Abstract: Methods for producing linearly amplified amounts of (+) strand RNA from an initial mRNA source are provided. In the subject methods, an initial mRNA source, e.g., total RNA, is converted to double-stranded cDNA using a second strand cDNA promoter-primer having a promoter sequence recognized by an RNA polymerase located at its 5′ end. The resultant double-stranded cDNA is then transcribed into (+) RNA. The subject methods find use in a variety of different applications in which the preparation of linearly amplified amounts of (+) RNA is desired. Also provided are kits for practicing the subject methods.

Abstract: A method of reading an array of moieties such as polynucleotides (for example, DNA) on at least a portion of a surface of a transparent slide which is opposite a first portion on the opposing surface, which array has been previously exposed to a sample. The method may include mounting the slide on a slide holder and retaining the slide thereon in an enclosed and protected environment in which the holder does not contact the previously exposed array and the array or dyes bound there to are not subject to external factors that might impact their measurement over time. The holder is then inserted into an array reader and the array read. A holder and slides that can be used in the method are also provided.

Abstract: Methods for evaluating whether a sample of at least one detectably-labeled target biomolecule is suitable for use in an array based assay are provided. The subject methods include: (1) providing a substrate having an evaluation array thereon; (2) contacting the evaluation array with the sample; (3) detecting any resultant target biomolecules to obtain signal data; and (4) processing the signal data to evaluate whether the sample is suitable for use in a biopolymeric array assay. Many embodiments of the subject methods include using a volume of sample that does not exceed about 5 &mgr;l and/or incubating the sample with the array for a period of time that does not exceed about 4 hours. Also provided are methods of performing array based assays that include the subject evaluation methods, and kits for practicing the subject methods.

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: Apparatus and methods are disclosed for conducting chemical reactions. The apparatus comprises a plurality of wells in a housing and a channel in the housing. The channel surrounds the plurality of wells and is adapted for filling with an amount of a fluid to form a convex meniscus extending above the top of the channel. In the method one or more liquid samples are placed in separate wells in a housing surface comprising a plurality of the wells. The volume of the liquid sample in each of the wells is sufficient to form a convex meniscus at the surface of each of the wells. The liquid samples are contacted with a plurality of arrays of chemical compounds. In one approach, the liquid samples are contacted with a substrate surface having a plurality of arrays of chemical compounds arranged on the substrate surface. Each of the arrays corresponds to a respective well in the housing.

Abstract: A method and apparatus for simultaneously conducting multiple chemical reactions combine a test sample with a chemical reactant in a plurality of closed reaction chambers to produce reaction products. The method comprises assembling a plate having the test sample in a plurality of spatially arranged wells with a microarray of similarly spatially arranged surface bound chemical reactants to form the sealed apparatus having the plurality of closed reaction chambers. The apparatus is sealed such that it is gas, liquid and/or fluid tight. The seal may be accomplished with a flexible array substrate or a flexible gasket, and one or more of mechanical clamps, external fluid pressure, radiation, heat, vacuum and an adhesive. The sealed apparatus can be subjected to various reaction conditions, such as intense mechanical agitation and a controlled temperature environment. A kit comprises one or more of the elements of the apparatus.

Abstract: Apparatus and methods are disclosed for determining a functional property of a fluid in a chamber. A support to which is bound a plurality of test elements is introduced into the chamber. Each of the test elements comprises a reaction domain and a detection domain. A fluid that is interactive with the reaction domains is introduced into the chamber. Fluid is removed from the chamber. The locations at which the fluid has not interacted with the reaction domains is determined by means of the detection domains. The locations are then related to the functional property of the fluid.

Abstract: Methods of performing array-based assays are provided. A feature of the subject methods is that a sample is initially contacted with a first substrate, i.e., a backing element, to produce a substrate supported sample. Next, the resultant substrate supported sample is contacted with an array of at least two different ligands, and the presence of any resultant surface bound binding complexes is detected. Also provided are backing elements, as well as kits and systems, for use in practicing the subject methods. The subject methods and compositions find use in any array based application, including genomic and proteomic applications.

Abstract: A method and system for normalizing two or more molecular array data sets. Input molecular array data sets are separately globally normalized by, for example, dividing the feature-signal magnitudes of each data set by the geometric mean of the feature-signal magnitudes of the data set. The globally normalized feature signal magnitudes within each data set are ranked in ascending order. A numeric function is created that relates feature-signal magnitudes of the data sets. Only a subset of the features, obtained by selecting features that are similarly ranked in the separate feature-signal-magnitude rankings for the data sets, is used to construct the numeric function. The numeric function is smoothed by one of many possible different smoothing procedures.

Abstract: A method and system for normalizing two or more molecular array data sets. Input molecular array data sets are separately globally normalized by, for example, dividing the feature-signal magnitudes of each data set by the geometric mean of the feature-signal magnitudes of the data set. The globally normalized feature signal magnitudes within each data set are ranked in ascending order. A numeric function is created that relates feature-signal magnitudes of the data sets. Only a subset of the features, obtained by selecting features that are similarly ranked in the separate feature-signal-magnitude rankings for the data sets, is used to construct the numeric function. The numeric function is smoothed by one of many possible different smoothing procedures.

Abstract: Methods for assaying a sample for the presence of one or more nucleic acid analytes, either qualitatively or quantitatively, are provided. In the subject methods, an array of DNA primers is contacted with the sample being assayed under conditions sufficient to produce labeled target nucleic acids enzymaticallyon the surface of the array at locations where a DNA primer has hybridized to a nucleic acid analyte to produce a duplex nucleic acid. The presence of labeled target nucleic acids on the array surface is then detected and used to determine the presence of the one or more nucleic acid analytes in the sample. Also provided are kits for practicing the subject methods. The subject invention finds use in a variety of different applications, including differential gene expression analysis.

Abstract: A method and apparatus for simultaneously conducting multiple chemical reactions combine a test sample with a chemical reactant in a plurality of closed reaction chambers to produce reaction products. The method comprises assembling a plate having the test sample in a plurality of spatially arranged wells with a microarray of similarly spatially arranged surface bound chemical reactants to form the sealed apparatus having the plurality of closed reaction chambers. The apparatus is sealed such that it is gas, liquid and/or fluid tight. The seal may be accomplished with a flexible array substrate or a flexible gasket, and one or more of mechanical clamps, external fluid pressure, radiation, heat, vacuum and an adhesive. The sealed apparatus can be subjected to various reaction conditions, such as intense mechanical agitation and a controlled temperature environment. A kit comprises one or more of the elements of the apparatus.

Abstract: Methods for efficiently depositing small quantities of a protein containing fluid onto the surface of a substrate are provided. A feature of the subject methods is that the deposition process does not substantially modulate the protein activity/functionality of the deposited fluid. In practicing the subject methods, a small volume of fluid containing the protein(s) of interest is front loaded into a thermal inkjet device. Next, a small quantity of the front loaded fluid is expelled onto the surface of a substrate. The subject methods find use in a variety of different applications where the deposition of small volumes of a fluid containing a protein of interest is desired.

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: 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: 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: A method of electrophoretically separating bioorganic molecules is disclosed. The method uses a slab electrophoresis gel and positively or neutrally charged dyes to prevent the dyes from interfering with the gel readout.