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The Microarray Analysis and Gene Expression Facility offers a comprehensive set of microarray based services to researchers in the academic, commercial and pharmaceutical communities. We provide:

Please see our acknowledgment policy.

• Free initial consultation to discuss experimental design to address all steps crucial for a successful microarray experiment
• RNA quality testing via the Agilent BioAnalyzer
• GeneChip® technology based expression analysis and SNP genotyping
• Array-based comparative genomic hybridization (CGH) with either BAC or Agilent oligonucleotide arrays
• Illumina BeadStation expression analysis (this service is provided by the Genetic Analysis Facility)
• Access to a wide variety of Data Analysis software on public computers for on-site microarray data analysis
• Statistical consultation services for simple and advanced data analysis

1. Facility Overview
2. Microarray Pricing
3. Sample Submission Guidelines
4. Sample Submission Forms
5. RNA BioAnalyzer Analysis
6. Data Analysis Software Available
7. Facility Contact

The Microarray Analysis and Gene Expression Facility offers Affymetrix GeneChip® analysis for both gene expression and genotyping, and array-based comparative genomic hybridization (CGH) with either BAC genomic DNA or oligonucleotide arrays. Affymetrix oligonucleotide GeneChip® microarrays are available for both RNA analysis of gene expression and DNA analysis for mapping, association or genomic copy-number studies. The facility obtains Affymetrix arrays at the Genome Canada Platform discount rate, which is among the most competitive in the world. The facility is an accredited Affymetrix Service Provider.

Affymetrix GeneChips® are also available for industrial customers at Industrial Tier 1 pricing. Contact the facility for more information.

For detailed information about this technology and further product information, please see www.affymetrix.com. The array CGH uses Agilent oligonucleotide arrays (www.agilent.com). Other array-based technologies can be provided on request. Please contact the facility.

TCAG offers Illumina genotyping and gene expression arrays. more details

The TCAG Microarray and Gene Expression Facility participates in the Genome Canada Platform blanket discount program that provides us with the best possible pricing for the most popular Affymetrix microarray products. We also offer further discounts on orders of 7 or more samples. The pricing below is calculated for the standard protocol for Canadian academic researchers and listed as unit price per sample. For non-Canadian or private sector users, pricing is typically only slightly higher and is still extremely competitive. Please contact us for details. For samples with less than 50ng total RNA, when additional amplification or Nugen kits are needed, there will be additional $200 to $250 charge per sample. For array-CGH, other arrays or services not listed in this table, please contact facility staff to obtain more information.

Gene Expression GeneChip	≤ 6 Samples	7-19 Samples	≥ 20 Samples
Single Cartridge Array Format
Human Gene 1.0 ST	$475	$450	$425
Mouse Gene 1.0 ST	$475	$450	$425
Rat Gene 1.0 ST	$475	$450	$425
Human exon 1.0 ST array	$750	$725	$700
Mouse exon 1.0 ST array	$750	$725	$700
Human Genome U133 Plus 2.0	$750	$725	$700
Mouse MOE 430 2.0	$750	$725	$700
Rat RAE 230 2.0	$725	$700	$675
Drosophila Genome 2.0	$575	$550	$525
miRNA 2.0	$500	$475	$450
E.Coli Genome 2.0	$450	$425	$400
Plate Array Format	≤ 24 Samples	25-96 Samples	≥ 96 Samples
Human Gene 1.1 Array	$400	$375	$350
DNA SNP chips	≤ 6 Samples	7-19 Samples	≥ 20 Samples
Human 50K (HindIII or XbaI)	$550	$500	$450
Human 250K (NspI or StyI)	$400	$375	$350
	≤ 22 Samples	23-44 Samples	≥ 44 Samples
Human 6.0 SNP array	$525	$500	$475
Mouse Genotyping Array	$650	$625	$600

Additional GeneChip® Services (Excluding Arrays)
Full service excluding chip (provided by client)	$250
Failed cRNA preparation due to RNA quality and/or quantity	$200
DNA prep for 250K SNP array	$175
DNA prep for 5.0 array, or 6.0 GW SNP array	$250
CHIP experiment	$150
GeneChip hybridization service	$70

Array CGH Experiments	Cost
Agilent Human or Mouse CGH products	call for information

All pricing is in Canadian dollars and excludes any applicable taxes.
* - Last Updated: October 29, 2010

See Illumina pricing

RNA/DNA microarray analysis
For RNA microarray analysis, we require high quality total RNA, shipped to us on dry ice. Affymetrix recommends some protocols for RNA preparation, but other methods can also be used. If you wish to prepare your own cRNA, protocols and recommended reagents are available from Affymetrix or other vendors.

Here are some general guidelines:

• Samples of high quality and purity are the most important factors for obtaining high quality data for any whole genome microarray analysis.
• Sample (total RNA or genomic DNA) should be in nuclease-free water with absolutely no SDS or any other detergent in the solution. Detailed information on quantity and quality requirement can be found in the Sample Requirement List.
• The amount of total RNA needed for GeneChip microarray analysis ranges from 5.0 ng to 10 ug depending upon the array or protocol used.
• For genomic DNA analysis, high quality DNA in low TE buffer is required and each sample should have an agarose gel picture.

RNA BioAnalyzer Analysis

• Please provide an additional aliquot of approximately 5 μl RNA at about 200 ng/μl, diluted in water and shipped to us on dry ice with the test sample.

Comparative Genomic Hybridization (CGH) Microarray Analysis
Spectral Genomics 1 Mb resolution BAC arrays are currently used for CGH studies. This technology co-hybridizes a "test" genomic DNA sample labeled with one fluor and a control genomic DNA sample labeled with a different fluor to a BAC genomic DNA microarray. For a complete overview of the Spectral Genomics array-based CGH see http://www.spectralgenomics.com.

• A minimum of 2 μg of DNA is needed for each test sample. It is recommended to quantify the DNA prior to shipping.
• For Agilent olignonucleotide array experiments, please contact us.

The following forms are in Microsoft Excel format

1. Affymetrix Gene Expression
2. Afymetrix Genotyping 96 well plate format
3. Affymetrix Genotyping
4. Bioanalyzer for Microarray
5. Aglient Microarray

Submit samples using the LabLink server

For instructions for creating and account, placing an order etc., download the following documents.

• TCAG LIMS placing an order
• Requesting a user ID

Agilent BioAnalyzer analysis of RNA samples is available. The fee is $10 for each RNA sample. this fee is waived for an RNA sample being used in for a GeneChip experiment.. Five μl of each RNA sample should be provided at a concentration of 200ng/μl, diluted in water. Please complete the request form from above link for BioAnalyzer service.

The facility has several public computer workstations available for customer use. Commercial software installed includes packages from from Affymetrix (Expression Console, Genotyping Console, AGCC), Agilent (Genomic Workbench), SpotFire (DecisionSite), Partek (Genomics Suite) and Ingenuity Pathway Analysis. In addition, the publicly available dCHIP package is installed for analysis of genomic copy number and loss of heterozygosity.