You should use 96-deepwell plates equipped with air-permeable sealing tape as a sterile barrier. The filling volume should not be greater than 500µL. Shake the plates with an orbital speed of 300 rpm and a shaking diameter of 50 mm. With smaller shaking diameters you should increase the shaking speed.
For further information consider the following publication:
Characterization of Gas-Liquid Mass Transfer Phenomena in Microtiter Plates
Hermann R., Lehmann M., Buechs, J.
Biotechnology and Bioengineering (2003); Vol. 81, No. 2, pp 178-186
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