Week 2 finished-

Wow- busy day on Friday! We started out down in the computer lab, working on MatLab, and I was also working on my graphs with Excel- which is a little different on my Mac. Trying to get the data I want to show up where I want was pretty frustrating - and I didn't get it done, so I will have to try to work on it this weekend some. I know there HAS to be a way to get all the pieces of info in there - I can draw it on a piece of paper - why can't I make it happen on the computer?

In MatLab we are trying to normalize the data we have, so three different files have pieces of information we need - the sequence depth is the total numbers of sequences on the entire chromosome 17 ( over 212000), and that is on one file. The region is the spot where transcription starts for one gene, and then you go out 5000 base pairs on each side, and we have a region for each gene (on chr 17 that is 1905 genes), and that is on another file. And the length of the gene is measured from the spot on the chromosome where the gene starts to where it ends - on another file. We put all those together to calculate a "normal" number for the gene expression compared to all the other gene expressions. So, in this program I have to figure out how to pull out the info that we need, and get it to all work together to give the results we need and save them. Then, I supposed we are going to do the same thing with the other cell line and compare them to see if there are any big differences.

Then we went upstairs to the wet lab where Micheal was extracting RNA from cells. We watched as he put in acid to break down the cells and did the process to get the RNA out. After that, he showed us how to split the cells that we were growing - a long process with many chemicals and a centrifuge, before we put the new cell samples back into the dishes and incubate. Never having done anything like this before I came here, I really need to get the basic idea of a clean zone about my sample down. I am never supposed to have my hand wave in the air above my sample, and beware of anything touching anything else. Someday Steven Spielberg or George Lucas can design a holographic sleeve you can assign around what you are supposed to keep clear of to remind you - that would help! We also were shown "The Cold Room", which is where you work with samples that need to stay at low temps. It is 4 degrees Celsius in there - which would feel pretty great at times, like after walking out to the parking lot to my car in the heat!

Keith came in last night for a visit - yay! So I am planning on some relaxation and fun, and brain down-time! Next week we will be taking classes in the morning, and going to the lab in the afternoon. Michael seems determined to get max productivity out of us - and I am learning a whole bunch from him. Of course, when you start with no knowledge at all like I am, you have no where to go but up!!

See you next week-

Leslie