Expression Profiling Service

The Microarray Unit is equipped with all major microarray expression platforms. Gene expression profiling is offered comprehensively, providing Affymetrix (cartridge based) and Illumina beadarray platforms with all their respective mRNA analysis opportunities. Agilent array platforms are mostly used for gene expression analysis in specific model systems (e.g. E. coli, Drosophila melongaster).

YOU supply

  • Completion of sample sheet
  • High-quality intact RNA (assess RNA quantity and integrity)
  • DNA Sample Concentration and Volume Requirements:
AffymetrixIllumina HT12Agilent
Chip-Format
(No.Samples/Chip)
1124/8
(depending on Chiptype)
Min. Concentration/sample50 ng/µl30 ng/µl50 ng/µl
Total RNA/sample>500 ng>500 ng>500 ng
Volume>8 µl>8 µl>8 µl

 

For lower RNA amounts please inquire.

  • All samples should be treated with DNase
  • Samples must be non-pathogenic and non-infectious (S1-Condition).
  • RNA samples must be provided in a 1.5ml-tube and on dry-ice

 

Please be aware: NO BIOLOGICAL REPLICATES = NO STATISTICS

Please consult the pricelist for detailed cost information.

 

We perform

  • Assistance with Experimental Design
  • Incoming QC for quality and concentration of all samples (Nanodrop ND-1000, Agilent 2100 Bioanalyzer)
  • Labeling and hybridization to the microarrays you request
  • Monitoring the quality at all steps
  • Basic Data Analysis

 

Output to you (see example expression data)

  • 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) on request
  • Raw data of microarrays (if possible, format compatible to GEO/Array Express)
  • 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
  • Group Comparisons

 

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.

 

Citing our service

Please cite our service in the acknowledgements part of your paper in case we've just performed the standard service. The following statement may be used.

"We thank the microarray unit of the DKFZ Genomics and Proteomics Core Facility for providing the Illumina Whole-Genome Expression Beadchips and related services."

last update:
26/04/2019
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