a) All cells (except for gametes) contain the same DNA. What makes cells unique is how they express this DNA - sometimes the difference between a healthy cell and a diseased cell is a simple change in gene expression. Microarray analysis allows us to compare gene expression by first creating a gene chip, in which specific DNA sequences are put into individual spots on the chip. Meanwhile, cDNA (complementary DNA) is created from mRNA found in the healthy and diseased cells. The cDNA is then added to the chip and the fragments bind to their complementary strands of DNA that were placed there originally. By analyzing the chip, we can see what sequences are being expressed based on where the cDNA binds. For instance, let's say that the cDNA from the diseased tissue is labeled red and the cDNA from the healthy tissue is labeled green. When we analyze the results, spots that are green indicate that those particular sequences are only expressed in healthy tissue. Spots that are red indicate sequences that are only expressed in diseased tissue. Spots that are yellow (red light + green light = yellow light) indicate sequences which are expressed in both and spots that don't turn any color are not expressed in either.
b) The purpose of this experiment is to analyze gene expression in lung cancer cells versus healthy lung cells by using microarrays. Potentially, by gaining more knowledge about gene expression in this way, we could develop ways to alter cancer cells or cure them somehow. The more we understand about what makes a cancer cell different, the closer we get to solving the problem.
c) Most of the techniques or materials were explained in part "a". The microarray chip serves to isolate known DNA sequences, so that when we apply the cDNA to the chip, we can determine which sequences are active. The red and green labels show us which sequences are specifically expressed in either, both, or neither of the two cell types. We will use pipetting techniques to transfer the cDNA to the miniature microarray.
d) For my hypothesis, I think genes which are involved in typical cell functions (such as protein synthesis or cell respiration) will be expressed in both the healthy and the cancer cells. I think genes which are involved in replication will likely be turned off in the cancer cells, since they are known to divide uncontrollably. After that, I will have to wait and see how the experiment turns out. The controls of this experiment are the DNA sequences on the microarray. We already know where specific sequences are located on the chip. The variables are the cDNA sequences, which are unknown (until they bond to the DNA on the chip of course).
Results:
The microarray results are shown above. Pink = expressed in lung cancer cells only (#1,5). Blue = expressed in healthy lung cells only (#3,6). Purple = expressed in both (#2). Clear = expressed in neither (#4).
