Monday, December 3, 2007

Field Trip!!!!

The moment we've been waiting for has finally come!!!!

We took a field trip to the microaray facilities at the University of Pennsylvania in order to scan our microarray slides. We all jumped into a van and Karl safely drove us (thanks Karl!). When we got there, we met Ben, who helped us with our scanning.

What's the whole scanning process all about?

Well, be patient and we'll tell you.

Basically, the microarray slide with our hybridized sample is exposed to UV light. This exposure causes the Cy3 to glow a green color and Cy5 a red color. When cy3 and cy5 overlap, they glow a yellow color.

So remember we labeled our control population cDNA with the cy5 dye and our treated population cDNA with a cy3 dye. Also remember that cDNA is a product of RNA so it is indicative of whether a gene is expressed or not. Also remember that the microarray slide has many spots on them, to which different cDNAs corresponding to different genes can bind.

Why do you have to remember so many things??

The answer is so that you will understand that a red signal for a certain spot on the microarray slide (which corresponds to a certain gene) means that the particular gene is expressed in the control population and not expressed in the heat shock treated group - hence, one might suspect that this gene is turned off during heat shock.

On the other hand, a green signal means that the particular gene is turned on during heat shock, and a yellow signal means that the gene is on in both populations.

By determining which genes are on and off, we can reveal 'heat shock' genes - that is, genes that are involved with the heat shock response.

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