Maria Foti

Genopolis will act as the Affymetrix Core Lab for Tolerage partners carrying out high quality whole genome-gene expression experiments and customized data analysis and data mining. The goal of Genopolis is to make its expertise available to the consortium, provide knowledgeable support in experimental design, high standard in executing experiments, and “state of the art data analysis” to identify pathways of differentially expressed genes in the respective experiments. The Genopolis facility is fully equipped and includes: Qiagen TissueLyser, Agilent 2100 Bioanalyser, NanoDrop ND-100 Spectrophotometer, Affymmetrix Platform (Affymetrix 450 hybridisation oven, Affmetrix GeneChip fluidics station, AffymetrixGeneChip scanners 3000), Applied Biosystems 7500 Real-Time PCR System.b

Experiment planning, consulting, and feasibility assessment

Microarray technology allows researchers to observe the expression levels of thousands of genes in one experiment. Robust experimental design is a fundamental starting point to ensure that microarray data is interpretable and statistically relevant. Therefore, it is essential to plan microarray experiments with a precise biological question in mind. It is also crucial to execute the experiments with extreme care. The experimental system/model should be well-characterized or well-defined with an independent experimental verification. Standardization of experimental protocols and data analysis are critical as well.

Genopolis helps the researchers to develop clearly defined microarray experiments enable them to reach their experimental goals.

Microarrays experiment quality controls

Stringent quality control measures throughout the work flow are applied to assure accurate and reliable results.

RNA quality is of fundamental importance in microarray experiments. RNA samples need to be intact and free of contaminants. Above all, differential degradation of RNA can lead to erroneous conclusions about both the relative and absolute mRNA levels in the sample.

Microarray Data Analysis

Elucidating the statistical relevance of the huge amount of data obtained when conducting microarray experiments is a challenge. Dealing with thousands and thousands of data points requires skillful statistical and computational support.

Genopolis established a bioinformatics core team that ensures state of the art microarray data analysis. An automated microarray data analysis (AMDA) pipeline provides the relevant information and the graphical representations necessary for a meaningful interpretation of the results. Differentially expressed genes are selected according to their significance level and clustered into groups of genes with similar expression profiles across the samples. Based on the experimental conditions provided by the researcher, our pipeline performs as follows:

data normalization and signal intensity summarization

selection and clustering of differentially expressed genes

clustering of differentially expressed genes with similar expression profiles across the samples

functional annotation of differentially expressed genes

The pipeline is used with a default choice of algorithms and parameters, but can be configured according to the user's needs. An analysis report (.pdf format) is generated, including references to the files containing the list of genes for each of the analysis steps performed

pathways of differentially expressed genes in the respective experiments.  The Genopolis facility is fully equipped and includes:  Qiagen TissueLyser, Agilent 2100 Bioanalyser, NanoDrop ND-100 Spectrophotometer, Affymmetrix Platform (Affymetrix 450 hybridisation oven, Affmetrix GeneChip fluidics station, AffymetrixGeneChip scanners 3000), Applied Biosystems 7500 Real-Time PCR System.