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Illumina Arrays: Overview & FAQ
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The PMGC is an experienced provider of Illumina array-based services. With the increased popularity of sequencing based RNA analysis, Illumina has unfortunately discontinued the production of their gene expression arrays. However, Illumina's DNA and epigenomic arrays continue to present a cost effective, robust platform. The PMGC offers a number of Illumina array-based solutions, primarily for human and mouse studies. The unique bead-based technology behind the Illumina arrays is robust, and provides excellent reproducibility and reliability.


Pricing: Please inquire
Pricing is highly dependent on experimental design - please allow us to help you find the most cost effective solution, take advantage of our complimentary experimental design consultation!

Contact:

Illumina Service Coordinator: Julie Tsao


Quick Questions:

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Where can I find more information about Illumina Array content?

For older expression based arrays, the PMGC has developed a powerful tool (ArrayTrans) to allow for researchers to easily search for genes or probes represented on Illumina human and mouse arrays. For additional information about the content of Illumina bead-arrays, including species other than human and mouse, please visit the Illumina website.

How much DNA is required for Illumina arrays

The amount of material required depends on the application. Illumina SNP arrays typically require 1 µg of genomic DNA at a concentration of at least 50 ng/µl. For methylation assays, 500 ng of bisulfite-converted DNA is required. Please refer to the specific pages for Gene Expression, SNP, or methylation profiling for more accurate guidelines on sample requirements.

Are there control probes on the Illumina arrays?

Yes, there are several types of control probes. Illumina provides control probes to test for hybridization, contamination, stringency, background, labelling, and housekeeping genes. For more details on Illumina probes please refer to this PDF from Illumina.

Is it possible to get data for each feature on the chip (instead of data averaged for each probe)?

Yes, this is known as bead-level data. Although we do not normally save bead-level data, if you need this let us know prior to your experiment.

What steps are taken to ensure the least amount of variability?

Microarray experiments are relatively complex, with numerous steps, reagents and instruments involved. Despite this, it has been shown in many studies that the leading causes of variance are both the facility that is performing the analysis followed by the technician that completes the experiment. All of our technicians are highly experienced and rigorously trained. Each project is assigned a specific technician who completes the entire project to minimize variability. Furthermore, wherever possible, we use arrays and reagents from the same lot. We use the same equipment (hybridization oven, scanner, etc.) throughout the project; all in an effort to ensure the tightest possible data.

Often a project is large enough that it will require multiple days worth of amplification, labelling, and hybridizing to complete. In these cases we work with the customer to identify which samples are replicates and we split these replicates across the various days to ensure that it is possible to control for any day-to-day variations that may occur.

What is the difference between a technical replicate and a biological replicate? Which type is most useful and how many replicates do I need?

A biological replicate involves independent samples (multiple patients, multiple biopsies from an individual patient, etc.). RNA or DNA would be extracted from unique biopsies, blood from unique patients or from independent cell cultures (i.e. individual culture dishes). The purpose of a biological replicate is to assess and control for biological diversity.

A technical replicate involves splitting a sample at some point and continuing on with the two aliquots as separate samples through the rest of the protocol. So for example, a technical replicate might involve taking one RNA sample and performing two independent amplifications and labellings from that initial sample. Similarly, if a labelled sample was split onto two arrays, that would be another type of technical replicate. Technical replicates provide an indication of measurement (or technical) error and are useful for diagnosing problems with the protocol, but offer little in the way of statistical power for a biological experiment.

The exact number of replicates required for an experiment is difficult to determine a priori without a proper power analysis. Such a power analysis is not always possible as it requires that you have an estimation of the overall variance, which you often do not have before you perform the experiment. We generally recommend doing as many biological replicates as your budget can accommodate. In general it is good to have at least three biological replicates per condition. For a more detailed determination of the number of replicates required, please contact us as we will be happy to help you design your experiment.

What kind of data will I receive with the optional data analysis?

All customers running an Illumina experiment through the PMGC will receive raw data files (both background subtracted and non-background subtracted) in tab-delimited text format.

Customers who opt for our additional data analysis service will also receive files from a quality control assessment, completed in R, as well as the appropriate statistics, heat-map and fold-change analysis for their data set. For a more detailed answer specific to the particulars of your experiment, please inquire with Carl Virtanen, our Bioinformatics Manager, at .