DNA Chips-How the genes were affected

Results from our last lab involving microarrays were some of the samples had pink in them! This symbolizes that they represented lung cancer. The samples that showed up blue meant that they appeared in both normal and cancerous cells. The fourth gene was clear, which meant that it was not present in either cell.

DNA Chips- how genes affect disease

In this next lab that we are doing in class, we will be examining how to use micorarray analysis. If a person wanted to find changes in transcription in a specific tissue, they would use this process. One microarray can contain over 30,000 "spots of DNA" where each spot represents a different gene. The first step is to make a DNA chip, that is arranged in a pattern and that represents part of a genome. The chip could then be used to analyze complementary DNAs that were made from mRNA isolated from the same tissue. The two samples of tissue are dyed and then applied to the prepared "chip". You can determine the extent of transcrition by observing how each dyed sample adheres to its complement. Once you find this out computer analysis will reveal what similarities the two samples of tissue could have.  The analysis allows scientists and doctors to find problems in certain tissues much earlier than ever before.

We will be studying six genes in this lab:
C4BPA- helps initiate part of our immune system to kill pathogens
ODC1- codes for an enzyme in the polyamine biosyntheis pathway
FGG- encoded in this gene is a part of fibrinogen, a protein found in the blood, creates blood clots
HBG1- expressed in liver, spleen, and bone marrow
SIAT9- catalyzes the formation of a protein called GM3
CYP24- catalyze many reactions involved in drug metabolism and the making of cholesterol, steroids and other lipids

CSI- We've gotcha now

In this lab we began our identification of the murderer by first putting our tube with the restriction enzymes in an ice bath. Then we collected our evidence from the crime scene, in five test tubes. We had narrowed it down to five suspects! We got a sample of each suspects DNA and placed them in test tubes, then we added 10 ul of the enzyme mix into the samples and mixed well. Next, we placed the test tubes into an incubator at 37 degrees Celsius for 45 minutes. Mr. Chugh took out our test tubes at the correct time and got them ready for when we returned the next day.  

The next day when we came back we removed the tubes from the water bath and then we gentle tapped the tubes on the table to bring the liquid to the bottom of the tubes. Next, we added 5 ul of loading dye into the separate tubes, collecting the samples in the end of each test tube. We took the agarose gel and placed it in the electrophoresis apparatus. We  checked that the wells of the agarose gels were near the black negative electrode and the bottom was near the red... But we found that our positive and negative was switched! So, we replugged the electrophoresis to correct the error. The next thing we did was using a separate tip for each sample we loaded the DNA samples into the gel and after putting the lid over the chambers we turned on the power. When we returned the next day, we could finally compare our results! We found the real murderer and solved our simulated crime scene investigation.