University Health Network Microarray Centre

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Sample Analysis Services

RNA

Looking for targets

Less than 100ng of each sample (picogram/low nanogram range)

When working with less than 100 ng of total RNA, an additional RNA amplification step will likely be necessary. For example, the Affymetrix platform requires a minimum of 100ng total RNA for labelling, however, one could amplify as little as 500 pg of total RNA using the NuGEN amplification method prior to labelling the sample and analysing it on an Affymetrix GeneChip.

For a complete comparison of platforms available for gene expression platforms, click here .

Please feel free to contact us for more information. We would be happy to meet with you to discuss your project. (geneservice@microarrays.ca)

Between 100 ng to 2 μg of each sample

If you have between 100 ng and 2 μg of total RNA, an additional RNA amplification step may not be required, depending on the platform you choose. Here is an example of the minimum amount of total RNA required by each platform for gene expression:

Affymetrix: 100 ng
Agilent: 2 μg
Illumina: 200 ng
NimbleGen: 10 μg
UHNMAC arrays: 10 μg

Over 10 μg of each sample (tissue culture, for example)

If you have more than 10 μg of total RNA, RNA amplification will not be necessary and your choice of platform will not be determined by your amount of starting material.

Yes

Labelling protocols and RNA amplification methods are available that have been optimised for degraded samples. Three of the platforms (Affymetrix, Agilent, and Illumina) have protocols for FFPE samples. Generally speaking, more RNA is required for degraded/partially degraded samples.

Not sure

The UHNMAC offers a RNA quality check using the Agilent 2100 Bioanalyzer .

Human

All platforms offer Human and Mouse arrays.

Mouse

All platforms offer Human and Mouse arrays.

Other

Custom printing is available on all platforms. Affymetrix, Agilent, and NimbleGen also have an extensive list of catalogue arrays for a wide variety of species.

Have targets ready for validation

Use Nanostring technology

Nanostrings (developed by Nanostring Technologies) are fluorescent barcodes that bind to target mRNA for digital gene expression analysis. The nCounter™ Analysis System measures RNA abundance by tagging with barcodes and counting individual mRNA molecules using a novel digital technology. This system is able to detect 1 copy of mRNA per cell, can evaluate up to 550 genes per reaction, and requires only 10-100 ng of total RNA for analysis. Nanostrings can be used to validate microarray results in addition to biomarker analysis and gene expression profiling involving hundreds of genes or a large number of samples. Catalogue assays (CodeSets) are available from Nanostring Technologies and Custom CodeSets can be specifically designed for your research.

Visit the Nanostring data validation page to learn more.

Perform array-based experiments on a different/low-density array platform

Array data can be validated using another array platform, often a low-density array like the Ziplex system (Xceed Molecular).

microRNA

microRNA profiling can be carried out using the Affymetrix, Agilent, and Illumina platforms. For Agilent and Illumina, Human and mouse catalogue arrays are available (Agilent also offers a rat catalogue array), and custom arrays are available for other organisms. Affymetrix’s microRNA GeneChip covers 71 different organisms. All platforms require 100-200 ng of total RNA (Agilent needs 100ng, Affymetrix and Illumina require a minimum of 200 ng total RNA)

Affymetrix miRNA Profiling
Agilent miRNA Profiling
Illumina miRNA Profiling

DNA

DNA methylation

1 μg

Of the three platforms (Agilent, Illumina, UHNMAC CpG arrays) that can be used for DNA methylation experiments, only the Illumina platform requires a minimum of 1 μg.

2 μg

Of the three platforms (Agilent, Illumina, UHNMAC CpG arrays) that can be used for DNA methylation experiments, the Illumina platform requires a minimum of 1 μg and the Agilent platform requires a minimum of 2 μg.

5 μg

Of the three platforms (Agilent, Illumina, UHNMAC CpG arrays) that can be used for DNA methylation experiments, any can be used if you have at least 5 μg of DNA.

Human

All platforms offer catalogue human arrays for DNA methylation.

Mouse

The Agilent and UHNMAC platforms offer catalogue mouse arrays (Illumina offers mouse content through custom arrays).

Other

Species other than human and mouse are available through custom printing on all platforms.

