I want to do gene expression analysis of cell lines exposed to pesticides with control cells using microarray. Which chip should I select for this study?
Probably you should check which of the available chips cover most of your interesting genes. If there are no chips for your organism/genes you can design your own using for example TherMODO (http://nar.oxfordjournals.org/content/37/3/e18.abstract). You can order such array in Agilent (for example).
Deer Deepa,
The choice of array depends on several aspects:
1. Do you have access to a core facility or a lab at your place?
2. What is your budget for the experiments?
3. Do you want to perform a genome-wide screen or a focused screen on a pre-defined set of genes?
Depending on these answers, it is easier to formulate an answer for your question.
We have started with Affymetrix arrays until 2005 and since then are using Illumina array technology with great success. The technology is very reliable and easy to analyze.
Greetings
JLS
I definitely agree with Joachim and have a few other suggestions.
1. http://www.sciencemag.org/site/products/dnamicro.xhtml#Types, this site will help you with a lot of recent info on companies that you may explore. You must read about the pioneering works from the labs of Pat Brown, Mark Schena and Ron Davis to understand the power of the technology and that it has developed a lot over the years with commercial availability.
A Microarray is an array of DNA molecules immobilized on a solid support, may be nylon membrane, glass or specialized chips called DNA chips. Suggested companies would be Clontech, Affymetrix, and Agilent Tech. And as JLS has said, it all depends on a lot of factors, whether you have an array core facility, your budget, or you would do-it-yourself on a small test budget. You could even start with membrane arrays and then go to glass or Chips depending on budget and core facitlity availability.
Also, remember your homework has to be complete all the way to how you plan to anaylze your results and you can discuss that with your co-workers and company about informatics or try the free available softwares. When you have finally decided you have to choose proper controls, repeat experiments and confirmations with other tests like real time PCRs will be required. Furthermore, you need to know the cell type well about growth and confluence. Because will will get a huge load of data that will require orderly analyses to understand your results. But I an sure it will be worth it and very promising, GOOD LUCK!
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