Transcription profiling of Arabidopis leaves from plants treated with antimycin A to trigger mitochondrial production of reactive oxygen species
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ABSTRACT: mitochondrial electron transport in Arabidopsis leaves was blocked by antimycin A treatment to trigger mitochondrial production of reactive oxygen species and to study transcriptional changes in response
Project description:Mitochondrial electron transport in Arabidopsis leaves was blocked by antimycin A treatment to trigger mitochondrial production of reactive oxygen species in a knockout line for a mitochondrial peroxidase (PrxII F) and to study transcriptional changes in response
Project description:Mitochondrial antioxidant defence was manipulated by dexamthasone inducible RNAi knockdown of the mitochondrial superoxide dismutase (MSD1) to study transcriptional changes in response.
Project description:We performed a dye-swap microarray experiment using a total of 24 Rat 15k cDNA duplicates microarrays. The study included RNA from samples with high expected differential gene expression termed high contrasts compared to self-self hybridization (rat cell lines AR42J and NRK52E). We than optimized a pipeline to maximize the number of genes found differentially expressed between the two different RNA samples while at the same time making sure that the methodology finds no differentially expressed genes in selfself experiments with the same cell lines. In this high-contrast vs. self-self method (HCSSM) significantly expressed genes is determined by estimating the false discovery rate (FDR) using a null distribution obtained from self-self experiment. The optimization criterion requires only 4 microarrays per evaluation, and the effects of blocking reagent dose, filtering, and background corrections methodologies were investigated. In our experiments a dose of 250 ng LNA dT blocker gave the highest number of differentially expressed genes. When the criterion was used to evaluate steps in the computational analysis of microarray data we found that no background correction and weight based filtering gave the largest number of differentially expressed genes. Background correction method, however, has a greater influence on the number of differentially expressed genes found than filtering.
Project description:3 different ES cell lines were compared in order to determine whether there are significant expression profile differences between ES cell lines, or whether the constraints of maintaining pluripotency in culture force a similar expression profile on cell lines derived from disparate sources. Our results indicate that the latter is more likely. We identified 21 genes that were significantly differentially regulated, either on comparison with the pooled control, or on direct comparison of individual ES cell line data from different slides. Using semi-quantitative RT-PCR on 3 separate isolates from each cell line, we have confirmed 4 of these genes as consistently differentially regulated, Hprt, and 3 others. We would conclude therefore that different ES cell lines at the same passage number in identical culture conditions show very similar expression profiles. Keywords: cell type comparison Cardiff University Array Facility NIA 15K slides were used in conjunction with 3 different RNA isolates from each of the ES cell lines. A pooled control was assembled using equal quantities of cells from each cell line, RNA was extracted and labelled, for use on every slide. Fluor switches were carried out, and 12 replicates were used for each cell line (3 biological replicates). The ES cell lines were each derived from different sources; IMT11 cells are derived from 129 strain mice. HM1 cells are also derived from 129 mice, but are missing a functional copy of Hprt. SHBl6.3 cells are derived from the less permissive C57Bl6/J mouse strain. Data were analysed as described in the GSM submissions.
Project description:MicroRNAs are small RNA species that regulate gene expression post-transcriptionally and are aberrantly expressed in many cancers including lymphoma. However, the role of microRNAs in the pathogenesis of multiple myeloma (MM) is poorly understood. We therefore elucidated the complete miRNome of purified tumor (CD138+) cells from 33 patients with MM, 5 patients with monoclonal gammopathy of undetermined significance (MGUS) and 9 disease controls. Unsupervised cluster analysis revealed that MM samples have a distinct microRNA expression profile. The majority of microRNAs aberrantly expressed in MM (109/129) were up-regulated. A comparison of these microRNAs with those aberrantly expressed in other B-cell and T-cell lymphomas revealed a surprising degree of similarity (~40%) suggesting the existence of a common lymphoma microRNA signature. We identified 39 microRNAs associated with the pre-malignant condition MGUS. Twenty-three (59%) of these were also aberrantly expressed in MM suggesting common microRNA expression events in MM progression. MM is characterized by multiple chromosomal abnormalities of varying prognostic significance. We identified specific microRNA signatures associated with the most common IgH translocations (t(4;14) and t(11;14)) and del(13q). Expression levels of these microRNAs were distinct between the genetic subtypes (by cluster analysis) and correctly predicted these abnormalities in >85% of cases using the support vector machine algorithm. Additionally, we identified microRNAs associated with light chain only myeloma, as well as IgG and IgA-type MM. Finally, we identified 32 microRNAs associated with event-free survival (EFS) in MM, ten of which were significant by univariate (logrank) survival analysis. In summary, this work has identified aberrantly expressed microRNAs associated with the diagnosis, pathogenesis and prognosis of MM, data which will prove an invaluable resource for understanding the role of microRNAs in this devastating disease. Plasma cells (CD138+) cells were purified from bone marrow samples of 33 patients with MM, 5 patients with monoclonal gammopathy of undetermined significance (MGUS) and 9 disease controls.
Project description:Silencing of DND1 in potato leads to resistance to late blight, powdery mildew and Botrytis cinerea. At the same time, however, it reduces plant growth and causes leaf necrosis. To get knowledge on the molecular events behind the pleiotropic effect of DND1 downregulation in potato transcriptome analysis were performed on three DND1 silenced lines in comparison with the potato cultivar ‘Désirée’ as a wild-type.
Project description:A custome-made 8x15k oligonucleotide limanda limanda microarray (Agilent) comprised of 14919 experimental probes, was used to characterize gene expression profiles of dab hepatocellular adenoma tumours from sites of different pollution status in Irish Sea.
Project description:Abstract: The mitochondrial electron transport chain is essential to Plasmodium and is the target of the antimalarial drug atovaquone. The mitochondrial genomes of Plasmodium sp. are the most reduced known, and the majority of mitochondrial proteins are encoded in the nucleus and imported into the mitochondrion post-translationally. Many organisms have signalling pathways between the mitochondria and the nucleus to regulate the expression of nuclear-encoded mitochondrially-targeted proteins, for example in response to mitochondrial dysfunction. We have studied the gene expression profiles of synchronous Plasmodium falciparum treated with an LD50 concentration of the complex III inhibitor antimycin A, to investigate whether such pathways exist in the parasite. There was a broad perturbation of gene expression. Some effects were attributable to a delay in the gene expression phase of drug-treated parasites. However, our data also indicated regulation of mitochondrial stress response genes and genes involved in pyrimidine biosynthesis. 3 biological replicates each for treated and untreated: control (1/2000 DMSO) and LD50 antimycin A, respectively. Normalised microarray data for antimycin A-treated parasites were contrasted against untreated (DMSO) controls.
Project description:This SuperSeries is composed of the following subset Series: GSE10413: Gene expression profiling of caffeic acid phenethyl ester-treated human umbilical vein endothelial cells-1 GSE10429: Gene expression profiling of caffeic acid phenethyl ester -treated human umbilical vein endothelial cells-2 Keywords: SuperSeries Refer to individual Series