Hello to all,
I am a masters student from Cologne, Germany and currently working on my thesis. One of my associate project involves to quantify the phenotype of nuclear orientation in some xyz gene knockdown in HEK293 (HUMAN EMBRYONIC KIDNEY cells) cell line. We have observed a phenotype of round or oval shape of nucleus oriented towards one particular pole in monolayers of cells during the knockdown. This phenotype is distinctive from the normal HEK293 cells. Now we wanted to quantify the nuclear orientation, size, during the knock downs, and a good data could help us, me, to propose a theory that nuclear polarization, is due to the specific knockdowns.
I am a new user to cell profiler, I am going though the instructions, but yet I would like to know the suggestions of this community in the following issues. 1. How many pictures should be considered ( > 1000 ) ? 2. What could be the best pipeline order for analysis, in according to your view ? 3. Could you suggest any controls? 4. What is the ideal Mammalian cell splitting ratios for especially cell profiler analysis, would you recommend any change in growth conditions ?
I would be glad to know your suggestions, and I think you will be the only community I could look for any discussion on this study.