Ottawa Genome Centre
Sample Submission Guidelines
RNA Sample Preparation
 Best results are obtained using 10 ug of recently isolated total cellular RNA utilizing the standard
Affymetrix target labelling protocol. Smaller starting amounts of RNA can also be labelled utilizing
the GeneChip Eukaryotic Small Sample Target Labelling protocol developed by Affymetrix. This
protocol requires 50 ng of starting total RNA and generates adequate labelled target through two
successive rounds of cDNA synthesis and in-vitro transcription.
 The method of isolation that produces the best results in our hands is Qiagen RNeasy Mini Kit (P/N
741104). If isolating RNA from tissue, initial isolation using Trizol (Invitrogen P/N 10296010)
followed by RNeasy column purification is recommended.
 The RNA should be resuspended in RNase free water. Please do not resuspend your samples in buffers
containing SDS, or other detergents, as they will inhibit the enzyme reaction used to synthesize the
target cRNA. Poor RNA quality can also lead to lower signals. The Genome Centre cannot absorb
costs to repeat experiments unless a chip defect is unambiguously detected.
*
Item
Concentration
Volume
Total RNA*, Affymetrix Standard
Target Labelling Protocol
2.0 ug/ul
10.0 ul
Total RNA*, Affymetrix Small Sample
Target Labelling Protocol
0.01-0.05 ug/ul
5.0 ul
Total RNA*, Agilent Bioanalyzer
0.01-0.05 ug/ul
5.0 ul
*
Please note that each individual sample must be submitted in duplicate: the first aliquot will be used for quality assessment
on the Bioanalyzer, the second aliquot will be used for the microarray experiment. Please label each aliquot on the top of the lid with a
“B” for the Bioanalyzer aliquot, and “M” for the microarray aliquot.
Request Forms
 In advance of shipment of the RNA samples please fax the completed request form to the attention of Pearl
Campbell (613) 737-8803.
 If your RNA sample has been obtained from human subjects, please include a copy of the appropriate ethics
review approval forms.

Upon receipt of your fax you will be given an approximate timeline for experiment completion.
Shipping
 The samples should be shipped via FedEx on dry ice to the OHRI (see the address below). It is important to
label the sample “Perishable”.
 For samples that have been accepted into the Stem Cell Genomics Project FedEx charges will be covered by
the Network. On the FedEx waybill please mark 123626583 in the box marked Account # and for Internal
Reference please mark 997319200.
 Please also include a copy of the previously faxed request form with the shipped samples.
Shipping Address
Pearl Campbell
Ottawa Health Research Institute
Ottawa Genome Centre
Gene Expression Facility, Lab 4B-100
501 Smyth Road
Ottawa, Ontario
Canada K1H 8L6
Tel:
(613) 737-8899 x73110
Data


Upon completion of your microarray experiments, all results will be saved to CD and will be shipped
directly to you via Federal Express. All Affymetrix files will be saved to CD (.exp, .dat, .cel, and .chp
files). Additionally, a tab delimited text file (.txt) will be generated from the .chp file.
Analysis of the data can be obtained for an hourly charge ($50.00 per hour).