Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Small RNA profiles of mycovirus-free and mycovirus-infected Aspergillus fumigatus isolates, created using ScriptMiner adapters

ABSTRACT: Small RNA libraries of 4 different mycovirus-infected and -free isogenic lines of A. fumigatus were constructed using Scriptminer adapters. sRNAomes were analysed and putative virus-derived small RNAs were identified. Analysis of small RNA profiles of 4 different mycovirus-infected A. fumigatus isolates

ORGANISM(S): Aspergillus fumigatus

SUBMITTER: Irina Mohorianu

PROVIDER: E-GEOD-61681 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:CRZ is a C2H2 zinc finger transcription factor activated by calcineurin, a protein phosphatase activated by calcium-calmodulin, in different stress conditions related with calcium cell accumulation. CRZ binds to a specific element on the promoter region of genes called CDRE (calcineurin-dependent response element) shown to be sufficient for calcium- and calcineurin-dependent gene expression. In order to investigate which pathways are involved under calcium stress conditions, we determined the transcriptional profile of A. fumigatus delta crzA mutant strain upon a time course 200 mM calcium chloride treatment. Conidia from the mutant and wild type strains were incubated at 37Â°C in complete medium for 16 hours and were challenged with 200 mM calcium chloride for 10 and 30 minutes. At each time point, the mycelia were harvested by centrifugation and used for competitive microarray hybridizations. We were able to observe a decreased mRNA expression of genes encoding inorganic ion transport proteins and lipid transport. In contrast, increased mRNA expression was observed for several genes involved in transcription, energy production and conversion, cell cycle control, cell division, chromosome partitioning, amino acid, lipid and carbohydrate transport and metabolism, nucleotide transport, cell wall and membrane biogenesis, posttranslation modifications, protein turnover, chaperones, inorganic ion transport, signal transduction mechanisms, intracellular trafficking, secretion and vesicular transport. Keywords: gene expression array-based (log2 ratio) For the time course microarray experiments, 5.0 x 108 conidia of A. fumigatus wild type [CEA17 delta akuB(KU80)] and delta crzA strains were inoculated in 300 ml of pre-warmed liquid cultures (YG) in 500-mL erlenmeyer flasks and allowed to grow for 16 hours in a reciprocal shaker (250 rpm) at 37Â°C. After this time, the cultures were added by calcium chloride (200 mM) and incubated for 10 and 30 more minutes before mycelia recovery and RNA extraction. Hybridization experiments were competitive using probes derived from calcium chloride shock cultures using the wild type strain exposed to calcium (10 or 30 minutes) as the reference RNA for every hybridizantion. Normalized signal intensities were used to generate relative hybridization ratios (query/reference). Following normalization, the values for each gene's in-slide replicates were averaged (median variance <0.01), and corresponding flip-dye replicates were averaged to compensate for dye-specific effects. These final, processed data are linked below as supplementary files.

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Small RNA profiles of mycovirus-free and mycovirus-infected Aspergillus fumigatus isolates, created using ScriptMiner adapters

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