Abstract: Methods and compositions for detecting cross-contamination between samples contacted with different arrays of a multi-array substrate are provided. The methods involve contacting sample to arrays of a multi-array substrate that contains cross-contamination probes in each of its arrays, and evaluating the resultant sample contacted arrays for cross-contamination between the samples. In many embodiments, the arrays of the multi-array substrate contain a set of cross-contamination probes for a corresponding set of cross-contamination targets in the sample(s). Kits and systems are provided for performing the invention. The subject methods may be used in a variety of different applications, such as gene expression analysis, DNA sequencing, mutation detection, as well as other genomics and proteomics applications.

Abstract: The subject invention provides devices and methods for contacting a fluid with a chemical array. Device embodiments include a reservoir plate that includes a support having a plurality of holes therethrough alignable with a chemical array when the reservoir plate and chemical array are operatively positioned relative to each other. Method for using the subject reservoir plates are also provided, as well as systems and kits.

Abstract: Apparatus and methods are disclosed for processing samples on the surface of supports that are contained in support housings. Biopolymer features are attached to the surfaces of the supports. An apparatus comprises an input element, a holding device for holding a plurality of support housings, one or more fluid dispensing stations, and an output element. Each of the support housings contains a support having attached thereto a plurality of biopolymer features. The holding device is movably mounted with respect to other components of the apparatus. The holding device is adapted to receive a support housing from the input element. The output element is adapted to receive a support housing from the holding device. The apparatus is adapted to index each support housing for a predetermined operation. In use, each of the support housings is moved to one or more processing stations by means of the movable holding device. The location and identity of each of the support housings is indexed.

Abstract: Methods and compositions for encoding and decoding array information on an array are provided. The methods involve contacting an array containing one or more array information features with a sample containing target that binds to at least one of the one or more array information features to produce at least one signal that provides information about the array.

Abstract: Methods and compositions for encoding array information on an array are provided. The methods involve contacting an array containing one or more array information features with a sample containing target that binds to at least one of the one or more array information features to produce at least one signal that provides information about the array. In many embodiments the signal is a symbol or a code, such as binary-code or non-binary-code, that provides the information about the array. Kits and systems are provided for performing the invention.

Abstract: Methods and compositions for detecting cross-contamination between samples contacted with different arrays of a multi-array substrate are provided. The methods involve contacting sample to arrays of a multi-array substrate that contains cross-contamination probes in each of its arrays, and evaluating the resultant sample contacted arrays for cross-contamination between the samples. In many embodiments, the arrays of the multi-array substrate contain a set of cross-contamination probes for a corresponding set of cross-contamination targets in the sample(s). Kits and systems are provided for performing the invention. The subject methods may be used in a variety of different applications, such as gene expression analysis, DNA sequencing, mutation detection, as well as other genomics and proteomics applications.

Abstract: Devices, apparatus and methods are disclosed for carrying out processing steps involved in chemical reactions such as hybridization reactions conducted on the surface of a substrate comprising chemical compounds such as biopolymer features. A device comprises a housing comprising a housing chamber. The housing comprises an opening through which a substrate may be inserted into the housing chamber. The device may also comprise a lift mechanism for moving the substrate in and out of the housing chamber in a controlled manner. At least one inlet may be in fluid communication with the housing chamber and at least one outlet may be in fluid communication with the housing chamber. Also disclosed are methods wherein the surface is brought into contact with a processing fluid; and, then, the surface is removed from contact with the fluid in a controlled manner at a rate that substantially eliminates droplet formation of the fluid on the surface of the substrate.