Abstract: Methods and compositions for producing labeled probe nucleic acids from genomic nucleic acid template are provided. In the subject methods, a conserved coding consensus region primer is employed to enzymatically generate a select set of labeled probe nucleic acids corresponding to coding regions of genes from a genomic template via a primer extension protocol. The subject methods find use in a variety of different applications, and are particularly suited for use in the preparation of labeled probe nucleic acids for use in array based comparative genomic hybridization applications. Also provided are kits for use in practicing the subject methods.

Abstract: A polynucleotide array, and methods of making and using such arrays. The array may include a first set of multiple features each of which has first polynucleotide molecules of at least 400 nucleotides in length, and a second set of features each of which has second polynucleotide molecules of no more than 100 nucleotides in length. The second set of features can be used as control features, or to replace failed sequences in an enzymatic amplification to produce first polynucleotides, or to detect polymorphisms or splice variants which may not be detected by a particular first polynucleotide.

Abstract: Methods for generating mixtures of nucleic acids, e.g., oligonucleotide primers, are provided. In the subject methods, an array is employed as template to generate mixtures of nucleic acids via a template driven primer extension reaction. In preferred embodiments, each probe on the array employed in the subject methods comprises a constant domain and a variable domain, where the constant domain is further characterized by having at least a recognition domain. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods. The subject methods find use in a variety of applications, including the generation of target nucleic acids from an mRNA sample for use in hybridization assays, e.g., differential gene expression analyses.

Abstract: A method of testing multiple fluid samples with multiple biopolymer arrays. A cover is assembled to a contiguous substrate carrying on a first side, multiple arrays each with multiple regions of biopolymers linked to the substrate, such that the cover and the substrate together form a plurality of chambers each containing a biopolymer array and each being accessible through its own port. Multiple fluid samples are introduced into respective chambers through a port of each such that the fluid samples contact respective arrays. A binding pattern of the arrays is observed. An apparatus and kit useful in such methods, are also provided.

Abstract: Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.

Abstract: Devices, apparatus and methods for conducting hybridization reactions are disclosed. An embodiment of a device comprises two chambers in fluid communication. Each of the chambers has an interior wherein one of the chambers has at least one interior dimension that is larger (larger chamber) than at least one interior dimension of the other of the chambers (smaller chamber). Each of the interiors comprises an array of features.

Abstract: Systems and methods for optimizing polymer analysis are provided. One such system includes a polymer analysis system having a polymer control system. The polymer analysis system is operative to: apply a set of conditions to a sample being analyzed by the polymer array, the set of conditions correspond to at least one characteristic of the polymer array; analyze the at least one characteristic using the polymer control system; and generate polymer array data.

Abstract: An apparatus and method for separating and identifying chemical moieties. The apparatus employs a microarray device coupled to a nanopore system. The apparatus both separates and identifies target molecules without the requirement of extraneous tags or fluorescent markers. Methods for using the apparatus are also disclosed.

Abstract: A method of using a chemical array unit having a chemical array with probes at multiple feature locations. A request for test may be read, which test uses a sub-array of the array. A pattern of the sub-array may be retrieved from a memory using the test request, which memory carries a pattern for the sub-array which is retrievable with the different test request. Also, a method of reading a chemical array unit which has been exposed to a sample, and feature locations of which have been rendered incapable of providing signal data representative of binding of a sample component. Further methods, apparatus, and computer program products are provided.

Abstract: An apparatus and method for separating and identifying chemical moieties. The apparatus employs a micro array device coupled to a detector such as a mass spectrometer system. The apparatus both separates and identifies target molecules without the requirement of extraneous tags or fluorescent markers. Methods for using the apparatus are also disclosed.

Abstract: Methods and compositions for performing template dependent nucleic acid primer extension reactions that produce a reduced complexity product are provided. In the subject methods, template RNA is contacted with a primer composition that includes both a universal, e.g., oligo dT, primer and at least one gene specific primer under template dependent primer extension reaction conditions, which step results in the production of a reduced complexity product as compared to the initial RNA template. The subject methods find use a variety of different applications, including the preparation of labeled nucleic acids, e.g., for use in differential gene expression analysis applications. Also provided are kits for practicing the subject methods.

Abstract: Array-based clinical assays and compositions for use in practicing the same are provided. A feature of the subject array-based clinical assays is that they include a sample quality evaluation step that is independent from the clinical assay step of the assays, where the sample quality evaluation step may be performed in a number of different ways. Also provided are compositions, devices and kits for use in practicing the subject methods.

