Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 48
Release date: Oct 18 2005
Last update date: Sep 10 2014
Access: Public
Diseases: Infection, Paracoccidioidomycosis, Eye Infections, Fungal
Dataset link Transcriptome analysis of Paracoccidioides brasiliensis cells undergoing the Mycelium-to-Yeast transition

Experimental Protocol


Microarray hybridizations were carried out with RNA obtained from cells harvested at 5, 10, 24, 48, 72 and 120 h after setting the temperature shift from 26 to 37oC. The RNA obtained from the original mycelial culture was taken as reference (t = 0 h). Each time point was analyzed with four independent hybridizations (two pairs of dye-swap hybridizations). The hybridizations labeled as "Exp1" and "Exp2" have been performed with independent RNA preparations. Since each biochip carried two replicas of the arrayed genes, a total of eight samples were generated for each timepoint. 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 24 hybridization files (four from each timepoint). These files have been loaded into the software TIGR MIDAS v. 3.03. 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

Repositories


GEO

GSE3238

BioProject

PRJNA92775

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Contact


Luiz Nunes