Try to trypsin after washing the cells with 1X PBS and for a longer duration (15 min). Add media and collect cells in a 15 ml tube and use 10 ml pipette to continuously forward-backward pipetting for 15-20 times. Centrifuge at 1200 rpm for 3 min at room temp. Add desired amount of media and use 10 ml pipette again for 15-20 times pipetting. Count the cells and do serial dilutions to get single cells per well of 96 well plate.
I am sorry I am here not for answer your question. I want to ask you which medium you are using for culture the mkn45 cells. Because I am going to culture it for my further experiment. Thank you very much.