Online Databases – The GEO DataSet Browser

A great way of gathering some preliminary data is to use the GEO DataSet Browser on NCBI. NCBI has many useful resources and this database is one. Examples of its use include look at gene expression changes in:

* tissues stimulated with steroids, drugs, and other compounds;

* control vs diseased tissues;

* the effect of age;

* etc

Here is a link to the GEO DataSet Browser:

http://www.ncbi.nlm.nih.gov/sites/GDSbrowser/

For those of you not familiar with it, just type in your search term in the search box e.g. “alzheimers disease stages”. Select a GDS dataset. Scroll down to the bottom and you should see 3 tabs “Expression Profiles”, “Data Analysis Tools” and “Sample Subsets”. The “Expression Profiles” tab will take you to the profiles of all the genes screened.  When you click on the “Data Analysis Tools” tab a new section will appear below. Type in the name of your GOI in the search box and you will be able to search for gene expression changes in your GOI. The “Sample Subsets” tab provides information about the samples used.

Gene Expression?

A very quick way to determine if a particular gene is expressed in your cells or tissue of interest is via LSBM.

RefExA contains gene expression data derived from microarray analysis of normal human tissues and cultured cell-lines. If you are ever wondering what cDNA template to use to test your new primers, it is worthwhile checking out RefExA to see if the tissue or cell type your template is derived from does express your GOI and to what extent. Sometimes a failed PCR may just be because the template of choice has little to no expression of your GOI.

Screen capture of ESR1 data from LSBM