STEMCORE LABORATORIES
501 SMYTH ROAD
OTTAWA, ONTARIO
CANADA K1H 8L6
(613) 737-8899 X73251
Dear Researcher,
Thank you for your interest in the OHRI Gene Expression Facility. Currently, our facility offers
Affymetrix GeneChip® technology which provides efficient access to genetic information using
miniaturized, high-density arrays of oligonucleotide probes. In order to initiate a GeneChip experiment at
the facility an Affymetrix GeneChip® Request Form must accompany the submitted RNA samples that are
prepared in accordance to the guidelines in the attached document. In an attempt to standardize our
protocols and minimize turnaround time we ask that the guidelines for concentrations and volumes for
RNA sample submission be followed as closely as possible. In addition to the sample submission
document you will also find enclosed a newly revised GeneChip® Request Form. Recently, quality
assessment measures for RNA samples submitted for microarray analysis have been implemented. Use of
the Agilent Bioanalyzer for this purpose is strongly recommended for each sample submitted and can be
indicated on the request form.
Upon completion of your microarray experiments, all results will be saved to CD and either you
will be contacted by email that your results are ready (customers in Ottawa only) or the results 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. The Affymetrix
files can only be used with Affymetrix software (GCOS, GDAS, and DMT) while the .txt file can be used
with third party microarray analysis software as well as with Microsoft Excel. One workstation is available
at the Genome Centre that can be accessed for data analysis. Data analysis services can also be purchased
from the Genome Centre.
Sincerely,
Kathy Sheikheleslamy
Manager,
StemCore Laboratories
STEMCORE LABORATORIES
501 SMYTH ROAD
OTTAWA, ONTARIO
CANADA K1H 8L6
(613) 737-8899 X73251
RNA Sample Submission Guidelines
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 50-100 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). 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
Total RNA, Affymetrix Standard
Target Labelling Protocol
Total RNA, Affymetrix Small Sample
Target Labelling Protocol
Total RNA, Agilent Bioanalyzer*Nano chips
Total RNA, Agilent Bioanalyzer*Pico chips
Concentration
2.0 ug/ul
Volume
10.0 ul
0.01-0.05 ug/ul
5.0 ul
50 ng/ul
500 pg/ul
5.0 ul
5.0 ul
*
Please note that if quality assessment of submitted total RNA samples via the Agilent Bioanalyzer is requested, a separate
aliquot must be provided.
In advance of shipment of the RNA samples please fax the completed request form to the
attention of Kathy Sheikheleslamy (613) 739-6294. 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. The
samples should be shipped on dry ice to the OHRI. It is important to label the sample
“Perishable”. Please also include a copy of the previously faxed request form with the shipped
samples. Investigators located in Ottawa may hand deliver samples directly to the Gene
Expression Facility weekdays, between the hours of 9:00 am and 4:00 pm. The samples should
be transported on ice.
Shipping Address:
Kathy Sheikheleslamy
StemCore Laboratories
Ottawa Health Research Institute
501 Smyth Road
Ottawa, Ontario
Canada K1H 8L6
Tel:
(613) 737-8899 x73251
Fax: (613) 739-6294
STEMCORE LABORATORIES
501 SMYTH ROAD
OTTAWA, ONTARIO
CANADA K1H 8L6
(613) 737-8899 X73251
E-mail: ksheikheleslamy@ohri.ca
Fee Schedule
GeneChip Array
Standard Target
Labelling Protocol
Small Sample Target
Labelling Protocol
Human Gene 1.0 ST Array
Human Genome U133A, B
$950
$1100
Human Genome U133 Plus 2.0
$1000
$1150
$450
Mouse Gene 1.0 ST Array
Mouse Genome MOE 430 A, B
$950
$1100
Mouse Genome MOE 430 v 2.0
$1000
$1150
$450
Rat Gene 1.0 ST Array
$450
Rat Genome RAE 230 A, B
$950
$1100
Rat Genome 230 v 2.0
$1000
$1150
Arabidopsis ATH1 Genome
$850
$1000
Bovine Genome
$850
$1000
Canine Genome
$850
$1000
C. elegans Genome
$850
$1000
Chicken Genome
$975
$1125
Citrus Genome Array
$975
$1125
Drosophila Genome
$850
$1000
E.coli Genome 2.0 Array
$750
Maize Genome Array
$850
$1000
Medicago Genome Array
$1000
$1150
STEMCORE LABORATORIES
501 SMYTH ROAD
OTTAWA, ONTARIO
CANADA K1H 8L6
(613) 737-8899 X73251
P. aeruginosa Genome
$850
Plasmodium/Anopheles Genome
Array
Poplar Genome Array
$850
$1000
$1000
$1150
Porcine Genome Array
$850
$1000
Rhesus Macaque Genome Array
$1000
$1150
Rice Genome Array
$1000
$1150
Soy Array
$1000
$1150
Sugar Cane Genome Array
$750
$900
Tomato Genome Array
$750
$900
Vitis vinifera (Grape) Genome
$850
$1000
Wheat Genome
$1000
$1150
Xenopus Genome
$850
$1000
Yeast Genome v2.0
$750
$900
Zebrafish Genome
$850
$1000
Test 3 Array (with genome array)
$175.00
$ 325.00
Test 3 Array (no genome array)
$400.00
$ 550.00
Human Tiling 2.0R Array
(A or B or C or D or E or F or G)
Human Tiling 2.0R Array Set
(ChIP, 7 Arrays)
Human Promoter 1.0R Array
(ChIP)
Human Tiling 1.0R Array Set
(14 Arrays)
Human Exon 1.0 ST Arrays
$1150
$4500
$1150
$5000
$1500
STEMCORE LABORATORIES
501 SMYTH ROAD
OTTAWA, ONTARIO
CANADA K1H 8L6
(613) 737-8899 X73251
Mapping 10K Array
$1000
Mapping 10K 2.0 Array
$1000
Mapping 100K Array
(50K Xba or 50K Hind)
Human Mapping 500K Array Set
(250K Nsp or 250K Sty)
Mouse Tiling 2.0R Array
(A or B or C or D or E or F or G)
Mouse Tiling 2.0R Array Set
(ChIP, 7 Arrays)
Mouse Promoter 1.0R Array
(ChIP)
Mouse Tiling 1.1R Array Set
(14 Arrays)
Mouse Exon 1.0 ST Array
$1100
Rat Exon 1.0 ST Array
$1500
Reagent Fee*
Bioanalyzer Fee
$1100
$1150
$4500
$1150
$5000
$1500
$200.00
Microarray Data Analysis
*
Updated January 2008
*
Reagent Fee for reactions not proceeding to hybridization with GeneChip®.
$ 350.00
$20.00 per sample
$75.00 per hour