Affymetrix Microarray Facility
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)
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
- 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
- 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
- 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.
Ottawa Hospital Research Institute
Sprott Center for Stem Cell Research
Room 5132, Critical Care Wing
501 Smyth Road
Ottawa, Ontario, Canada K1H 8L6
613.737.8899 x73251 (lab phone)