Expression Profiling Service

Welcome to the DKFZ Microarray Core Facility. We provide access to full service of state-of-the-art molecular profiling based on Illumina technology for members of DKFZ, NCT and their collaborators (via DKFZ accounts).

We support Illumina expression profiling using whole genome BeadChip® Sentrix arrays

• HumanHT-12 v4
  
• mouseWG-6 v2
  
• mouseRef-8 v2
  
• RatRef12

Make sure to provide the appropriate number of RNA samples for a series of experiments. Sentrix arrays require 6, 8, or 12 samples in parallel (see Sentrix number above).

YOU supply

As starting material we take total RNA at a concentration of at least 50 ng/µl and 500 ng in total, that is quality checked and has a defined concentration. You may provide the samples together with the signed expression profiling sample submission form, after logging into the GPCF web (see left menu).

Please be aware: NO BIOLOGICAL REPLICATES = NO STATISTICS

What we do

We perform incoming QC for quality and concentration of all samples (Nanodrop ND-1000, Agilent 2100 Bioanalyzer).
Upon acceptation of samples we perform labeling and hybridization to the microarrays you request, monitoring the quality at all steps.
Image acquisition, single chip analysis as well as normalization across all of your samples is performed, and in depth analysis support via practical software training is provided

Output to you

• All RNA and labeling QC data (conc. of input RNA, quality of input RNA, conc. of double stranded cDNA, conc. of labeled cRNA, quality of cRNA)
• Raw data of microarrays
• Individual chip QC (for chip integrity and hybridization success)
• Raw data evaluation (box plots)
• Interpreted data (numerical readout and gene annotation for microarray elements (probe sets)
• Normalization across each chip
• Normalization (if wanted) for complete sets of experiments

What's next?

You may unlock the insights buried in your experimental data, applying statistical analysis using DKFZ' in-house Chipster installation that makes use of R and Bioconductor packages and a Java GUI. Pathway analysis tools like Ingenuity Pathway Analysis or DAVID are also available via direct links, or provision of a computer workstation at GPCF (booking system for Ingenuity). Check out our webpage for more details and to get access.

For more Information, please review the FAQ site on expression profiling and the respective glossary.

Please consult the pricelist for detailed cost information.