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Title: Effects of soil properties and time of exposure on gene expression of Enchytraeus albidus (Oligochaeta)      
dateReleased:
09-06-2011
description:
Changes in soil properties (e.g. pH, organic matter content, granulometry) can influence chemical toxicity to organisms and act alone as stressors. Previous studies on Enchytraeus albidus showed that changes in soil properties caused effects on reproduction and avoidance behavior and also oxidative stress. In addition, results at the transcritptomic level indicated changes in gene expression profile due to soil properties changes. In this study, E. albidus was exposed to modified versions of the artificial standard OECD soil (different pH, OM and clay content) in different exposure times (2, 4 and 8 days). The gene expression profile was characterized using a class comparison statistical analysis. Results indicated that the transcriptional response was time dependent, with different genes being affected at different time points. Results also showed some genes (and biological functions) being affected in a soil specific way. Fluorescently labelled cDNA, from enchytraeids exposed during 2, 4 and 8 days OECD standard soil (Cy3) and to the different exposure conditions (modified OECD soil) (Cy5), was synthesized for microarray analysis and hybridizations were performed. After scanning (Agilent Microarray Scanner from Agilent Technologies), spots were identified and ratios quantified using Quantarray (Packard Biochip Technologies). Statistical analysis of the microarrays was performed using BRB Array Tools version 3.8.1 Stable Release (). After background subtraction, the replicated spots within each array were averaged, and microarrays were normalized using loess method (Smith and Speed, 2003). Statistical class comparison between groups of arrays was performed between each exposure condition and the respective “control” (exposure in OECD standard soil, for each time of exposure) using two-sample T-test and 95% of confidence level for the assessment of differentially expressed genes.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-27700
refinement:
raw
alternateIdentifiers:
27700
keywords:
functional genomics
dateModified:
05-03-2014
availability:
available
types:
gene expression
name:
Enchytraeus albidus
ID:
A-GEOD-11360
name:
EBT_UA_Enchytraeus albidus_version2
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-27700/E-GEOD-27700.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-27700/E-GEOD-27700.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=GSE27700
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