Transcriptomics platform


An Agilent DNA microarray platform was established at the department allowing the processing of any 1 x 3 inch (25mm x 75mm) glass slide format (custom-made or catalog arrays). The system consists of the following equipment (for further details of the microarray hardware please visit the Agilent homepage):

  • Nanodrop ND-1000 UV-Vis spectrophotometer enabling highly accurate quantification of RNA/DNA samples in as little as 1 µl volumes.
  • 2100 Bioanalyzer to confirm quality (and quantity) of nucleic acid samples before entering the labelling and hybridisation workflow.
  • Microarray hybridisation oven equipped with a rotator rack to hold Agilent SureHyb microarray chambers.
  • Microarray scanner which is a 48-slide scanning system that can read any 1 * 3 inch glass slide microarray. It allows fast scanning at 5 and 10 microns, poses a dynamic autofocus to keep features in focus all times, an extended dynamic range of 104 for high sensitivity and enables scanning at different saturation levels.
  • Feature Extraction software (v 9.5) enabling seamless extraction of data from images as soon as they are obtained from the scanner. The software automatically finds and places grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. It provides an application-specific quality report and analyses Agilent-specific controls ("spike-in"). Data are provided as MAGE-ML or tab-delimited text files compatible with GeneSpring or other microarray data analysis applications.
  • GeneSpring software (v 7.3, v 11.02) which offers a wide range of tools for analysing, visualizing (e.g. statistical tests such as t-test, 2-way ANOVA, K-mean or QT-clustering, principal component analysis) and managing of microarray data coming from different platforms.

The workflow is schematically illustrated in figure 1:

The technical platform is available for internal as well as external users. We offer partial or complete support for sample preparation, labelling (one or dual colour) and hybridisation. In addition to the processing of microarrays, Agilent provided a web-based application tool to design customized microarrays (

For further details please contact: sophia.sonnewald (at)