Transcription profiling of Arabidopsis Ler/Cvi recombinant inbred line popultion to assess natural variation in gene expression
Ontology highlight
ABSTRACT: To assess natural variation in gene expression in Arabidopsis thaliana, genome wide gene expression variation was analyzed in a Ler/Cvi recombinant inbred line (RIL) population.The variation in expression could be explained for many genes by expression quantitative trait loci (eQTLs). These eQTLs are combined with regulator candidate gene selection to generate genetic regulatory networks.
Project description:Plant hypocotyls elongate in response to darkness. The response to darkness is gated by the circadian clock, such that wild-type plants (Col) only respond to darkness with growth once every 24 hours, whereas arrhythmic lines, such as CCA1-34, will respond to darkness with growth at any time of day. The experiment here was designed to find genes whose expression was correlated with growth. It should also pick up other genes that are gated by the circadian clock or that are direct targets of CCA1. Experiment Overall Design: Two genotypes were uses, wild-type (Col) and the arrhythmic CCA1-34 line that overexpresses the CCA1 protein. Plants were entrained in short day conditions for four days and then subjected light/dark pulses consisting of 160 minutes of light and 320 minutes of dark. We collected samples 120 minutes into the first and last dark periods of the day, corresponding to 280 and 1240 minutes after dawn. At the 280 minute time point Col plants are growing in response to darkness. At the 1240 minute time point Col plants are not growing. CCA1-34 plants are growing at both time points. The collection regime was continued for three days for a total of three temporal replicates for each time point/genotype combination.
Project description:To determine the pleiotropic effect of the ABC transporter gene (Atpdr2) mutation, we performed the microarray analyses on the root tissues of Arabidopsis thaliana wild type (Col-0) and Atpdr2 mutant.
Project description:Microarray gene expression analysis were performed to identify genes responding to Fusarium graminearum inoculation and genes that show a differential regulation between the resistant c.v. Sumai-3 and the susceptible near isogenic lines. Sumai-3 is a Chinese wheat cultivar, the most commonly used source of resistance to Fusarium head blight (FHB) disease. NIL-3 and NIL-4 are near isogenic lines susceptible to FHB and are derived from a cross between Sumai-3 and Chuan980, a susceptible wheat cultivar, followed by seven generations of marker assisted backcrossing with the recurrent parent Sumai-3 and selection for FHB susceptibility in each generation by artificial inoculation with F. graminearum. A combination of DNA markers including simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs) were used to screen for DNA polymorphisms between Sumai-3 and its susceptible NILs. Polymorphic markers were mapped using a mapping population. The analysis indicated 7 polymorphisms between the susceptible NILs and the resistant Sumai-3. The analysis indicated that NIL-3 differs from Sumai-3 at chromosome 3BS and NIL-4 differs from Sumai-3 at chromosome 2AL region.
Project description:Exercise has an measureable impact on gene expression profiles of white blood cells. While subpopulations of white blood cells undergo specific changes in answer to physical load we focused on pan T-lymphocytes and Monocytes. These cells are in direct contact to organs influenced by exercise and additionally should be affected by alterations of nutrient and gas composition in blood, which occur as a consequence of exercise. We screened the gene expression profiles of top athletes at the beginning and the end of the Tour de France 2005 and at at the annual rest period in order to find functional processes that are differentially expressed in answer to the longtime and high load training and competition. Therefor we filtered out genes with significant changes in gene expression more than 1.5fold between two of the three conditions and build overlap lists of this list and GO (gene ontology) lists and KEGG (kyoto encyclopedia of genes and genomes) lists. We observed a strong decline in immune functions and an equal decline in metabolic processes. Experiment Overall Design: 12 professional cyclists from two german top teams gave written agreement to participate to this study. We collected 12ml of whole blood at each time point and isolated T-lymphocytes out of 4ml and monocytes out of 8ml whole blood. The experimental groups are divided into rest (6 replicates in Tcells/ 7 replicates in Monocytes), start (10 replicates in each cell type) and final (8 replicates in Tcells/ 9 replicates in Monocytes). This means that we collected samples at the beginning and the end of the Tour de France and during the annual rest period of the athletes.
Project description:Time courses of gene expression profiles of primary human umbilical vein endothelial cells (HUVEC) during infection with piliated and adherent wild-type (WT), frpC/frpA-deficient mutant, or the non-adherent (?pilD) Neisseria meningitidis MC58 bacteria defective in production of the type IV pilus, were analyzed respectively. Total RNA isolated from uninfected HUVEC (reference) and HUVEC after 1, 4 or 6 hours of infection with N. meningitidis mutants was labeled according to standard Affymetrix protocol and hybridized to HG-U133A GeneChips. Data were analyzed by Robust Multi-array Analysis algorithm. For every condition at least two biological replicates were analyzed, totally representing 23 Affymetrix GeneChips.
Project description:These gene expression profiles were measured to create a broad and balanced control for any project that examines gene expression changes in men exposed to a defined stimulus (see series 5105). Experiment Overall Design: 9 healthy men (aged 21 to 44) gave written agreement to participate to this study. At the time of blood withdrawal all participants were non-smokers, with normal BMI and did not obtain any medicamentation. We collected 12ml of whole blood and isolated T-lymphocytes out of 4ml and monocytes out of 8ml whole blood.
Project description:Transcriptional profiling of A. thaliana seedlings (early development) at 7 time points We investigate biomass heterosis by scoring partial correlations of transcriptional profiles. We compare 4 genotypes: Col-0 (homozygous parental line), C24 (homozygous parental line), Col-0xC24 and C24xCol-0 (crossings) using 2-4 replicates each
Project description:Transcriptomic profiling of laser microdissected epidermis and subepidermis cells from expanding green fruit rind of Citrus clemenules using the cDNA microarray CFGP-Citrus_20k.
Project description:Lung alveolarization is a complex process that involves interactions between several cell types and leads to considerable increase in gas-exchange surface area. The step designated secondary septation includes elastogenesis from interstitial fibroblasts. We used microarrays to detail the global programme of fibroblast gene expression that underly secondary septation, and identified numerous genes that undergo signficant changes in expression Experiment Overall Design: Rat lung fibroblats were extemporaneously isolated at successive stages of postnatal development that flank the septation period for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates from three different litters were prepared for each time point.
Project description:identification of genetic differences and similarities between clinical isolates of s.pneumonie of the same sequence type and /or serotype