depending on which specific chemotaxis assay you use,

migrating cells can either be attached/stuck under the pore membrane AFTER they migrated through it, i.e. the underside, opposite side

or if the membrane is not sticky, have passed through and collected in the bottom/recipient chamber

so either on the membrane, or in suspension at the recipient well or measure both and add!

in general, assuming you have a chemo attractant in the lower media chamber, the migrated cells are the ones in the lower chamber-can be attached to the well floor or in solution or attached to the side of the membrane that faces the lower media chamber.

Hi,

If cells having adherent properties then migrated cells usually attached to the lower side of membrane. However if cells grow in suspension then migrated cells goes to the chemotaxis containing chamber lower chamber .

Hi Subodh, I agree with Chris and Dhiraj, in that if you are looking at  migration of an adherent cell line in a transwell assay, then they only migrate on a solid surface. 

Adherent cells usually migrate to the underside of the transwell insert in response to a cemoattractant and stay there. These cells only fall to the bottom chamber if they are overcrowded, or dying. 

Migration of a non-adherent cell line using transwell inserts, however,  is a whole different story.

Thank you all for your concern on my problem and your informative answers.