Gene Discovery Core Facility

Genechips allow the simultaneous analysis of expression levels for thousands of genes in normal and pathological tissues and hold great promise in molecular medicine, notably in cancer research. The great biological and clinical diversity present in human tumors is poorly characterized by the current classification systems. Genechips can provide a better understanding of oncogenesis, leading to improvements in cancer management. To improve cancer chemotherapy, a better understanding of the involved signal transduction networks is essential. Therefore, not only expression profiling data from relevant tumor specimens have do be converted into signaling information but also proteomic, metabolomic and transcriptomic data sources have to be collected, integrated and analyzed, respectively.

Expression Profiling Unit (EPU):
Head: R. Kofler
Methods, Services and Prices Version 24.7.2006
DNA microarray analyses allow simultaneous monitoring of genome-wide transcriptional responses activated by individual or complex signals. It represents the current state-of-the-art technology for a number of biologic questions such as identification of individual differentially expressed genes in the entire genome (candidate gene search) or complex expression profiles and regulatory networks to classify biologic entities or predict responses (e.g., by cluster analyses).Wet lab technology: Usually the RNA is provided by the user. We require 3-5µg total RNA of high quality. Lower amounts (100-1000ng) can be processed by a second round amplification procedure upon request. For RNA preparation we recommend a combination of the TriReagent preparation method (Molecular Research Center, Cincinnati, OH) with the RNeasy protocol (Quiagen, Hilden, Germany). We routinely reassess RNA quantity and integrity by OD260/280 measurements and Agilent lab-on-a-chip technology (2100 Bioanalyzer, Agilent, Palo Alto, CA). Quality requirements are OD260/280 ratios of 1.8 to 2.2 and an 18S to 28S ratio of about 1.8 to 2.2. Target labelling and hybridization. Hybridization target preparations are performed according to protocols recommended by Affymetrix (Affymetrix Technical Manual). Briefly, 1.5µg total RNA is reverse transcribed into cDNA using an oligo(dT)-T7 promotor primer and transformed into double stranded cDNA by E.coli DNA polymerase using the Affymetrix one cycle cDNA synthesis kit. After purification of double stranded cDNA with the Affymetrix GeneChip Sample Cleanup Module, biotin-labeled cRNA is produced by T7 polymerase (Affymetrix IVT Labeling kit). After Agilent-based quantification and integrity control, 20 µg cRNA is fragmented by alkaline treatment (Affymetrix GeneChip Sample Cleanup Module) and 15 µg fragmented cRNA added to the hybridization cocktail (300 µl final volume). The arrays are washed and stained according to the recommended Fluidics Station protocol (EukGE-WS2 version 5_450). Fluorescence signal intensities from each feature on the microarrays are determined using the Affymetrix GeneChip Scanner 3000 and the GCOS software (version 1.2) according to the manufacturer‘s recommendations. Data processing and presentation. The raw data from all arrays of a given experiment are normalized using the RMA package for R by R. Irrizary (Biostat. 4: 249-264; 2003). The final data will be provided as expression values for the 54,000 probe sets (original Affymetrix cel.files and xls.files) and one set of regulation tables (xls.files), if requested. Additional bioinformatic services are offered by GDCF-Bioinformatics Unit (F. Überall).  For detailed information please visit the EPU homepage.


Functional Gene expression Bioinformatics Unit (FGBU)
Head: F. Ueberall
Methods, Services and Prizes (Version 21.2.2005)
In order to get out the most biologically meaningful information of your microarray data, a combination of bioinformatical, biostatistical and methods from computer science is essential. The aim of the Functional Gene expression Bioinformatics Unit is: to develop and establish software-tools for the identification of new target genes and pathways, to provide a basis for the development of specific molecular-based anticancer drugs and to classify tumors with multivariate biostatistical analysis of operational and external expression profiles of homogeneous diagnostic and prognostic groups as well as for identification of new clinically and biologically relevant tumor subclasses. For a detailed pricing list please contact F. Ueberall.

Genotyping Unit (GU):
Head: F. Kronenberg
Methods, Services and Prizes (Version 21.2.2005)
Together with the Division of Genetic Epidemiology of the Innsbruck Medical University our unit offers a wide variety of help for: project planning including study design (case-control or family-based designs), logistics for genetic field work, sampling of material including biobanking, pipetting by robots, sequencing, genotyping, genetic analysis of data (association studies and linkage analysis). Following the needs of our partners we offer various modules which depends also whether the partners would like us to do the work collaborative or as a service. For detailed information see our homepage.