Well, when I did transfection in 96 wells plate, first I seeded each well with 1x104 cells and filled each well with 200 uL of DMEM. Then I put the plate in an incubator for 24 hours. After that, I withdrawn the DMEM and washed each well with PBS for 2 times. This because in my case, the cells that I used in a 96 well grown 60-65% (of confluence) in 24 hours when I seeded the well with 1.000 cells in each well. So you will need to do a growth curve to determine how much cells and how much time do you will need to achieve 60-65% in confluence per well. After that, you will can do the transfection protocol normally.
Be careful to assure equal spreading of the cells. Avoid making bubbles, as in this case the cells wont attach to the surface where the bubble is!
SECOND day: check the cells on the microscope. Carefully select the concentration of cells that corresponds to 60% of confuency. Only these wells will be used for the transfection!
Then, suck off the media and put 100 uL DMEM.
Prepare the reagent transfection mixture:
Recommended Reagent:DNA ratio for most of the cells is 3.0 :1; it means:
in a eppendorf tube add 2.2 µg of DNA, 6.6 µl of FuGENE® HD reagent and OptiMEM till 103 µl. MIX THOROUGHLY! Then incubate the mixture for 15 minutes; then from this mixture, add 10 µL per well.