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general FAQ
- What services are offered at the UHNMAC?
Please visit our Services Overview page for the most up-to-date list of services we offer.
- Are you interested in collaborations?
The UHNMAC is interested in participating in collaborative research projects with academic and commercial groups. We could contribute valuable array expertise to a project, including experimental design, performing the experiments, data analysis, etc. If you are interested in a collaborative project with us, please contact Neil Winegarden at .
- What are microarrays?
There are many different types of microarrays used for very different tasks. We make cDNA, oligonucleotide, and CpG island microarrays at the UHN Microarray Centre. A (perhaps over) simplified description of a microarray is a glass slide with a large number of different cDNA (or oligonucleotides) spotted on it.
Visit NCBI's Microarray Factsheet for more details.- What exactly are on the microarrays?
On the human and mouse cDNA microarrays, PCR amplified EST clones. On the yeast arrays, PCR amplified ORF clones. The 34.6k human oligonucleotide array consists of 70-mer oligonucleotides based on the Ensembl Human 13.31 database. The human and mouse CpG island arrays contain PCR amplified clones from a CpG library obtained at the Sanger Institute.
- What are EST clones?
EST stands for expressed sequence tags. Essentially something that has been identified as a potential mRNA which has been isolated, catalogued and cloned. Each EST has a clone ID that usually stays with that clone. The assignment of the EST to a particular gene or mRNA is often done by sequence similarity though, which means that as new genes are found, old assignments are changed. On some occasions, an EST is mislabelled and the ID itself must change as well.
- Where did you get the clone sets from?
The different clone sets are produced by different groups/organisations but in brief:
- All of our current human clones are from Image Consortium
- Our Yeast collection is from Research Genetics (Invitrogen)
- Our Mouse Collection is from National Institute of Aging
- Our CpG clone collection (human and mouse) is from the Sanger Institute
- How do you know what a particular clone corresponds to?
Most of the core annotations (clone Ids) we have were provided with the clone sets. However, we have found that these annotations (especially those from Image Consortium) are not perfect (Nucleic Acids Research, 2001, 29(2):582-588) so as a result we are sequencing all of our clone sets. The Human 1.7k and 19k sequences are complete and are available for download on our Gene Lists page.
- How can I get a clone for further verification?
We can provide Image Consortium Clones to researchers so they can sequence or use for Northern blots. We do charge a nominal fee on a per clone basis for cost recovery. Just send an email to . Mouse clones must be obtained from NIA through their distribution channels. Human and Mouse CpG clones can be through the Sanger Institute. Yeast ORFs were derived from Research Genetic Genepairs (Invitrogen) so there are no clones to distribute.
- How do I analyse my data?
This is really a very broad question that is often asked soon after our users realize exactly how much data is produced from microarrays. There are numerous analysis packages (some commercial, some free) available that would help you do some of the work but much like a car won't go very far if you don't know how to drive, you won't get much out of these packages unless you understand the principals behind them. Statistics plays a large part in microarrays so read up on it. It is also a good idea to read microarray papers to see how other people analyse their data. The Microarray Centre offers a Data Analysis and Bioinformatics service.
- Why are there a small number of redundant spots on the 19k array?
Some spots are purposely spotted more than once as a positive control. The libraries themselves were thought to be made up of non-redundant ESTs when they were purchased. However, through our bioinformatics efforts, and the increasing amount of data available, we have found that some of the ESTs do map to the same Unigene, thereby contributing to the increase of redundant clones within the set.
- What are focused arrays and do you make any?
Focused microarrays are comprised of clones representing certain classes or families of genes; often genes associated with a particular pathway, chromosome, or disease. Such focused content is often used for validation and/or disease-specific studies. The UHNMAC currently does not manufacture focused arrays, however, such arrays can be made as part of our custom arraying service.