I have used Triazol extraction protocol depending on the size of the Transwell inserts and the number of cells you have seeded on them. First I washed the cells with PBS and then added the half the amount of Triazol to the transwell and pipette up and down and I sometiles use a tip to scratch the member to ensure complete separation of the cells. I withdraw the triazol and put them in an eppendorf tube then add the other half of Triazol to the transwell with pipetting up and down to get any further attached cells. and then follow the normal Triazol extraction protocol.