Transcriptional profiles of T.rubrum treated with PHS11A
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ABSTRACT:
ORGANISM(S): Trichophyton rubrum
SUBMITTER: Qi Jin
PROVIDER: E-GEOD-6403 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:T. rubrum was treated with PH11B,a potent eucaryotic fatty acid synthase inhibtor. A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and transcriptional profiles of the responses to PH11B were determined. Some class-specific and mechanism-independent changes in gene expression were found. Keywords: fatty acid synthase inhibition The expression profiles of Trichophyton rubrum treated with PH11B were compared to those of Trichophyton rubrum without drug. Each treatment has three replicates.
2007-11-21 | E-GEOD-6336 | biostudies-arrayexpress
Project description:One antifungal agent, terbinafine(TRB), has specific activity against dermatophytes.A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and transcriptional profiles of the responses to TRB were determined. Some class-specific and mechanism-independent changes in gene expression were found. Keywords: original article The expression profiles of Trichophyton rubrum treated with TRB were compared to those of Trichophyton rubrum without drug. Each treatment has three replicates.
2010-06-26 | E-GEOD-6951 | biostudies-arrayexpress
Project description:Trichophyton rubrum, an anthropophilic and cosmopolitan fungus, is the most common agent of superficial mycoses, causing rarely deep dermatophytosis in immunocompromised hosts. In this study, an infection condition of T. rubrum was modeled by adding human skin sections into a limited medium containing glucose to monitor T. rubrum gene expression patterns using cDNA microarrays on a global level. We found that exposure to human skin resulted in up-regulation of the expression levels of T. rubrum genes related to many cellular and biological processes, including transcription and translation, metabolism and secondary transport, stress response, and signaling pathways. These results provide a reference set of T. rubrum genes whose expression patterns change upon infection and reveal previously unknown genes that probably corresponding to proteins that should be considered as virulence factor candidates and potential new drug targets for T. rubrum infections.
2011-10-02 | E-GEOD-15532 | biostudies-arrayexpress
Project description:A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and comparative genome hybridization based on microarray procedures were carried out. Dermatophyte species are classified into three genera: Epidermophyton, Microsporum, and Trichophyton. To determine the relationship between these three groups comparative genome hybridization were used in our experiment. Trichophyton rubrum genmic DNA was reference DNA and labelled by Cy3 while the other dermatophytes genomic DNA were test DNA and labelled by CY5. Test and reference DNA were co-hybridized with the T. rubrum cDNA microarray and the numbers of genes shared between each species and T. rubrum were determined. Keywords: Comparative Genomic Hybridization We used a Trichophyton rubrum cDNA microarray prepared in our lab through comparative genome hybridization of genomic DNA of 21 dermatophyte strains (belonging to 20 species) to elucidate the taxonomy and evolution profiles of 20 dermatophyte species. The numbers of genes shared between each species and T. rubrum were determined. Each strain DNA hybridized for 3 times. The slides were separated into three groups base on different datasets.
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Project description:A whole genome DNA microarray was used to undertake a global transcriptional analysis of nitrogen fixation and ammonium repression in Pseudomonas stutzeri A1501. The aim of this study was to identify the genes that are up-regulated under nitrogen fixation conditions and rapidly down-regulated as soon as 10 min after ammonia shock. The expression changed genes may be the candidate genes for the ammonia signal transmission or be involved in the nitrogen regulatory mechanism. First, P. stutzeri A1501 was treated with 0.1 mM ammonia and 0.5% Oxygen tension until the nitrogenase activity was detectable. Then the cells were sudden shifted from the nitrogen fixation conditions to the ammonia repression conditions by addition of 20 mM ammonia for 10min. Subsequently, the bacterium was collected and began the RNA extraction process. Thus, we compare the expression profilings in these two conditions in order to identify the candidate genes.
2010-05-14 | E-GEOD-14775 | biostudies-arrayexpress
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Project description:Due to the lack of controlled microarray experimental data, evaluation of gene identification methods has been performed using simulated data. As the ability of these approaches to mimic actual experimental data is questionable, conclusions drawn can be misleading. We applied spike-in approaches to develop experimental benchmark data and used it to evaluate various gene identification methods. mRNA that correspond to specific spots on a microarray were obtained by in-vitro transcription of selected clones. They were then spiked in at 11 varying concentrations to a common pool of mRNA, creating a set of known differentially expressed genes. mRNA was obtained from mouse ATCC CRL1606 hybridoma cells. From self hybridization results 200 genes that consistently exhibited a log ratio value close to 0 were randomly selected across a range of intensity. In-vitro transcripts of these 200 genes were obtained from their respective clones. From RNA gel electrophoresis and test array results, 169 of the 200 transcripts were deemed successful. Experiments were then conducted by spiking these 169 transcripts to the common pool of mRNA extracted from the hybridoma cells. With exception of the spiked in genes, the experimental set-up is identical to a self hybridization. This experiment is thus different from other microarray experiments as the set of differentially expressed genes is known as they have been artificially created. Spiked in genes were introduced at 11 concentrations: 0pmol (self hybridization), 0.025pmol, 0.05pmol, 0.10pmol, 0.15pmol, 0.20pmol, 0.25pmol, 0.5pmol, 0.75pmol 1pmol and 2pmol. For concentrations 0pmol, 0.05pmol, 0.10pmol, 0.25pmol, 0.50pmol and 0.75pmol, 6 replicates were obtained. For concentrations 0.025pmol, 0.15pmol, 0.20pmol, 1pmol and 2pmol, 3 replicates were obtained. Dye swaps were not performed for these experiments.
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