Abstract: Ligand array assays and compositions for use in practicing the same are provided. A feature of the subject methods is that they include a wash step in which the ligand displaying surface of a sample exposed array is washed with a low surface tension fluid, e.g., acetonitrile. Also provided are kits for use in practicing the subject methods. The subject methods and kits find use in a variety of ligand array based applications, including genomic and proteomic applications.

Abstract: Ligand array assays and compositions for use in practicing the same are provided. A feature of the subject methods is that they include a wash step in which the ligand displaying surface of a sample exposed ligand array is washed with organic wash fluid, e.g., propylene carbonate. Also provided are kits for use in practicing the subject methods. The subject methods and kits find use in a variety of ligand array based applications, including genomic and proteomic applications.

Abstract: A method, apparatus and kit forms a plurality of closed reaction chambers to simultaneously conduct multiple chemical reactions. The apparatus includes a plate of wells and an array of sets of bound chemical reactants. A well has a deformable closed end and an open end opposite the closed end. When assembled together, the array covers open ends of the wells in the plate to form a reaction assembly having a plurality of closed cells that is one or more of gas, liquid and/or fluid tight. The deformable closed end of the well is flexible such that a test sample is displaced toward a set of chemical reactants in a closed cell for mixing. The array may include spatially arranged prongs distally extending from a support with the sets of chemical reactants bound to distal ends of prongs.

Abstract: Comparative genomic hybridization assays and compositions for use in practicing the same are provided. A characteristic of the subject comparative genomic hybridization assays is that solid support immobilized oligonucleotide feature elements, e.g., in the form of an array, are employed. Specifically, at least first and second nucleic acid populations prepared from genomic templates are contacted with a plurality of distinct oligonucleotide feature elements immobilized on a solid support surface and the binding of the at least first and second populations is then evaluated. Also provided are kits for use in practicing the subject methods.

Abstract: Methods of detecting the presence of a nucleic acid analyte in a sample are provided. In the subject methods, a sample suspected of having an analyte is contacted with an array, and any resultant binding complexes on the surface of the array are detected to determine the presence or absence of the analyte in the sample. A feature of the subject methods is that the sample includes at least a first unlabeled nucleic acid made up of at least two types of nucleotides. Also provided are kits for use in practicing the subject methods.

Abstract: Methods and devices for detecting deposition unit misalignment, e.g., printhead misalignment, of an in situ polymeric, e.g., a nucleic acid, array synthesis device are provided. In accordance with the subject methods, at least one test probe feature is synthesized on a substrate using an in situ polymeric array, e.g., nucleic acid array or protein array, synthesis device. The at least one test probe feature is then contacted with at least two different distinguishably labeled targets, e.g., target nucleic acids. The binding of the targets to the at least one test probe feature is then evaluated to detect any misalignment, e.g., deposition unit or pulse jet misalignments, of the synthesis device. Also provided are substrates having at least one test probe feature and at least one polymeric array, as well as methods of using the substrates in array assays. Also included are kits for use in practicing the subject methods.

Abstract: Methods and devices for producing a polymer at a location of a substrate are provided. In the subject methods, a fluid droplet containing a first monomer labeled with a first detectable label is deposited from a fluid deposition device onto a location of a substrate surface having a second monomer labeled with a second detectable label. The first and second detectable labels are then detected to determine any misalignment between the fluid deposition device and the location of the substrate surface during deposition. Also provided are algorithms that perform the subject methods, as well as fluid deposition devices that include the subject algorithms. The subject invention also includes arrays produced according to the subject methods and kits that include the subject arrays.

Abstract: The present invention provides for assaying as few as a single microarray of a chemical array of microarrays at a time without contamination or damage to a remainder of the microarrays. A chemical array apparatus, system and method comprise a microarray attached to a surface of a planar substrate and a breakaway seal or barrier applied to the substrate surface to surround the microarray. The breakaway seal provides the microarray fluid isolation and is manipulatable. The system further comprises a cover extending over and in contact with the breakaway seal to cover the microarray. The method further comprises processing a microarray of the chemical array with a fluid, and breaking away a portion of the breakaway seal to create a gap. The gap releases the fluid in a direction away from remaining microarrays of the chemical array. A removable cover overlies a microarray on the chemical array apparatus.