The Hospital for Sick Children TCAG logo DGV image PGP image

Mailing List

CBW logo

Canadian Bioinformatics Workshops

University of Waterloo award

TCAG Facilities

Microarray Analysis - Gene Expression and Genotyping

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

Please see our acknowledgment policy and terms of use.

We provide

  • Free initial consultation to discuss experimental design to address all steps crucial for a successful microarray experiment
  • RNA quality testing via the Agilent BioAnalyzer
  • Expression analysis and SNP genotyping on Affymetrix GeneChip or Illumina iScan technology
  • Array-based comparative genomic hybridization (CGH)
  • 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. Affymetrix platform

Overview

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 is an accredited Affymetrix Service Provider. For detailed information about this technology and further product information, please see www.affymetrix.com.

Pricing
Gene Expression GeneChip ≤ 24 Samples 25-48 Samples ≥ 49 Samples
Single Cartridge Array Format
Human Gene 2.0 ST $320 $310 $300
Mouse Gene 2.0 ST $320 $310 $300
Rat Gene 2.0 ST $320 $310 $300
Human Transcriptome 2.0 $555 $540 $525
Mouse Transcriptome array $555 $540 $525
Human Genome U133 Plus 2.0 $475 $460 $445
Human PrimeView Array $230 $220 $210
miRNA 4.0 $445 $430 $415
E.Coli Genome 2.0 $475 $450 $425
Plate Array Format ≤ 24 Samples 25-96 Samples ≥ 97 Samples
Human Gene 2.1 Array $310 $300 $290
Mouse Gene 2.1 Array $310 $300 $290
miRNA 4.1 Array $280 $270 $260
DNA SNP chips ≤ 22 Samples 23-44 Samples ≥ 44 Samples
Human CytoScan HD array $700 $675 $650
Human 6.0 SNP array $550 $525 $500
Additional GeneChip® Services (Excluding Arrays)
Full service excluding chip (provided by client) $150
Failed cRNA preparation due to RNA quality and/or quantity $150
DNA prep for 5.0 array, or 6.0 GW SNP array $250
GeneChip hybridization service $70
  • Additional charges may apply for samples with less than 50ng total RNA, when additional amplification or Nugen kits are needed.
  • Gene 1.0 ST arrays are available for model organisms: (see detailed list on www.affymetrix.com). For pricing and processing please contact the facility.
  • Human CytoScan HD array and assay are available. Please contact the facility. for more information.

Sample preparation and submission

All RNA samples have to be delivered or shipped to the facility in dry ice.

2. Illumina platform

Overview

TCAG offers genotyping on any publicly available Illumina microarray including:

  • Whole-genome genotyping and copy number analysis using Infinium Omni arrays
  • Focused genotyping arrays, non-human chips, etc.
  • Custom genotyping panels using Illumina's Goldengate assay (96 and 384-3,072 SNP panels) or iSelect (3,000 to 1M custom SNPs)

For more information on Illumina's suite of products, visit www.illumina.com.

Pricing
Whole-genome Genotyping <= 96 samples 97-480 samples > 480 samples
Human Omni2.5-8 array $280 $270 $260
Human Omni2.5Exome-8 array $285 $275 $265
Human Omni5Exome-4 array $440 $430 $420
Human CoreExome-24 array $95 $90 $85
Human OmniExpress-24 array $165 $155 $145
Human PsychArray-24 $110 $105 $100
Human OncoArray-500k $115 $110 $105
DNA Methylation profiling
Human MethylationEPIC array $500 $490 $480
Bisulphate Conversion $20 $15 $15
Custom and Focused content SNP genotyping # SNPs # samples Price
iSelect custom genotyping panel 7,600-60,800 ≥ 1152 Please enquire
Custom SNP genotyping panels (any species) 96 or 384-1,536 ≥ 96 Please enquire

Additional charges may apply for samples with less than 50ng total RNA, when additional amplification or Nugen kits are needed.

Sample preparation and submission

All RNA samples have to be delivered or shipped to the facility in dry ice.

3. Agilent Platform

Overview

Comparative Genomic Hybridization (CGH) Microarray Analysis

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 genomic DNA microarray. The array CGH uses Agilent oligonucleotide arrays (www.agilent.com). Other array-based technologies can be provided on request. Please contact the facility.

Sample preparation

  • A minimum of 2 µg of DNA is needed for each test sample. It is recommended to quantify the DNA prior to shipping.

Samble submission

4. RNA BioAnalyzer Analysis

Overview

To verify quantity and quality of RNA samples for any downstream application, Agilent BioAnalyzer analysis (Acrobat 56 KB) is available.

Pricing

The fee is $10 for each RNA sample. This fee is waived for an RNA sample being used in an array experiment at TCAG.

Sample preparation

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

    (*if also submitting for one of our microarray services).

Samble submission

5. Sample submission for Microarray or Bioanalyzer experiments

Request your service using the Clarity LabLink server. For instructions on creating an account, placing an order etc., download the following document.

The following forms are used to upload requests to your Microarray LabLink account. All forms are in Excel format unless otherwise indicated.

Samples should be delivered to:

TCAG Microarray Facility
Attention: Dr. Chao Lu

The Centre for Applied Genomics
The Hospital for Sick Children
Peter Gilgan Centre for Research and Learning
686 Bay Street, Room 139800
Toronto, Ontario
M5G 0A4, Canada

6. Data Analysis Software Available

The facility has several public computer workstations available for customers to use with data generated at TCAG. 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.

Facility Contact

Chao Lu

The Centre for Applied Genomics
The Hospital for Sick Children
Peter Gilgan Centre for Research and Learning
686 Bay Street, Room 139800
Toronto, Ontario
M5G 0A4, Canada
Tel.: 416-813-8059, Internal: 308059
Fax: 416-813-8319, Internal: 208319
Email: