Abstract: An apparatus for transfer of a liquid using a diaphragm that separates a working fluid volume from a working air volume and can controllably induce a change pressure to draw or expel a target fluid into a tube. The apparatus is particularly suitable for automated processing of nucleic acids and other samples includes a disposable container comprising a tray and a flexible barrier. The barrier is configured to seal with a top edge of the tray, providing a closed, aseptic work area within the sealed tray. A pipette head and/or other sample manipulation device can be attached to the inside of the barrier under the diaphraghm, and the barrier can include an interface for a robotic arm or other device. When the barrier is sealed over the tray, the barrier separates the contents of the tray from the robot or other manipulation device.