Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 24
Release date: Sep 8 2011
Last update date: Mar 23 2012
Access: Public
Chemicals: Copper
Dataset link Effect of Cu-Nanoparticles versus Cu-salt in Enchytraeus albidus (Oligochaeta): differential gene expression through microarray analysis

Experimental Protocol


Fluorescently labelled cDNA, from enchytraeids exposed during 2 days to control soil (from Hygum site in Denmark) and to the different exposure conditions (Cy5), was synthesized for microarray analysis and hybridizations were performed. After scanning, spots were identified and ratios quantified using the QuantArray (Packard Biochip Technologies). Statistical analysis of the microarrays was performed using limmaGUI package (1.18.0) (Smyth, 2005) in the R (2.8.0) software environment (http://www.R-project.org/). After being submitted to local background subtraction, microarrays were normalized using global loess method. To statistically evaluate the differential gene expression between the different conditions, a gene-per-gene linear model (limma – linear model for microarray analysis) and empirical Bayes methods were applied. The results were then corrected for multiple testing using the Benjamini-Hochberg’s method (adjusted p<0.05 was considered significant) (Benjamini and Hochberg, 1995).

Repositories


GEO

GSE26331

ArrayExpress

E-GEOD-26331

BioProject

PRJNA136907

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Contact


Susana Gomes
Susana Isabel Lopes Gomes