An apparatus of conducting electrophoresis experiments including a container for receiving an electrophoresis buffer and a buffer core assembly for holding gel-containing cassettes that are immersed in the buffer for molecular separation of an electrophoresis sample. The buffer core assembly defines a flow path for the electrophoresis buffer which can be circulated by means of a heat exchanger and a pump to effect controlled heat exchange between the buffer and the cassette surfaces thereby maintaining the gel and the electrophoresis process at a desirable temperature uniformly over the surfaces of the gel cassette. The buffer core assembly also has upper well for receiving a second electrically chargeable buffer in contact with the gel so as to impose an electric field on the gel for the electrophoresis in conjunction with the first buffer. The well is isolated from the first buffer to prevent mixing of the buffers and to reduce the risk of an electrical short.