Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 6
Release date: Jun 16 2009
Last update date: Mar 21 2012
Access: Public
Diseases: Mycoses
Dataset link Identification of osmotic stress-responsive genes dependent on HogA and AtfA in Aspergillus nidulans

Experimental Protocol


Conidia of wild type or each mutant were cultured at 37C in 100ml CD medium containing 2% glucose for 18h, and 50 ml of 3 M sorbitol was added (final concentration; 1 M) or equivalent volume of water (as a control) for 15 min. The mycelia were harvested and frozen in liquid nitrogen, ground to powder, and used for RNA preparation. mRNA was purified and used for hybridization experiments. A total of 2 hybridizations were performed for each microarray experiment described in the summary. The following replicates were carried out: 1. In-slide replicates were carried out for each analysis. 2. Dye swap replicates were carried out for each experiment. The slides were scanned with an Axon GenePix 4000B scanner (Molecular Devices). The resulting TIFF images were imported into GenePix Pro and fluorescent intensity of spots were calculated for each of the Cy3 and Cy5 channels. Global normalization was applied to all analyses. Following normalization, spots whose Cy3 or Cy5 intensity was less than 0 were removed from the data set (the exceptional case was that intensity of the other channel was more than 100). The dye-swap replicates and in-slide replicates were subjected to all analyses. Finally, gene expression ratios (channel 2/channel 1) were calculated for each replicates. Gene expression was considered to be significantly higher or lower whenever the spot intensity changed by at least 2-fold in all four replicates for each experiment.

Repositories


GEO

GSE16566

ArrayExpress

E-GEOD-16566

BioProject

PRJNA116207

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Contact


Daisuke Hagiwara