Affymetrix Microarray Facility

Sample Submission Form


Currently, the StemCore Microarray Facility offers Affymetrix Genechip Technology® for gene expression and DNA Analysis profiling. This technology provides efficient access to genetic information using miniaturized, high-density arrays of oligonucleotide probes. If sample quantity is limited, current protocols in place allow us to process samples that are at concentrations as low as 50 ng/µl. Quality assessment measures for total and mRNA samples are available. Use of the Agilent Bioanalyzer for this purpose is strongly recommended for each sample submitted and can be indicated on the request form. This service can also be requested for RNA that will not be utilized for a GeneChip experiment.

  • GeneChip Hybridization Oven (64 GeneChip capacity)
  • Two Fluidics Stations (12 GeneChip capacity in one 8 hour shift)
  • Scanner (36 GeneChip capacity in one 8 hour shift)
Services Provided

We are pleased to announce that we are now able to provide access to the full line of Affymetrix Gene Expression and DNA Analysis products including:

  • miRNA 2.0, 3.0 and 4.0 Array
  • Human Gene 1.0 ST, 2.0 ST Array
  • Human Exon 1.0 ST Array
  • Human Promoter 1.0R Array
  • Human Transcriptome 2.0 Array
  • Human SNP 6.0 Array
  • Mouse Gene 1.0 ST, 2.0 ST Array
  • Mouse Exon 1.0 ST Array
  • Mouse Promoter 1.0R Array
  • Rat Gene 1.0 ST, 2.0 ST Array
  • Rat Exon 1.0 ST Array
  • Model Organism Arrays (Xenopus, Zebrafish, C.elegans, P. aeruginosa, etc.)
  • Tiling Arrays

Technical specifications regarding the full Affymetrix product line can be found at

  • Samples from local researchers should be dropped off at the Microarray Facility Monday-Friday between the hours of 9:00 AM and 4:00 PM along with a fully completed Request Form. Please make sure to indicate RNA concentration for each sample and ensure that the label on the tube exactly matches the sample name given on the request form.
  • Samples from external sources should be shipped to the above mailing address via Federal Express or Purolator to the attention of Kathy Sheikheleslamy. In advance of shipment of the RNA samples please fax the completed request form to Kathy Sheikheleslamy at (613) 739-6294. If your RNA sample has been obtained from human subjects, please include a copy of the appropriate ethics review approval forms. The samples should be shipped on dry ice to the Stemcore Laboratory (see address below). It is important to label the sample "Perishable". Please also include a copy of the previously faxed request form with the shipped samples.
  • Results can generally be obtained within 2 working weeks from date of submission.
  • All samples are processed on a first come first served basis.
  • Laboratories will be charged for all reactions processed barring any technical issues encountered
  • Your results which include the Affymetrix files (.exp, .dat, .cel, and .chp) as well as a .txt file of probeset values and quality assessment analysis will be saved into a drop box and be available for your retrieval. When your experiment has been completed you will receive an email informing you of completion of the experiment and the link to drop box.

Please refer to the attached fee schedule for specific services offered and associated costs. This schedule is applicable to academic researchers only. Commercial researchers should inquire for pricing and availability

RNA Sample Preparation

Best results are obtained using 300 ng of recently isolated total cellular RNA utilizing the whole transcript ST Labeling protocol.

The method of isolation that produces the best results in our hands is Qiagen RNeasy Mini Kit (P/N 741104). The RNA should be resuspended in RNase free water. Please do not resuspend samples in buffers containing SDS, or other detergents, as they will inhibit the enzymatic reactions used to synthesize the target cDNA.

Reaction Submission Format

In order to minimize error and reduce turnaround time we will only accept samples that are provided in the following format:

  • Each sample should be provided in a 1.5 ml microfuge tube.
  • Please provide a separate aliquot of the sample if both Affymetrix microarray analysis and Agilent Bioanalyzer quality assessment is required
  • The microfuge tube should clearly be labeled with black indelible ink with the sample name as well as the requestor’s initials.
  • Please ensure that the name on the microfuge tube corresponds exactly to the name indicated on the request form.
Mailing Address

Ottawa Hospital Research Institute
Sprott Center for Stem Cell Research
StemCore Laboratories
Room 5132, Critical Care Wing
501 Smyth Road
Ottawa, Ontario, Canada K1H 8L6

Contact Information

Kathy Sheikheleslamy
613.737.8899 x73251 (lab phone)
613.739.6294 (fax)

Affymetrix GeneChip Technical Variability