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Title: Global modulation of gene expression in Paracoccidioides brasiliensis in response to thioridazine      
dateReleased:
12-31-2013
description:
Phenothiazines are antipsychotic drugs used in the treatment of schizophrenia, which have been shown to present antimicrobial activity (in vitro and in vivo) against a great variety of pathogenic microorganisms, including bacteria, parasites (protozoa and helmints) and fungi. In this study, we used competitive microarray hybridization to evaluate the effects of increasing concentrations of the piperidinic phenothiazine derivative thioridazine (TR) on the transcriptome of Paracoccidioides brasiliensis, the causative agent of paracoccidioidomycosis (PCM) - the most common systemic mycosis in Latin America. These analyses showed that the presence of TR affected expression of more than 1,800 genes from this fungus, including genes related to cellular processes such as cell wall metabolism and drug resistance. Microarray hybridizations were carried out with amplified RNA (aRNA), which was produced starting with total RNA extracted from cells treated with thioridazine (15, 20 or 25 µM) for 168 hours. The aRNA synthesized from cells unexposed to TR was taken as reference. Each treatment was analyzed with two independent hybridizations (a pair of hybridizations, with dye-swaps within each pair). Since each biochip carried two replicas of the arrayed genes, a total of four intensity readings were generated for each element in the microarray.The data has been filtered, normalized and adjusted as described in the "data processing" box for each individual sample. Dye swap consistency checking has been performed between equivalent experimental pairs with the aid of the software TIGR MIDAS v2.19 and inconsistent spots have been flagged and excluded from further analyses. The values obtained from each dye swap pair have been averaged and consolidated into a single data file, generating a total of 8 hybridization files (four from each treatment concentration). These files have been loaded into the software TIGR Multi-Experiment Viewer, v.3.1 Experiments were then normalized and genes that displayed statistically significant modulation were identified by one-way ANOVA, considering p < 0.01 as a cutoff value. A list of statisticaly significant, modulated genes was created, showing the average log ratio for each one of these genes, within each time point.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-41881
refinement:
raw
alternateIdentifiers:
41881
keywords:
functional genomics
dateModified:
06-02-2014
availability:
available
types:
gene expression
name:
Paracoccidioides brasiliensis
ID:
A-GEOD-2780
name:
Paracoccidioides brasiliensis microarray v1
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-41881/E-GEOD-41881.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-41881/E-GEOD-41881.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41881
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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