I do the procedure as below, I am getting result always,
first i seed the cells then i will treat the cells by different dilutions of drug from 100 to 1.5ug/ml, this is all in 96 well plare, and triplicate, after incubation time (24,48 and 72) i will not remove any media, depend on media availble in each well i will add 10ul of mtt solution to each 100ul of media in each well, then after 4hrs i will remove the complete media by taking the 96wel in 45" angle, remove the media carefully, the tips should not touch bottom of the wells, then add 100ul of DMSO, read in 570nm.
If your cells are detaching from the bottom when you are removing the media, it may because of the plate which is not good quality. or it may because of the cell line you are using...
are you sure that the MTT solution should be filtered, while you add the MTT solution, means you are killing the cell any way, and cross contamination does not give any sense...
I have one idea for you, but its depend on your experiment, if you using anexin v assay, you do not need to do it by flowcytometry, you can use by florescence microscope which you need to have chamberslide, here you can observe the cells by flourcsence microscope whith out disturbing the cell surface...
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