Affymetrix GeneChips use a single color detection system different to the traditional two-colour “cDNA array” technology. This method allows you to generate and easily compare gene expression data generated at different times and locations. Introducing new data points to experiments is easy and allows complex experiments to be built up over time.
Pricing is dependant on the type of array you are using and where you are based. All prices are exclusive of VAT. Contact us for a detailed quote.
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recommend isolating RNA using the Qiagen RNeasy kits. If you use Trizol
or other extraction methods then you must perform a clean-up of your
RNA using the Qiagen RNeasy kits before submitting your samples. We
routinely request 20ug of total RNA at a minimum concentration of 1ug/ul,
in DEPC-treated water. You should provide a gel image of the RNA alongside
a marker. 10ug is the recommended amount of starting total RNA required
for each GeneChip analysis. We would encourage you to send as much RNA
as possible as this will allow us to repeat any failed samples immediately
without your having to grow plants and extract RNA again.
Include replicates! All experiments should be planned with the help of a qualified and experienced statistician if possible. We recommend that you preapre at least one set of replicate material more than you want to include in the final experiment. If there is a problem with one or more of your samples you have material ready for analysis and will not have to grow new plants or obtain more tissue. Journals are becoming stricter in assessing the statistical interpretations you claim in your papers, if you are asked for more replication you can quickly get this data back to referees.
Your experimental system should be well defined and the approprate controls included. Analysis of your system for genes that you know to be affected using Northern or RT-PCR analysis can save you a lot of money on wasted chips. All experiments should be carried out in triplicate if possible. The Affymetrix GeneChip system is a reliable and robust tool for gene expression monitoring, your greatest source of variation is biological and you should perform biological replicate analysis.
Sample preparation by the Service Provider:
be cleaned, if necessary, using Qiagen RNeasy columns. cDNA synthesis
and cRNA in vitro transcription reactions are not guaranteed. The user
must meet the costs associated with repeating failed reactions. The
Service Provider will inform you of any failures and subsequent cost
implications before proceeding.
Clean-up of RNA
Hybridsation cocktail set up
Small Sample Labelling Protocol
does it cost per chip?
What do I
get for my money?
How much RNA
Small Sample Protocol: You can start with as little as ng quantities of total RNA. The protocol uses a two round strategy to amplify the necessarry amount of cRNA for GeneChip analysis. You cannot directly compare data from small sample protocol experiments with those using the standard protocol. If you can produce enough total RNA for the standard protocol this is the one we would recommend.
How long will
How do I analyse
Do I need replicates?
The JGL cannot guarantee the results from gene expression analysis.You should perform confirmatory analysis such as Northern blots or RT-PCR on interesting genes.