DNA-protein binding sites (ChIP-on-chip)

Between 4 μg and 9 μg

The Agilent platform requires 4 μg of PCR amplified material for ChIP-chip experiments, and the Affymetrix platform requires at least 9 μg.

For a complete comparison of platforms available for ChIP-chip experiments, click here .

Please feel free to contact us for more information. We would be happy to meet with you to discuss your project. (geneservice@microarrays.ca)

More than 10 μg

Any of the three platforms (Affymetrix, Agilent, and UHNMAC CpG arrays) can be used for ChIP-on-Chip experiments if you have more than 10 μg of PCR amplified sample. The Agilent platform requires 4 μg of PCR amplified DNA, the Affymetrix platform requires 9 μg, and the UHNMAC array platform requires 10 μg.

Human or mouse

Affymetrix, Agilent, and the UHNMAC platforms offer human and mouse catalogue arrays for ChIP-on-Chip studies.

Other

Affymetrix and Agilent offer catalogue arrays for a number of model species including rat, yeast, Drosophila, C. elegans, and Arabidopsis. Other species are available through custom printing on all platforms.

Chromosomal copy number (aCGH)

Human, mouse, or rat

For human, mouse and rat samples, the Agilent platform offers aCGH arrays in several formats including 244K, 2x105K, and 4x44K. More information about aCGH can be found here.

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Please feel free to contact us for more information. We would be happy to meet with you to discuss your project. (geneservice@microarrays.ca)

Other

Custom printing (any species, any format) is available on the Agilent platform.

Click here to find out more about eArray - custom Agilent printing.

SNP detection

SNP detection is offered using the Affymetrix platform. The Affymetrix® Genome-Wide Human SNP Array 6.0 features more than 1.8 million markers for genetic variation, including more than 906,600 SNPs and more than 946,000 probes for the detection of copy number variation. Please visit the Affymetix SNP page for more information.

Protein

Size and concentration determination

Depending on the number of protein samples, protein size and concentration can be determined using the Agilent 2100 Bioanalyzer or the Caliper LabChip. The Agilent 2100 Bioanalyzer can analyse up to 12 samples per chip, while the Caliper LabChip is a high throughput solution for protein samples in 96-well or 384-well plates.

Protein expression profiling

The Bio-Plex (from Bio-Rad) is a multiplex analysis system that can simultaneously analyse up to 100 different biomolecules. This fast and reproducible multiplex system has small sample requirements and offers greater flexibility than planar arrays. There are hundreds of “off-the-shelf” Bio-Plex/xMAP (Luminex) assays available from vendors such as Bio-Rad, Invitrogen, Luminex, Millipore, and others. Custom assays are also available.

Cytokine/chemokine detection

HLA testing

Phosphoprotein detection

Data analysis & Bioinformatics

UHNMAC microarray data analysis services

The UHNMAC offers an optional microarray data analysis package for our service clients and for clients with their own array data. This optional package includes extensive quality control, filtering, and data normalisation as well as statistical analyses (clustering and T-tests/ANOVA) using R/Bioconductor and GeneSpring software. To learn more, please see Analysis & Bioinformatics . For general questions, or to obtain a service quote, please contact our Bioinformatics Manager, Carl Virtanen.

UHNMAC bioinformatics services

The UHNMAC Bioinformatics team also carries out bioinformatics services such as sequence and SNP analysis from raw chromatograms, BLAST searches, multiple alignments and trees, primer design, antibody epitope prediction, and computer programming. Please contact us to discuss your needs.

UHNMAC cDNA & CpG island array databases

User publications
1. involving UHNMAC microarrays
2. involving UHNMAC services
3. authored by UHNMAC staff

Technical support

Contact our Technical Support Specialist

Our Technical Support Specialist is available during regular office hours (usually Monday – Friday, 9am – 4pm, excluding holidays).

E-mail: help@microarrays.ca
Phone: 416-581-7623
Toll-free: 1-877-294-4410 (in Canada & USA)

View technical documents (technical notes)
View Frequently Asked Questions (FAQ) and troubleshooting tips
1. UHNMAC microarray products
  1. View gene lists (cDNA, Human CpG, Mouse CpG)
Brief description of each array (number of spots, origin of clones)
Optimised protocols to use with our array products

Microarray platform comparison
Pricing
Scientific resources