So in the lab that I'm working in the knocked down alpha 3 beta 1 integrin. They knocked down alpha 3 the same way that other lab from last week knocked down UPF1 by making the mRNA double stranded so the cell automatically degrades it. Alpha 3 in a integrin involved in a host of cell functions but for my purposes it happens to interact with Nonsense Mediated Decay. When alpha 3 is down regulated NMD functions normally, but when alpha 3 is upregulated NMD is suppressed. When UPF1 is down regulated NMD is also suppressed. My job was to compare the results from that two different labs got with regard to the fold change of other proteins, the thinking behind that being that if alpha 3 was upregulated and UPF1 was down regulated that means NMD won't be occurring so more mistakes would make into the protein formation stage. I was to look and see what proteins exactly were being upregulated while alpha 3 was being upregulated and UPF1 was being downregulated.
I did this by scanning through hundreds of lines of a spread sheet that had factors that I need like fold change. Fold changes are basically the difference in prevalence for when alpha 3 is knocked down versus when it wasn't. I ended up finding 6 that were upregulated while alpha 3 was upregulated and UPF1 was downregulated out of a possible 1,180 proteins. Oddly enough this exercise was more or less a warmup to get me acquainted with how to do a little bit of bioinformatics.
0 Comments
Leave a Reply. |
Michaela BentonI'm lucky enough to go to this amazing school that has this amazing program that lets me learn amazing things. Archives
December 2017
Categories
|