Patent ID: 8088573

Claim:
A method of performing a chemical reaction on a substrate having at least one target location that contains a sample of biological material, comprising; (a) mounting a substrate on a mounting region in a cartridge base that supports the substrate in a fixed position relative to the base with the top surface of the substrate facing away from the cartridge base, the substrate having a plurality of target locations that each contain a sample of biological material; (b) locating a reaction containment member over the top surface of the substrate, (c) aligning the reaction containment member with the substrate while moving the reaction containment member relative to the substrate such that a bottom surface of the reaction containment member is juxtaposed with a top surface of the substrate and the reaction containment member and the substrate collectively form a plurality of chambers, each chamber being located directly over at least one respective target location, the reaction containment member having an outer peripheral shape and size which substantially conforms with the shape and size of the substrate when viewed from the top, the aligning step further comprising releasably securing a cartridge cover in mating engagement with the cartridge base to secure the substrate and reaction containment member in position with the bottom surface of the reaction containment member juxtaposed with the top surface of the substrate and each chamber located over at least one respective target location, the cartridge cover having an aperture positioned over the substrate and reaction containment member when the cartridge cover is secured to the cartridge base; (d) dispensing selected fluids into chambers through ports in the reaction containment member which are accessible through the aperture in the cartridge cover, whereby each target location is exposed to a selected fluid; (e) conducting a chemical reaction within each chamber using the selected fluid; (f) heating the substrate to increase the temperature within the same chambers in which steps (d) and (e) were previously performed; wherein steps (d), (e) and (f) are all performed while the substrate remains in a stationary position, wherein the reaction containment member has a back plate and the step of aligning the reaction containment member with the substrate comprises coupling the back plate and reaction containment member to the cartridge cover while allowing some movement between the back plate and cartridge cover, and moving the cartridge cover into mating engagement with the cartridge base such that an alignment member between the cartridge base and back plate moves the reaction containment member into alignment with the substrate such that each chamber is located over at least one respective target location on the substrate.