Affymetrix Arrays

Types of Service:

  • Complete protocol for Affymetrix hybridization experiments from total RNA (provided by user)
  • Synthesis of cRNA and cDNA
  • Fragmentation and Labeling
  • Sample purification
  • Hybridization
  • Washing and Scanning

Types of Arrays:

  • 3' IVT arrays (Genome arrays)
  • Gene arrays (Whole transcript genome arrays)
  • Exon arrays
  • Tiling arrays
    • Promotor Arrays
    • ENCODE Arrays


  • Human
  • Rat
  • Mouse
  • Zebrafish
  • Drosophila
  • C. elegans
  • S. cerevisiae
  • E. coli
  • Arabidopsis
  • and others




Please contact us before starting a project to make optimal arrangements for good results. This includes a mandatory quality check procedure we kindly ask our user to carry out.
Additionally we like to ask your respect the guidelines regarding your samples:


Assay Type Array Type Total RNA
Expression 3' IVT 100ng - 3ug
Whole transcriptom Gene, Exon 100 - 1.2ug
Transcript mapping Tiling, Promotor, Exon 3ug

Note: a low input protocol is available for whole transcript GeneChip arrays, please inquire for more details.

Please send only the ammount of sample, which is necessary for the number of requests, as we can store samples only for a six months at maximum. We are sorry, but we can't take any responsibility for excess of material.

The RNA sample should be intact. Please check by Gel picture, Bioanalyzer or Experion plots showing 18S/28S (16S/23S) bands.

The RNA should be free of any enzymatic inhibitors. Please perform an Oligo-dT primed Reverse Transcription PCR (RT-PCR) as a functional test. Either one amplicon in the sizes range of 500-1000 bp or two shorter one at each end of the same transcript should be detectable on a gel.



Users who are not working at the Heidelberg campus of EMBL should send the samples on dry ice at the beginning of the week, to prevent any damage. Please parafilm top of the each tube and place them into a separate bag or a box before putting them into the box with the dry ice pellets.

Please label the samples in a clearly readable form according to the request number you got from the online registration system.

Arrays results files will be made available to you for a period of six months maximum, please ensure your data is saved and backed up during this time.