BioChip-Labor

The biochip core facility of the Institute for Cell Biology (IFZ), University of Duisburg-Essen, has been established in 2000 by a consortium headed by Prof. Tarik Möröy (Institute for Cell Biology). During the following years, the spectrum of microarray applications has been extended, the GeneChip platform has been updated and additional equipment has been purchased. Currently, the biochip lab is able to offer state-of-the-art microarray and real-time PCR services to all members of the medical faculty and the university of Duisburg-Essen. The facility is headed by PD Dr. rer. nat. Ludger Klein-Hitpass, an experienced molecular biologist, who is supported by one technician.

The microarray platform of the IFZ Biochip lab consists of an up-to-date Affymetrix GeneChip System, including Hybridization Oven 640, Fluidics Station 450, and  GeneChip Scanner 3000 with G7 update and workstation. This platform allows processing and scanning of all currently available Affymetrix arrays including

1. 1. 1.    Conventional 3’-IVT expression arrays for whole genome expression analysis of samples from human, mouse, rat and many other organisms.

1. 1. 2.    Exon arrays for whole transcript detection and analysis of alternative splicing (human, mouse, rat).

1. 1. 3.    Whole genome mapping arrays (Human Mapping 100K, 500K, SNP5.0, SNP6.0) for genotyping, copy number and LOH analysis.

1. 4.    Tiling arrays for the analysis of immunoprecipitated DNA fragments (ChIP-on-chip) to map transcription factor binding sites and chromatin modifications.

The biochip lab at the IFZ provides full microarray service to all members of the medical faculty and collaborating scientists mainly following protocols established by the manufacturer (Affymetrix). In addition, a number of protocols for amplification of very small RNA samples (<50 ng) from NuGEN have been established. Microarray expression service includes RNA quality control, one- and two-cycle protocol based sample amplification and labelling for all microarray applications, array hybridization, staining and scanning. Expression services further include image analysis using various signal summarization methods, quality control, as well as statistical and bioinformatical analyses, including hierarchical clustering (Spotfire, Partek GS), significance analysis of microarrays (SAM), Anova (Partek GS), Gene Ontology enrichment analysis (GOstat) as well as Gene Set Enrichment Analysis (GSEA). Mapping array analysis includes QC and genotype determination. Loss of heterozygosity and copy number variations are determined with CNAG3.0 (up to the 500K array version) or Partek GS.  Tiling arrays, such as the Human, Mouse and Rat Promoter 1.0R arrays for ChIP-on-chip analysis can be analyzed using the Affymetrix TAS and IGB tools.

For validation of microarray data as well as other applications, the Biochip lab provides PCR service on an up-to-date real-time PCR system (Applied Biosystems HT7900 Sequence Detection System). This system is also suitable for real-time PCR-based expression analysis with Taqman probes or SYBRgreen in the conventional 96-well format:

1. 1. 1.    Real-time PCR-based expression analysis of up to 384 mRNA transcripts in a single run with Applied Biosystems Signature or Custom Low Density Arrays (384-well microfluid cards).

1. 1. 2.    Real-time PCR-based determination of genotypes using Taqman SNP genotyping assays.

1. 1. 3.    Real-time PCR-based expression analysis of selected microRNAs of interest with Taqman microRNA assays (Applied Biosystems) in the conventional 96-well format.

1. 4.    MicroRNA screening using Applied Biosystems real-time PCR-based Taqman microRNA Low Density Arrays (384-well microfluid cards), which detect about 360 different human microRNA species.

Again, the Biochip lab at the IFZ provides full PCR service, including RNA quality control, cDNA synthesis for real-time PCR applications, PCR setup, primary data analysis and QC.

As a core facility, the Biochip lab will be responsible for the central purchase of all microarrays and reagents from Affymetrix, which ensures special discounts. For all services, customers will be charged with the costs of the arrays and reagents.