family of transcription factors in plants. - Xylogenesis is a fundamental developmental process that is specific of vascular plants. It allows the formation of xylem, also called wood in trees, a complex tridimensional tissue composed of different cell types. This process occurs through the control of fundamental cell mechanisms like cell division and differentiation, secondary cell wall synthesis, lignin deposition and programmed cell death. Xylogenesis is controlled spatially and temporally by specific genetic programs that involve hundreds of genes. For instance, lignin biosynthetic genes, CAD and CCR, are specifically expressed during xylogenesis through MYB transcription factor binding sites, a process that seems to be common to all vascular plants. We have cloned two xylem specific MYB transcription factors, EgMYB1 et EgMYB2, in Eucalyptus. Interestingly, they are able to bind MYB consensus sequences of CAD and CCR promoters in vitro and to modulate CAD and CCR expression in vivo. When overexpressed in Arabidopsis or tobacco, they affect xylem structure by changing cell wall structure and quality. To follow expression changes of Arabidopsis genes in transgenic plants overexpressing Eg MYB1 and EgMYB2 should help us to find out which genes might be target of those transcription factors. This should help us to decipher the actual role of those two MYBs in xylogenesis, two new members of a large family of transcription factors in plants. Keywords: gene knock in (transgenic)
Project description:The gene expression profiles of the differentiating xylem of 91 Eucalyptus grandis backcross individuals were characterized following a loop design (Churchill, G.A. Nat Genet. 2002 Dec;32 Suppl:490-5). In this design, RNA from genotype 1666 (labeled with Cy5) was hybridized with RNA from genotype 1667 (labeled with Cy3) on the first slide(GEO accession number GSM7637); the same genotype 1667 (now labeled with Cy5) was compared with genotype 1669 (Cy3) on the second slide (GSM7638), and so on. The loop was completed when genotype 1666 (Cy3) was contrasted to individual 1796 (Cy3) on slide GSM7727. Therefore, 91 individuals (genotypes) from the E. grandis backcross population were analyzed in two replicates, one with RNA labeled with Cy3 and the other with Cy5. Keywords = Eucalyptus, xylem, microarray Keywords: ordered
Project description:The gene expression profiles of the differentiating xylem of 91 Eucalyptus grandis backcross individuals were characterized following a loop design (Churchill, G.A. Nat Genet. 2002 Dec;32 Suppl:490-5). In this design, RNA from genotype 1666 (labeled with Cy5) was hybridized with RNA from genotype 1667 (labeled with Cy3) on the first slide(GEO accession number GSM7637); the same genotype 1667 (now labeled with Cy5) was compared with genotype 1669 (Cy3) on the second slide (GSM7638), and so on. The loop was completed when genotype 1666 (Cy3) was contrasted to individual 1796 (Cy3) on slide GSM7727. Therefore, 91 individuals (genotypes) from the E. grandis backcross population were analyzed in two replicates, one with RNA labeled with Cy3 and the other with Cy5. Keywords = Eucalyptus, xylem, microarray